Science.gov

Sample records for phototropin lov domain

  1. Dynamic Switching Mechanisms in LOV1 and LOV2 Domains of Plant Phototropins

    PubMed Central

    Freddolino, Peter L.; Dittrich, Markus; Schulten, Klaus

    2006-01-01

    LOV domains are the light-sensitive portion of plant phototropins. They absorb light through a flavin cofactor, photochemically form a covalent bond between the chromophore and a cysteine residue in the protein, and proceed to mediate activation of an attached kinase domain. Although the photoreaction itself is now well-characterized experimentally and computationally, it is still unclear how the formation of the adduct leads to kinase activation. We have performed molecular dynamics simulations on the LOV1 domain of Chlamydomonas reinhardtii and the LOV2 domain of Avena sativa, both before and after the photoreaction, to answer this question. The extensive simulations, over 240 ns in duration, reveal significant differences in how the LOV1 and LOV2 domains respond to photoactivation. The simulations indicate that LOV1 activation is likely caused by a change in hydrogen bonding between protein and ligand that destabilizes a highly conserved salt bridge, whereas LOV2 activation seems to result from a change in the flexibility of a set of protein loops. Results of electrostatics calculations, principal component analysis, sequence alignments, and root mean-square deviation analysis corroborate the above findings. PMID:16935961

  2. Different role of the Jalpha helix in the light-induced activation of the LOV2 domains in various phototropins.

    PubMed

    Koyama, Takayuki; Iwata, Tatsuya; Yamamoto, Atsushi; Sato, Yoshiaki; Matsuoka, Daisuke; Tokutomi, Satoru; Kandori, Hideki

    2009-08-18

    Phototropins (phot) are blue light receptors in plants which are involved in phototropism, stomatal opening, and chloroplast movements. Phototropin has two LOV domains (LOV1 and LOV2), and the LOV2 domain is responsible for activation of Ser/Thr kinase. There is an alpha-helix at the C-terminal side of the LOV2 domain, which is called the Jalpha helix. The functional importance of the Jalpha helix has been established for Arabidopsis phot1, where light-induced structural perturbation takes place in the Jalpha helix during the photocycle of LOV2 domains. However, the present FTIR study reports a different role of the Jalpha helix in light-induced signal transduction of LOV2 domains. Here we construct LOV2 domains with (LOV-Jalpha) and without (LOV-core) the Jalpha helix for Arabidopsis phot1 and phot2 and Adiantum neochrome 1 and compare their light-induced difference FTIR spectra. Light-induced protein structural changes differ significantly between LOV-Jalpha and LOV-core for Arabidopsis phot1 [Yamamoto, A., Iwata, T., Sato, Y., Matsuoka, D., Tokutomi, S., and Kandori, H. (2009) Biophys. J. 96, 2771-2778]. In contrast, the difference spectra are identical between LOV-Jalpha and LOV-core for Adiantum neochrome 1. In Arabidopsis phot2, the protein structural changes are intermediate between Arabidopsis phot1 and Adiantum neochrome 1. These results suggest that the conformational changes of the Jalpha helix and the interaction between the LOV-core and the Jalpha helix are different among phototropins. The role of the Jalpha helix for signal transduction in phototropins is discussed. PMID:19601589

  3. Photo-cycle dynamics of LOV1-His domain of phototropin from Chlamydomonas reinhardtii with roseoflavin monophosphate cofactor

    NASA Astrophysics Data System (ADS)

    Tyagi, A.; Penzkofer, A.; Mathes, T.; Hegemann, P.

    2010-09-01

    The wild-type phototropin protein phot from the green alga Chlamydomonas reinhardtii consists of two N-terminal LOV domains LOV1 and LOV2 with flavin mononucleotide (FMN) cofactor and a C-terminal serine-threonine kinase domain. It controls multiple steps in the sexual lifecycle of the alga. Here the LOV1-His domain of phot with modified cofactor is studied. FMN is replaced by roseoflavin monophosphate (8-dimethylamino-8-demethyl-FMN, RoFMN). The modified LOV1 domain is called RoLOV1. The photo-dynamics consequences of the cofactor change are studied. The absorption, emission, and photo-cyclic behaviour of LOV1-His and RoLOV1-His are compared. A spectroscopic characterisation of the cofactors FMN and RoFMN (roseoflavin) is given.

  4. Crystallization and preliminary X-ray diffraction anaylsis of the LOV1 domains of phototropin 1 and 2 from Arabidopsis thaliana

    SciTech Connect

    Nakasako, Masayoshi; Hirata, Michihiro; Shimizu, Nobutaka; Matsuoka, Daisuke; Oka, Toshihiko; Yamamoto, Masaki; Tokutomi, Satoru

    2008-07-01

    Crystals of the LOV1 domains of phototropin 1 and 2 from A. thaliana were obtained which diffracted X-rays to a resolution of at least 2.1 Å. Phototropin is a blue-light receptor protein in plants that is responsible for phototropic responses, stomata opening and photo-induced relocation of chloroplasts. Higher plants such as Arabidopsis thaliana have two isoforms of phototropin: phototropin 1 and phototropin 2. Both isoforms comprise a tandem pair of blue-light-absorbing light–oxygen–voltage domains named LOV1 and LOV2 in the N-terminal half and a serine/threonine kinase domain in the C-terminal half. The LOV1 domain is thought to function as a dimerization site. In the present study, recombinant LOV1 domains of A. thaliana phototropin 1 and phototropin 2 were crystallized. The crystal of the LOV1 domain of phototropin 1 belonged to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 61.2, b = 64.9, c = 70.8 Å, and diffracted X-rays to a resolution of 2.1 Å. The crystal of the LOV1 domain of phototropin 2 belonged to space group P2{sub 1}, with unit-cell parameters a = 32.5, b = 66.5, c = 56.7 Å, β = 92.4°, and diffracted X-rays to beyond 2.0 Å resolution. In both crystals, two LOV1 domains occupied the crystallographic asymmetric unit.

  5. Primary photophysics of the FMN binding LOV2 domain of the plant blue light receptor phototropin of Avena sativa

    NASA Astrophysics Data System (ADS)

    Schüttrigkeit, Tanja A.; Kompa, Christian K.; Salomon, Michael; Rüdiger, Wolfhart; Michel-Beyerle, Maria E.

    2003-11-01

    The temporal evolution of the initially excited singlet state of flavine mononucleotide, which is the cofactor in the LOV2 domain of the blue photoreceptor phototropin, has been studied in picosecond time-resolved fluorescence and femtosecond time-resolved absorption experiments. In the LOV2-WT protein of Avena sativa singlet-triplet intersystem crossing proceeding within 2.3 ns is the primary process which increases the triplet yield by a factor of 1.23 as compared to a mutant where cysteine 39 is replaced by alanine. This flavin triplet state is responsible for the formation of a cysteinyl-flavin adduct which triggers the unique photocycle of the LOV2 domain and thus the sensoric function of the blue light receptor phototropin.

  6. Low-temperature and time-resolved spectroscopic characterization of the LOV2 domain of Avena sativa phototropin 1

    NASA Astrophysics Data System (ADS)

    Gauden, Magdalena; Crosson, Sean; van Stokkum, I. H. M.; van Grondelle, Rienk; Moffat, Keith; Kennis, John T. M.

    2004-09-01

    The phototropins are plant blue-light receptors that base their light-dependent action on the reversible formation of a covalent bond between a flavin mononucleotide (FMN) cofactor and a conserved cysteine residue in light, oxygen or voltage (LOV) domains. The spectroscopic properties of the LOV2 domain of phototropin 1 of Avena sativa (oat) have been investigated by means of low-temperature absorption and fluorescence spectroscopy and by time-resolved fluorescence spectroscopy. The low-temperature absorption spectrum of the LOV2 domain showed a fine structure around 473 nm, indicating heterogeneity in the flavin binding pocket. The fluorescence quantum yield of the flavin cofactor increased from 0.13 to 0.41 upon cooling the sample from room temperature to 77 K. A pronounced phosphorescence emission around 600 nm was observed in the LOV2 domain between 77 and 120 K, allowing for an accurate positioning of the flavin triplet state in the LOV2 domain at 16900 cm-1. Fluorescence from the cryotrapped covalent adduct state was extremely weak, with a fluorescence spectrum showing a maximum at 440 nm. Time-resolved fluorescence experiments utilizing a synchroscan streak camera revealed a singlet-excited state lifetime of the LOV2 domain of 2.4 ns. FMN dissolved in aqueous solution showed a pH-dependent lifetime ranging between 2.9 ns at pH 2.0 to 4.7 ns at pH 8.0. No spectral shifting of the flavin emission was observed in the LOV2 domain nor in FMN in aqueous solution.

  7. Time-resolved Fourier transform infrared study on photoadduct formation and secondary structural changes within the phototropin LOV domain.

    PubMed

    Pfeifer, Anna; Majerus, Teresa; Zikihara, Kazunori; Matsuoka, Daisuke; Tokutomi, Satoru; Heberle, Joachim; Kottke, Tilman

    2009-02-18

    Phototropins are plant blue-light photoreceptors containing two light-, oxygen-, or voltage-sensitive (LOV) domains and a C-terminal kinase domain. The two LOV domains bind noncovalently flavin mononucleotide as a chromophore. We investigated the photocycle of fast-recovery mutant LOV2-I403V from Arabidopsis phototropin 2 by step-scan Fourier transform infrared spectroscopy. The reaction of the triplet excited state of flavin with cysteine takes place with a time constant of 3 micros to yield the covalent adduct. Our data provide evidence that the flavin is unprotonated in the productive triplet state, disfavoring an ionic mechanism of bond formation. An intermediate adduct species was evident that displayed changes in secondary structure in the helix or loop region, and relaxed with a time constant of 120 micros. In milliseconds, the final adduct state is formed by further alterations of secondary structure, including beta-sheets. A comparison with wild-type adduct spectra shows that the mutation does not interfere with the functionality of the domain. All signals originate from within the LOV domain, because the construct does not comprise the adjacent Jalpha helix required for signal transduction. The contribution of early and late adduct intermediates to signal transfer to the Jalpha helix outside of the domain is discussed. PMID:19217862

  8. Mutations in N-terminal Flanking Region of Blue Light-sensing Light-Oxygen and Voltage 2 (LOV2) Domain Disrupt Its Repressive Activity on Kinase Domain in the Chlamydomonas Phototropin*

    PubMed Central

    Aihara, Yusuke; Yamamoto, Takaharu; Okajima, Koji; Yamamoto, Kazuhiko; Suzuki, Tomomi; Tokutomi, Satoru; Tanaka, Kazuma; Nagatani, Akira

    2012-01-01

    Phototropin is a light-regulated kinase that mediates a variety of photoresponses such as phototropism, chloroplast positioning, and stomata opening in plants to increase the photosynthetic efficiency. Blue light stimulus first induces local conformational changes in the chromophore-bearing light-oxygen and voltage 2 (LOV2) domain of phototropin, which in turn activates the serine/threonine (Ser/Thr) kinase domain in the C terminus. To examine the kinase activity of full-length phototropin conventionally, we employed the budding yeast Saccharomyces cerevisiae. In this organism, Ser/Thr kinases (Fpk1p and Fpk2p) that show high sequence similarity to the kinase domain of phototropins exist. First, we demonstrated that the phototropin from Chlamydomonas reinhardtii (CrPHOT) could complement loss of Fpk1p and Fpk2p to allow cell growth in yeast. Furthermore, this reaction was blue light-dependent, indicating that CrPHOT was indeed light-activated in yeast cells. We applied this system to a large scale screening for amino acid substitutions in CrPHOT that elevated the kinase activity in darkness. Consequently, we identified a cluster of mutations located in the N-terminal flanking region of LOV2 (R199C, L202L, D203N/G/V, L204P, T207I, and R210H). An in vitro phosphorylation assay confirmed that these mutations substantially reduced the repressive activity of LOV2 on the kinase domain in darkness. Furthermore, biochemical analyses of the representative T207I mutant demonstrated that the mutation affected neither spectral nor multimerization properties of CrPHOT. Hence, the N-terminal flanking region of LOV2, as is the case with the C-terminal flanking Jα region, appears to play a crucial role in the regulation of kinase activity in phototropin. PMID:22291022

  9. Detecting a new source for photochemically induced dynamic nuclear polarization in the LOV2 domain of phototropin by magnetic-field dependent (13)C NMR spectroscopy.

    PubMed

    Kothe, Gerd; Lukaschek, Michail; Link, Gerhard; Kacprzak, Sylwia; Illarionov, Boris; Fischer, Markus; Eisenreich, Wolfgang; Bacher, Adelbert; Weber, Stefan

    2014-10-01

    Phototropin is a flavin mononucleotide (FMN) containing blue-light receptor, which regulates, governed by its two LOV domains, the phototropic response of higher plants. Upon photoexcitation, the FMN cofactor triplet state, (3)F, reacts with a nearby cysteine to form a covalent adduct. Cysteine-to-alanine mutants of LOV domains instead generate a flavin radical upon illumination. Here, we explore the formation of photochemically induced dynamic nuclear polarization (CIDNP) in LOV2-C450A of Avena sativa phototropin and demonstrate that photo-CIDNP observed in solution (13)C NMR spectra can reliably be interpreted in terms of solid-state mechanisms including a novel triplet mechanism. To minimize cross-polarization, which transfers light-induced magnetization to adjacent (13)C nuclei, our experiments were performed on proteins reconstituted with specifically (13)C-labeled flavins. Two potential sources for photo-CIDNP can be identified: The photogenerated triplet state, (3)F, and the triplet radical pair (3)(F(-•)W(+•)), formed by electron abstraction of (3)F from tryptophan W491. To separate the two contributions, photo-CIDNP studies were performed at four different magnetic fields ranging from 4.7 to 11.8 T. Analysis revealed that, at fields <9 T, both (3)(F(-•)W(+•)) and (3)F contribute to photo-CIDNP, whereas at high magnetic fields, the calculated enhancement factors of (3)F agree favorably with their experimental counterparts. Thus, we have for the first time detected that a triplet state is the major source for photo-CIDNP in a photoactive protein. Since triplet states are frequently encountered upon photoexcitation of flavoproteins, the novel triplet mechanism opens up new means of studying electronic structures of the active cofactors in these proteins at atomic resolution. PMID:25207844

  10. Physiological roles of the light, oxygen, or voltage domains of phototropin 1 and phototropin 2 in Arabidopsis.

    PubMed

    Cho, Hae-Young; Tseng, Tong-Seung; Kaiserli, Eirini; Sullivan, Stuart; Christie, John M; Briggs, Winslow R

    2007-01-01

    Phototropins (phot1 and phot2) are plant blue-light receptors that mediate phototropism, chloroplast movement, stomatal opening, rapid inhibition of growth of etiolated seedlings, and leaf expansion in Arabidopsis (Arabidopsis thaliana). Their N-terminal region contains two light, oxygen, or voltage (LOV) domains, which bind flavin mononucleotide and form a covalent adduct between a conserved cysteine and the flavin mononucleotide chromophore upon photoexcitation. The C-terminal region contains a serine/threonine kinase domain that catalyzes blue-light-activated autophosphorylation. Here, we have transformed the phot1 phot2 (phot1-5 phot2-1) double mutant with PHOT expression constructs driven by the cauliflower mosaic virus 35S promoter. These constructs encode either wild-type phototropin or phototropin with one or both LOV-domain cysteines mutated to block their photochemistry. We selected multiple lines in each of the eight resulting categories of transformants for further physiological analyses. Specifically, we investigated whether LOV1 and LOV2 serve the same or different functions for phototropism and leaf expansion. Our results show that the LOV2 domain of phot1 plays a major role in phototropism and leaf expansion, as does the LOV2 domain of phot2. No complementation of phototropism or leaf expansion was observed for the LOV1 domain of phot1. However, phot2 LOV1 was unexpectedly found to complement phototropism to a considerable level. Similarly, transformants carrying a PHOT transgene with both LOV domains inactivated developed strong curvatures toward high fluence rate blue light. However, we found that the phot2-1 mutant is leaky and produces a small level of full-length phot2 protein. In vitro experiments indicate that cross phosphorylation can occur between functional phot2 and inactivated phot1 molecules. Such a mechanism may occur in vivo and therefore account for the functional activities observed in the PHOT transgenics with both lov domains

  11. FMN binding and photochemical properties of plant putative photoreceptors containing two LOV domains, LOV/LOV proteins.

    PubMed

    Kasahara, Masahiro; Torii, Mayumi; Fujita, Akimitsu; Tainaka, Kengo

    2010-11-01

    LOV domains function as blue light-sensing modules in various photoreceptors in plants, fungi, algae, and bacteria. A LOV/LOV protein (LLP) has been found from Arabidopsis thaliana (AtLLP) as a two LOV domain-containing protein. However, its function remains unknown. We isolated cDNA clones coding for an LLP homolog from tomato (Solanum lycopersicum) and two homologs from the moss Physcomitrella patens. The tomato LLP (SlLLP) contains two LOV domains (LOV1 and LOV2 domains), as in AtLLP. Most of the amino acids required for association with chromophore are conserved in both LOV domains, except that the amino acid at the position equivalent to the cysteine essential for cysteinyl adduct formation is glycine in the LOV1 domain as in AtLLP. When expressed in Escherichia coli, SlLLP binds FMN and undergoes a self-contained photocycle upon irradiation of blue light. Analyses using mutant SlLLPs revealed that SlLLP binds FMN in both LOV domains, although the LOV1 domain does not show spectral changes on irradiation. However, when Gly(66) in the LOV1 domain, which is located at the position equivalent to the essential cysteine of LOV domains, is replaced by cysteine, the mutated LOV1 domain shows light-induced spectral changes. In addition, all four LOV domains of P. patens LLPs (PpLLP1 and PpLLP2) show the typical features of LOV domains, including the reactive cysteine in each. This study shows that plants have a new LOV domain-containing protein family with the typical biochemical and photochemical properties of other LOV domain-containing proteins such as the phototropins. PMID:20826774

  12. Comparative investigation of the LOV1 and LOV2 domains in Adiantum phytochrome3.

    PubMed

    Iwata, Tatsuya; Nozaki, Dai; Tokutomi, Satoru; Kandori, Hideki

    2005-05-24

    Phototropin (phot) is a blue-light photoreceptor for phototropic responses, relocation of chloroplasts, and stomata opening in plants. Phototropin has two chromophore-binding domains named LOV1 and LOV2 in its N-terminal half, each of which binds a flavin mononucleotide (FMN) noncovalently. The C-terminal half is a Ser/Thr kinase. A transgenic study of Arabidopsis suggested that only LOV2 domain is necessary for the kinase activity, whereas X-ray crystallographic structures of LOV1 and LOV2 domains are almost identical. These facts imply that the detailed structures and/or structural changes are different between LOV1 and LOV2 domains. In this study, we compared light-induced structural changes of the LOV1 and LOV2 domains of a phototropin, Adiantum phytochrome3 (phy3), by means of UV-visible and Fourier transform infrared (FTIR) spectroscopy. Photochemical properties of an adduct formation between FMN and a cysteine are essentially similar between phy3-LOV1 and phy3-LOV2. On the other hand, the S-H group of the reactive cysteine forms a hydrogen bond in phy3-LOV1, which is strengthened at low temperatures. This is possibly correlated with the fact that no adduct formation takes place for phy3-LOV1 at 77 K as revealed by the UV-visible absorption spectra. The most prominent difference was seen in the amide-I vibration that monitors the secondary structure of peptide backbone. Protein structural changes in phy3-LOV2 involve the regions of loops, alpha-helices, and beta-sheets, which differ significantly among various temperatures. Extended protein structural changes are probably correlated with the signal transduction activity of LOV2. In contrast, protein structural changes were very small in phy3-LOV1, and they were almost temperature independent. The photocycle of phy3-LOV1 takes 3.1 h, being more than 100 times longer than that of phy3-LOV2. These facts suggest that Adiantum phy3-LOV1 does not work for light sensing, being consistent with the previous transgenic

  13. Designing photoswitchable peptides using the AsLOV2 domain

    PubMed Central

    Lungu, Oana I.; Hallett, Ryan A.; Choi, Eun Jung; Aiken, Mary J.; Hahn, Klaus M.; Kuhlman, Brian

    2012-01-01

    Summary Photocontrol of functional peptides is a powerful tool for spatial and temporal control of cell signaling events. We show that the genetically encoded light-sensitive LOV2 domain of Avena Sativa phototropin 1 (AsLOV2) can be used to reversibly photomodulate the affinity of peptides for their binding partners. Sequence analysis and molecular modeling were used to embed two peptides into the Ja helix of the AsLOV2 domain while maintaining AsLOV2 structure in the dark, but allowing for binding to effector proteins when the Jα helix unfolds in the light. Caged versions of the ipaA and SsrA peptides, LOV-ipaA and LOV-SsrA, bind their targets with 49-fold and 8-fold enhanced affinity in the light, respectively. These switches can be used as general tools for light dependent co-localization, which we demonstrate with photoactivable gene transcription in yeast. PMID:22520757

  14. Photochemical properties of the flavin mononucleotide-binding domains of the phototropins from Arabidopsis, rice, and Chlamydomonas reinhardtii.

    PubMed

    Kasahara, Masahiro; Swartz, Trevor E; Olney, Margaret A; Onodera, Akihiko; Mochizuki, Nobuyoshi; Fukuzawa, Hideya; Asamizu, Erika; Tabata, Satoshi; Kanegae, Hiromi; Takano, Makoto; Christie, John M; Nagatani, Akira; Briggs, Winslow R

    2002-06-01

    Phototropins (phot1 and phot2, formerly designated nph1 and npl1) are blue-light receptors that mediate phototropism, blue light-induced chloroplast relocation, and blue light-induced stomatal opening in Arabidopsis. Phototropins contain two light, oxygen, or voltage (LOV) domains at their N termini (LOV1 and LOV2), each a binding site for the chromophore flavin mononucleotide (FMN). Their C termini contain a serine/threonine protein kinase domain. Here, we examine the kinetic properties of the LOV domains of Arabidopsis phot1 and phot2, rice (Oryza sativa) phot1 and phot2, and Chlamydomonas reinhardtii phot. When expressed in Escherichia coli, purified LOV domains from all phototropins examined bind FMN tightly and undergo a self-contained photocycle, characterized by fluorescence and absorption changes induced by blue light (T. Sakai, T. Kagawa, M. Kasahara, T.E. Swartz, J.M. Christie, W.R. Briggs, M. Wada, K. Okada [2001] Proc Natl Acad Sci USA 98: 6969-6974; M. Salomon, J.M. Christie, E. Knieb, U. Lempert, W.R. Briggs [2000] Biochemistry 39: 9401-9410). The photocycle involves the light-induced formation of a cysteinyl adduct to the C(4a) carbon of the FMN chromophore, which subsequently breaks down in darkness. In each case, the relative quantum efficiencies for the photoreaction and the rate constants for dark recovery of LOV1, LOV2, and peptides containing both LOV domains are presented. Moreover, the data obtained from full-length Arabidopsis phot1 and phot2 expressed in insect cells closely resemble those obtained for the tandem LOV-domain fusion proteins expressed in E. coli. For both Arabidopsis and rice phototropins, the LOV domains of phot1 differ from those of phot2 in their reaction kinetic properties and relative quantum efficiencies. Thus, in addition to differing in amino acid sequence, the phototropins can be distinguished on the basis of the photochemical cycles of their LOV domains. The LOV domains of C. reinhardtii phot also undergo light

  15. Signaling mechanisms of LOV domains: New insights from molecular dynamics studies

    PubMed Central

    Freddolino, Peter L.; Gardner, Kevin H.; Schulten, Klaus

    2013-01-01

    Phototropins are one of several classes of photoreceptors used by plants and algae to respond to light. These proteins contain flavin-binding LOV (Light-Oxygen-Voltage) domains that form covalent cysteine-flavin adducts upon exposure to blue light, leading to the enhancement of phototropin kinase activity. Several lines of evidence suggest that adduct formation in the phototropin LOV2 domains leads to the dissociation of an alpha helix (Jα) from these domains as part of the light-induced activation process. However, crystal structures of LOV domains both in the presence and absence of the Jα helix show very few differences between dark and illuminated states, and thus the precise mechanism through which adduct formation triggers helical dissociation remains poorly understood. Using Avena sativa phototropin 1 LOV2 as a model system, we have studied the interactions of the LOV domain core with the Jα helix through a series of equilibrium molecular dynamics simulations. Here we show that conformational transitions of a conserved glutamine residue in the flavin binding pocket are coupled to altered dynamics of the Jα helix both through a shift in dynamics of the main β-sheet of the LOV domain core and through a secondary pathway involving the N-terminal A′α helix. PMID:23407663

  16. Mechanism-Based Tuning of a LOV Domain Photoreceptor

    SciTech Connect

    Zoltowski, B.; Vaccaro, B; Crane, B

    2009-01-01

    Phototropin-like LOV domains form a cysteinyl-flavin adduct in response to blue light but show considerable variation in output signal and the lifetime of the photo-adduct signaling state. Mechanistic studies of the slow-cycling fungal LOV photoreceptor Vivid (VVD) reveal the importance of reactive cysteine conformation, flavin electronic environment and solvent accessibility for adduct scission and thermal reversion. Proton inventory, pH effects, base catalysis and structural studies implicate flavin N5 deprotonation as rate-determining for recovery. Substitutions of active site residues Ile74, Ile85, Met135 and Met165 alter photoadduct lifetimes by over four orders of magnitude in VVD, and similar changes in other LOV proteins show analogous effects. Adduct state decay rates also correlate with changes in conformational and oligomeric properties of the protein necessary for signaling. These findings link natural sequence variation of LOV domains to function and provide a means to design broadly reactive light-sensitive probes.

  17. Mechanism Based Tuning of a LOV Domain Photoreceptor

    PubMed Central

    Zoltowski, Brian D.; Vaccaro, Brian; Crane, Brian R.

    2010-01-01

    Phototropin-like LOV domains form a cysteinyl-flavin adduct in response to blue light, but show dramatic variation in output signal and the lifetime of the photo-adduct signaling state. Mechanistic studies of the slow-cycling fungal LOV-photoreceptor Vivid reveal the importance of reactive cysteine conformation, flavin electronic environment and solvent accessibility for adduct scission and thermal reversion. Proton inventory, pH-effects, base catalysis and structural studies implicate flavin N5 deprotonation as rate-determining for recovery. Substitutions of active site residues Ile74, Ile85, Met135 and Met165 alter photoadduct lifetimes by over four orders of magnitude in VVD and similar changes in other LOV proteins show analogous effects. Adduct state decay rates also correlate with changes in conformational and oligomeric properties of the protein necessary for signaling. These findings link natural sequence variation of LOV domains to function and provide a means to design broadly reactive light-sensitive probes. PMID:19718042

  18. Modulating LOV Domain Photodynamics with a Residue Alteration outside the Chromophore Binding Site†

    PubMed Central

    Song, Sang-Hun; Freddolino, Peter L.; Nash, Abigail I.; Carroll, Elizabeth C.; Schulten, Klaus; Gardner, Kevin H.; Larsen, Delmar S.

    2011-01-01

    Phototropins, a class of light-activated protein kinases, are essential for several blue light responses in plants and algae, including phototropism. These proteins contain two internal light, oxygen, and voltage sensitive (LOV) domains, which bind flavin chromophores and undergo a reversible photochemical formation of a cysteinyl-flavin adduct as part of the light sensing process. While the photodynamic properties of such photosensory domains are dictated by interactions between the chromophore and surrounding protein, more distant residues can play a significant role as well. Here we explore the role of the Phe434 residue in the photosensory response of the second LOV domain of Avena sativa phototropin 1 (AsLOV2), a model photochemical system for these LOV domains. Phe434 lies over 6 Å from the FMN chromophore in AsLOV2; nevertheless, a F434Y point mutation is likely to change several structural features of the chromophore binding site, as we demonstrate using molecular dynamics simulations. Transient absorption signals spanning 15 decades in time were compared for wildtype AsLOV2 and the F434Y mutant, showing that the latter has significantly altered photodynamics including (i) a faster intersystem crossing leading to triplet formation on a nanosecond time scale, (ii) biphasic formation of adduct state kinetics on the microsecond time scale, and (iii) greatly accelerated ground-state recovery kinetics on a second time scale. We present mechanistic models that link these spectroscopic differences to changes in the configuration of the critical cysteine residue and in the chromophore’s accessibility to solvent and oxygen according to MD trajectories and purging experiments. Taken together, these results demonstrate the importance of residues outside the chromophore-binding pocket in modulating LOV domain photodynamics. PMID:21323358

  19. Molecular mechanism of phototropin light signaling.

    PubMed

    Okajima, Koji

    2016-03-01

    Phototropin (phot) is a blue light (BL) receptor kinase involved in the BL responses of several species, ranging from green algae to higher plants. Phot converts BL signals from the environment into biochemical signals that trigger cellular responses. In phot, the LOV1 and LOV2 domains of the N-terminal region utilize BL for cyclic photoreactions and regulate C-terminal serine/threonine kinase (STK) activity. LOV2-STK peptides are the smallest functional unit of phot and are useful for understanding regulation mechanisms. The combined analysis of spectroscopy and STK activity assay in Arabidopsis phots suggests that the decay speed of the photo-intermediate S390 in LOV2 is one of the factors contributing to light sensitive kinase activity. LOV2 and STK are thought to be adjacent to each other in LOV2-STK with small angle scattering (SAXS). BL irradiation induces LOV2-STK elongation, resulting in LOV2 shifting away from STK. The N- and C-terminal lateral regions of LOV2, A'α-helix, Jα-helix, and A'α/Aβ gap are responsible for the propagation of the BL signal to STK via conformational changes. The comparison between LOV2-STK and full-length phot from Chlamydomonas suggests that LOV1 is directly adjacent to LOV2 in LOV2-STK; therefore, LOV1 may indirectly regulate STK. The molecular mechanism of phot is discussed. PMID:26815763

  20. Photochemical Reactions of the LOV and LOV-Linker Domains of the Blue Light Sensor Protein YtvA.

    PubMed

    Choi, Seokwoo; Nakasone, Yusuke; Hellingwerf, Klaas J; Terazima, Masahide

    2016-06-01

    YtvA is a blue light sensor protein composed of an N-terminal LOV (light-oxygen-voltage) domain, a linker helix, and the C-terminal sulfate transporter and anti-σ factor antagonist domain. YtvA is believed to act as a positive regulator for light and salt stress responses by regulating the σB transcription factor. Although its biological function has been studied, the reaction dynamics and molecular mechanism underlying the function are not well understood. To improve our understanding of the signaling mechanism, we studied the reaction of the LOV domain (YLOV, amino acids 26-127), the LOV domain with its N-terminal extension (N-YLOV, amino acids 1-127), the LOV domain with its C-terminal linker helix (YLOV-linker, amino acids 26-147), and the YLOV domain with the N-terminal extension and the C-terminal linker helix (N-YLOV-linker, amino acids 1-147) using the transient grating method. The signals of all constructs showed adduct formation, thermal diffusion, and molecular diffusion. YLOV showed no change in the diffusion coefficient (D), while the other three constructs showed a significant decrease in D within ∼70 μs of photoexcitation. This indicates that conformational changes in both the N- and C-terminal helices of the YLOV domain indeed do occur. The time constant in the YtvA derivatives was much faster than the corresponding dynamics of phototropins. Interestingly, an additional reaction was observed as a volume expansion as well as a slight increase in D only when both helices were included. These findings suggest that although the rearrangement of the N- and C-terminal helices occurs independently on the fast time scale, this change induces an additional conformational change only when both helices are present. PMID:27203230

  1. Light signal transduction pathway from flavin chromophore to the J alpha helix of Arabidopsis phototropin1.

    PubMed

    Yamamoto, Atsushi; Iwata, Tatsuya; Sato, Yoshiaki; Matsuoka, Daisuke; Tokutomi, Satoru; Kandori, Hideki

    2009-04-01

    In the plant blue-light sensor phototropin, illumination of the chromophoric LOV domains causes activation of the serine/threonine kinase domain. Flavin mononucleotide (FMN) is a chromophore molecule in the two LOV domains (LOV1 and LOV2), but only LOV2 is responsible for kinase activation. Previous studies reported an important role of an additional helix connected to the C-terminal of LOV2 (Jalpha helix) for the function of phototropin; however, it remains unclear how the Jalpha helix affects light-induced structural changes in LOV2. In this study we compared light-induced protein structural changes of the LOV2 domain of Arabidopsis phot1 in the absence (LOV2-core) and presence (LOV2-Jalpha) of the Jalpha helix by Fourier-transform infrared spectroscopy. Prominent peaks were observed only in the amide-I region (1650 (-)/1625 (+) cm(-1)) of LOV2-Jalpha at physiological temperatures (>/=260 K), corresponding to structural perturbation of the alpha-helix. The peaks were diminished by point mutation of functionally important amino acids such as Phe-556 between FMN and the beta-sheet, Gln-575 being hydrogen-bonded with FMN, and Ile-608 on the Jalpha helix. We thus conclude that a light signal is relayed from FMN through these amino acids and eventually changes the interaction between LOV2-core and the Jalpha helix in Arabidopsis phot1. PMID:19348760

  2. Vibrational spectroscopy of an algal Phot-LOV1 domain probes the molecular changes associated with blue-light reception.

    PubMed

    Ataka, K; Hegemann, P; Heberle, J

    2003-01-01

    The LOV1 domain of the blue light Phot1-receptor (phototropin homolog) from Chlamydomonas reinhardtii has been studied by vibrational spectroscopy. The FMN modes of the dark state of LOV1 were identified by preresonance Raman spectroscopy and assigned to molecular vibrations. By comparing the blue-light-induced FTIR difference spectrum with the preresonance Raman spectrum, most of the differences are due to FMN modes. Thus, we exclude large backbone changes of the protein that might occur during the phototransformation of the dark state LOV1-447 into the putative signaling state LOV1-390. Still, the presence of smaller amide difference bands cannot be excluded but may be masked by overlapping FMN modes. The band at 2567 cm(-1) is assigned to the S-H stretching vibration of C57, the residue that forms the transient thio-adduct with the chromophore FMN. The occurrence of this band is evidence that C57 is protonated in the dark state of LOV1. This result challenges conclusions from the homologous LOV2 domain from oat that the thiolate of the corresponding cysteine is the reactive species. PMID:12524299

  3. A search for radical intermediates in the photocycle of LOV domains.

    PubMed

    Kutta, Roger Jan; Magerl, Kathrin; Kensy, Uwe; Dick, Bernhard

    2015-02-01

    LOV domains are the light sensitive parts of phototropins and many other light-activated enzymes that regulate the response to blue light in plants and algae as well as some fungi and bacteria. Unlike all other biological photoreceptors known so far, the photocycle of LOV domains involves the excited triplet state of the chromophore. This chromophore is flavin mononucleotide (FMN) which forms a covalent adduct with a cysteine residue in the signaling state. Since the formation of this adduct from the triplet state involves breaking and forming of two bonds as well as a change from the triplet to the singlet spin state, various intermediates have been proposed, e.g. a protonated triplet state (3)FMNH(+), the radical anion (2)FMN˙(-), or the neutral semiquinone radical (2)FMNH˙. We performed an extensive search for these intermediates by two-dimensional transient absorption (2D-TA) with a streak camera. However, no transient with a rate constant between the decay of fluorescence and the decay of the triplet state could be detected. Analysis of the decay associated difference spectra results in quantum yields for the formation of the adduct from the triplet of ΦA(LOV1) ≈ 0.75 and ΦA(LOV2) ≈ 0.80. This is lower than the values ΦA(LOV1) ≈ 0.95 and ΦA(LOV2) ≈ 0.99 calculated from the rate constants, giving indirect evidence of an intermediate that reacts either to form the adduct or to decay back to the ground state. Since there is no measurable delay between the decay of the triplet and the formation of the adduct, we conclude that this intermediate reacts much faster than it is formed. The LOV1-C57S mutant shows a weak and slowly decaying (τ > 100 μs) transient whose decay associated spectrum has bands at 375 and 500 nm, with a shoulder at 400 nm. This transient is insensitive to the pH change in the range 6.5-10.0 but increases on addition of β-mercaptoethanol as the reducing agent. We assign this intermediate to the radical anion which is protected

  4. Recording of Blue Light-Induced Energy and Volume Changes within the Wild-Type and Mutated Phot-LOV1 Domain from Chlamydomonas reinhardtii

    PubMed Central

    Losi, Aba; Kottke, Tilman; Hegemann, Peter

    2004-01-01

    The time-resolved thermodynamics of the flavin mononucleotide (FMN)-binding LOV1 domain of Chlamydomonas reinhardtii phot (phototropin homolog) was studied by means of laser-induced optoacoustic spectroscopy. In the wild-type protein the early red-shifted intermediate LOV715 exhibits a small volume contraction, ΔV715 = −1.50 ml/mol, with respect to the parent state. LOV715 decays within few μs into the covalent FMN-Cys-57 adduct LOV390, that shows a larger contraction, ΔV390 = −8.8 ml/mol, suggesting a loss of entropy and conformational flexibility. The high energy content of LOV390, E390 = 180 kJ/mol, ensures the driving force for the completion of the photocycle and points to a strained photoreceptor conformation. In the LOV-C57S mutated protein the photoadduct is not formed and ΔV390 is undetected. Large effects on the measured ΔVs are observed in the photochemically competent R58K and R58K/D31Q mutated proteins, with ΔV390 = −2.0 and −1.9 ml/mol, respectively, and ΔV715 ≈ 0. The D31Q and D31N substitutions exhibit smaller but well-detectable effects. These results show that the photo-induced volume changes involve the protein region comprising Arg-58, which tightly interacts with the FMN phosphate group. PMID:14747340

  5. Crystal structures and molecular mechanism of a light-induced signaling switch: The Phot-LOV1 domain from Chlamydomonas reinhardtii.

    PubMed

    Fedorov, Roman; Schlichting, Ilme; Hartmann, Elisabeth; Domratcheva, Tatjana; Fuhrmann, Markus; Hegemann, Peter

    2003-04-01

    Phot proteins (phototropins and homologs) are blue-light photoreceptors that control mechanical processes like phototropism, chloroplast relocation, or guard-cell opening in plants. Phot receptors consist of two flavin mononucleotide (FMN)-binding light, oxygen, or voltage (LOV) domains and a C-terminal serine/threonine kinase domain. We determined crystal structures of the LOV1 domain of Phot1 from the green alga Chlamydomonas reinhardtii in the dark and illuminated state to 1.9 A and 2.8 A resolution, respectively. The structure resembles that of LOV2 from Adiantum (Crosson, S. and K. Moffat. 2001. PROC: Natl. Acad. Sci. USA. 98:2995-3000). In the resting dark state of LOV1, the reactive Cys-57 is present in two conformations. Blue-light absorption causes formation of a proposed active signaling state that is characterized by a covalent bond between the flavin C4a and the thiol of Cys-57. There are differences around the FMN chromophore but no large overall conformational changes. Quantum chemical calculations based on the crystal structures revealed the electronic distribution in the active site during the photocycle. The results suggest trajectories for electrons, protons, and the active site cysteine and offer an interpretation of the reaction mechanism. PMID:12668455

  6. Functional and topological diversity of LOV domain photoreceptors

    PubMed Central

    Glantz, Spencer T.; Carpenter, Eric J.; Melkonian, Michael; Boyden, Edward S.; Wong, Gane Ka-Shu; Chow, Brian Y.

    2016-01-01

    Light–oxygen–voltage sensitive (LOV) flavoproteins are ubiquitous photoreceptors that mediate responses to environmental cues. Photosensory inputs are transduced into signaling outputs via structural rearrangements in sensor domains that consequently modulate the activity of an effector domain or multidomain clusters. Establishing the diversity in effector function and sensor–effector topology will inform what signaling mechanisms govern light-responsive behaviors across multiple kingdoms of life and how these signals are transduced. Here, we report the bioinformatics identification of over 6,700 candidate LOV domains (including over 4,000 previously unidentified sequences from plants and protists), and insights from their annotations for ontological function and structural arrangements. Motif analysis identified the sensors from ∼42 million ORFs, with strong statistical separation from other flavoproteins and non-LOV members of the structurally related Per-aryl hydrocarbon receptor nuclear translocator (ARNT)-Sim family. Conserved-domain analysis determined putative light-regulated function and multidomain topologies. We found that for certain effectors, sensor–effector linker length is discretized based on both phylogeny and the preservation of α-helical heptad repeats within an extended coiled-coil linker structure. This finding suggests that preserving sensor–effector orientation is a key determinant of linker length, in addition to ancestry, in LOV signaling structure–function. We found a surprisingly high prevalence of effectors with functions previously thought to be rare among LOV proteins, such as regulators of G protein signaling, and discovered several previously unidentified effectors, such as lipases. This work highlights the value of applying genomic and transcriptomic technologies to diverse organisms to capture the structural and functional variation in photosensory proteins that are vastly important in adaptation, photobiology, and

  7. Functional and topological diversity of LOV domain photoreceptors.

    PubMed

    Glantz, Spencer T; Carpenter, Eric J; Melkonian, Michael; Gardner, Kevin H; Boyden, Edward S; Wong, Gane Ka-Shu; Chow, Brian Y

    2016-03-15

    Light-oxygen-voltage sensitive (LOV) flavoproteins are ubiquitous photoreceptors that mediate responses to environmental cues. Photosensory inputs are transduced into signaling outputs via structural rearrangements in sensor domains that consequently modulate the activity of an effector domain or multidomain clusters. Establishing the diversity in effector function and sensor-effector topology will inform what signaling mechanisms govern light-responsive behaviors across multiple kingdoms of life and how these signals are transduced. Here, we report the bioinformatics identification of over 6,700 candidate LOV domains (including over 4,000 previously unidentified sequences from plants and protists), and insights from their annotations for ontological function and structural arrangements. Motif analysis identified the sensors from ∼42 million ORFs, with strong statistical separation from other flavoproteins and non-LOV members of the structurally related Per-aryl hydrocarbon receptor nuclear translocator (ARNT)-Sim family. Conserved-domain analysis determined putative light-regulated function and multidomain topologies. We found that for certain effectors, sensor-effector linker length is discretized based on both phylogeny and the preservation of α-helical heptad repeats within an extended coiled-coil linker structure. This finding suggests that preserving sensor-effector orientation is a key determinant of linker length, in addition to ancestry, in LOV signaling structure-function. We found a surprisingly high prevalence of effectors with functions previously thought to be rare among LOV proteins, such as regulators of G protein signaling, and discovered several previously unidentified effectors, such as lipases. This work highlights the value of applying genomic and transcriptomic technologies to diverse organisms to capture the structural and functional variation in photosensory proteins that are vastly important in adaptation, photobiology, and optogenetics

  8. Photo-reduction of flavin mononucleotide to semiquinone form in LOV domain mutants of blue-light receptor phot from Chlamydomonas reinhardtii.

    PubMed

    Song, S-H; Dick, B; Penzkofer, A; Hegemann, P

    2007-04-01

    The photo-excitation dynamics of the mutants LOV1-C57S and LOV2-C250S of the LOV-domains of the phototropin photoreceptor phot from the green alga Chlamydomonas reinhardtii is investigated by absorption and fluorescence studies. The LOV domains fused to a maltose binding protein (MBP) are expressed in Escherichia coli. The mutants were studied under aerobic conditions in aqueous solution at pH 8. Blue-light exposure reduced the fully oxidized flavin mononucleotide, FMN(ox), to FMN semiquinone, FMNH*, (quantum efficiency around 1%) which further reduced to FMN hydroquinone, FMN(red)H(2) or FMN(red)H(-) (quantum efficiency ca. 3 x 10(-5)). In the dark both reduced forms recovered back to the oxidized form on a minute timescale. Besides photoreduction, blue-light photo-excitation of the mutants resulted in photoproduct formation (efficiency in the 2 x 10(-4) - 10(-3) range). Photo-reaction schemes for the mutants are discussed. PMID:17292618

  9. Metagenome-based screening reveals worldwide distribution of LOV-domain proteins.

    PubMed

    Pathak, Gopal P; Losi, Aba; Gärtner, Wolfgang

    2012-01-01

    Metagenomes from various environments were screened for sequences homologous to light, oxygen, voltage (LOV)-domain proteins. LOV domains are flavin binding, blue-light (BL)-sensitive photoreceptors present in 10-15% of deposited prokaryotic genomes. The LOV domain has been selected, since BL is an ever present and sometimes harmful environmental factor for microbial communities. The majority of the metagenome material originated from the Sargasso Sea Project and from open-ocean sampling. In total, more than 40 million open reading frames were investigated for LOV-domain sequences. Most sequences were identified from aquatic material, but they were also found in metagenomes from soil and extreme environments, e.g. hypersaline ponds, acidic mine drainage or wastewater treatment facilities. A total of 578 LOV domains was assigned by three criteria: (1) the highly conserved core region, (2) the presence of minimally 14 essential amino acids and (3) a minimal length of 80 amino acids. More than three quarters of these identified genes showed a sequence divergence of more than 20% from database-deposited LOV domains from known organisms, indicating the large variation of this photoreceptor motif. The broad occurrence of LOV domains in metagenomes emphasizes their important physiological role for light-induced signal transduction, stress adaptation and survival mechanisms. PMID:22044076

  10. A dominant mutation in the light-oxygen and voltage2 domain vicinity impairs phototropin1 signaling in tomato.

    PubMed

    Sharma, Sulabha; Kharshiing, Eros; Srinivas, Ankanagari; Zikihara, Kazunori; Tokutomi, Satoru; Nagatani, Akira; Fukayama, Hiroshi; Bodanapu, Reddaiah; Behera, Rajendra K; Sreelakshmi, Yellamaraju; Sharma, Rameshwar

    2014-04-01

    In higher plants, blue light (BL) phototropism is primarily controlled by the phototropins, which are also involved in stomatal movement and chloroplast relocation. These photoresponses are mediated by two phototropins, phot1 and phot2. Phot1 mediates responses with higher sensitivity than phot2, and phot2 specifically mediates chloroplast avoidance and dark positioning responses. Here, we report the isolation and characterization of a Nonphototropic seedling1 (Nps1) mutant of tomato (Solanum lycopersicum). The mutant is impaired in low-fluence BL responses, including chloroplast accumulation and stomatal opening. Genetic analyses show that the mutant locus is dominant negative in nature. In dark-grown seedlings of the Nps1 mutant, phot1 protein accumulates at a highly reduced level relative to the wild type and lacks BL-induced autophosphorylation. The mutant harbors a single glycine-1484-to-alanine transition in the Hinge1 region of a phot1 homolog, resulting in an arginine-to-histidine substitution (R495H) in a highly conserved A'α helix proximal to the light-oxygen and voltage2 domain of the translated gene product. Significantly, the R495H substitution occurring in the Hinge1 region of PHOT1 abolishes its regulatory activity in Nps1 seedlings, thereby highlighting the functional significance of the A'α helix region in phototropic signaling of tomato. PMID:24515830

  11. Photocontrolled Exposure of Pro-apoptotic Peptide Sequences in LOV Proteins Modulates Bcl-2 Family Interactions.

    PubMed

    Mart, Robert J; Meah, Dilruba; Allemann, Rudolf K

    2016-04-15

    LOV domains act as biomolecular sensors for light, oxygen or the environment's redox potential. Conformational changes upon the formation of a covalent cysteinyl flavin adduct are propagated through hydrogen-bonding networks in the core of designed hybrid phototropin LOV2 domains that incorporate the Bcl homology region 3 (BH3) of the key pro-apoptotic protein BH3-interacting-domain death agonist (BID). The resulting change in conformation of a flanking amphiphilic α-helix creates a light-dependent optogenetic tool for the modulation of interactions with the anti-apoptotic B-cell leukaemia-2 (Bcl-2) family member Bcl-xL . PMID:26493687

  12. Unfolding of the C-Terminal Jα Helix in the LOV2 Photoreceptor Domain Observed by Time-Resolved Vibrational Spectroscopy.

    PubMed

    Konold, Patrick E; Mathes, Tilo; Weiβenborn, Jörn; Groot, Marie Louise; Hegemann, Peter; Kennis, John T M

    2016-09-01

    Light-triggered reactions of biological photoreceptors have gained immense attention for their role as molecular switches in their native organisms and for optogenetic application. The light, oxygen, and voltage 2 (LOV2) sensing domain of plant phototropin binds a C-terminal Jα helix that is docked on a β-sheet and unfolds upon light absorption by the flavin mononucleotide (FMN) chromophore. In this work, the signal transduction pathway of LOV2 from Avena sativa was investigated using time-resolved infrared spectroscopy from picoseconds to microseconds. In D2O buffer, FMN singlet-to-triplet conversion occurs in 2 ns and formation of the covalent cysteinyl-FMN adduct in 10 μs. We observe a two-step unfolding of the Jα helix: The first phase occurs concomitantly with Cys-FMN covalent adduct formation in 10 μs, along with hydrogen-bond rupture of the FMN C4═O with Gln-513, motion of the β-sheet, and an additional helical element. The second phase occurs in approximately 240 μs. The final spectrum at 500 μs is essentially identical to the steady-state light-minus-dark Fourier transform infrared spectrum, indicating that Jα helix unfolding is complete on that time scale. PMID:27537211

  13. Structural Tuning of the Fluorescent Protein iLOV for Improved Photostability*

    PubMed Central

    Christie, John M.; Hitomi, Kenichi; Arvai, Andrew S.; Hartfield, Kimberly A.; Mettlen, Marcel; Pratt, Ashley J.; Tainer, John A.; Getzoff, Elizabeth D.

    2012-01-01

    Fluorescent proteins derived from light, oxygen, or voltage (LOV) domains offer advantages over green fluorescent protein (GFP) from their small size and efficacy under anaerobic conditions. The flavoprotein improved LOV (iLOV) was engineered from the blue light receptor phototropin as a reporter of viral infection. To inform the molecular basis for the improved, photoreversible, fluorescent properties of iLOV, we employed directed evolution and determined five LOV crystallographic structures. Comparative structural analyses between iLOV and its progenitors reveal mutation-induced constraints in the environment of the flavin mononucleotide (FMN) chromophore; in iLOV, the methyl group of Thr-394 “crowds” the FMN isoalloxazine ring, Leu-470 triggers side chain “flipping” of Leu-472, and the terminal FMN phosphate shows increased anchoring. We further engineered iLOV variants that are readily detectable in bacterial and mammalian cells due to order-of-magnitude photostability increases. Structure determination of a resulting representative photostable iLOV (phiLOV) variant reveals additional constraints on the chromophore. Aromatic residues Tyr-401 and Phe-485 in phiLOV sandwich the FMN isoalloxazine ring from both sides, whereas Ser-390 anchors the side chain of FMN-interacting Gln-489 Our combined structural and mutational results reveal that constraining the FMN fluorophore yields improved photochemical properties for iLOV and its new photostable derivative. These findings provide a framework for structural fine-tuning of LOV scaffold proteins to maximize their potential as oxygen-independent fluorescent reporters. PMID:22573334

  14. Engineering and Application of LOV2-Based Photoswitches.

    PubMed

    Zimmerman, S P; Kuhlman, B; Yumerefendi, H

    2016-01-01

    Cellular optogenetic switches, a novel class of biological tools, have improved our understanding of biological phenomena that were previously intractable. While the design and engineering of these proteins has historically varied, they are all based on borrowed elements from plant and bacterial photoreceptors. In general terms, each of the optogenetic switches designed to date exploits the endogenous light-induced change in photoreceptor conformation while repurposing its effect to target a different biological phenomenon. We focus on the well-characterized light-oxygen-voltage 2 (LOV2) domain from Avena sativa phototropin 1 as our cornerstone for design. While the function of the LOV2 domain in the context of the phototropin protein is not fully elucidated, its thorough biophysical characterization as an isolated domain has created a strong foundation for engineering of photoswitches. In this chapter, we examine the biophysical characteristics of the LOV2 domain that may be exploited to produce an optogenetic switch and summarize previous design efforts to provide guidelines for an effective design. Furthermore, we provide protocols for assays including fluorescence polarization, phage display, and microscopy that are optimized for validating, improving, and using newly designed photoswitches. PMID:27586333

  15. Exploring the multiscale signaling behavior of phototropin1 from Chlamydomonas reinhardtii using a full-residue space kinetic Monte Carlo molecular dynamics technique.

    PubMed

    Peter, Emanuel; Dick, Bernhard; Stambolic, Ivan; Baeurle, Stephan A

    2014-09-01

    Devising analysis tools for elucidating the regulatory mechanism of complex enzymes has been a challenging task for many decades. It generally requires the determination of the structural-dynamical information of protein solvent systems far from equilibrium over multiple length and time scales, which is still difficult both theoretically and experimentally. To cope with the problem, we introduce a full-residue space multiscale simulation method based on a combination of the kinetic Monte Carlo and molecular dynamics techniques, in which the rates of the rate-determining processes are evaluated from a biomolecular forcefield on the fly during the simulation run by taking into account the full space of residues. To demonstrate its reliability and efficiency, we explore the light-induced functional behavior of the full-length phototropin1 from Chlamydomonas reinhardtii (Cr-phot1) and its various subdomains. Our results demonstrate that in the dark state the light oxygen voltage-2-Jα (LOV2-Jα) photoswitch inhibits the enzymatic activity of the kinase, whereas the LOV1-Jα photoswitch controls the dimerization with the LOV2 domain. This leads to the repulsion of the LOV1-LOV2 linker out of the interface region between both LOV domains, which results in a positively charged surface suitable for cell-membrane interaction. By contrast, in the light state, we observe that the distance between both LOV domains is increased and the LOV1-LOV2 linker forms a helix-turn-helix (HTH) motif, which enables gene control through nucleotide binding. Finally, we find that the kinase is activated through the disruption of the Jα-helix from the LOV2 domain, which is followed by a stretching of the activation loop (A-loop) and broadening of the catalytic cleft of the kinase. PMID:24623633

  16. Vibrational assignment of the flavin-cysteinyl adduct in a signaling state of the LOV domain in FKF1.

    PubMed

    Kikuchi, Sadato; Unno, Masashi; Zikihara, Kazunori; Tokutomi, Satoru; Yamauchi, Seigo

    2009-03-01

    LOV domains belong to the PAS domain superfamily, which are found in a variety of sensor proteins in organism ranging from archaea to eukaryotes, and they noncovalently bind a single flavin mononucleotide as a chromophore. We report the Raman spectra of the dark state of LOV domain in FKF1 from Arabidopsis thaliana. Spectra have been also measured for the signaling state, where a cysteinyl-flavin adduct is formed upon light irradiation. Most of the observed Raman bands are assigned on the basis of normal mode calculations using a density functional theory. We also discuss implication for the analysis of the infrared spectra of LOV domains. The comprehensive assignment provides a satisfactory framework for future investigations of the photocycle mechanism in LOV domains by vibrational spectroscopy. PMID:19708118

  17. Lighting Up Clostridium Difficile: Reporting Gene Expression Using Fluorescent Lov Domains

    PubMed Central

    Buckley, Anthony M.; Jukes, Caitlin; Candlish, Denise; Irvine, June J.; Spencer, Janice; Fagan, Robert P.; Roe, Andrew J.; Christie, John M.; Fairweather, Neil F.; Douce, Gillian R.

    2016-01-01

    The uses of fluorescent reporters derived from green fluorescent protein have proved invaluable for the visualisation of biological processes in bacteria grown under aerobic conditions. However, their requirement for oxygen has limited their application in obligate anaerobes such as Clostridium difficile. Fluorescent proteins derived from Light, Oxygen or Voltage sensing (LOV) domains have been shown to bridge this limitation, but their utility as translational fusions to monitor protein expression and localisation in a strict anaerobic bacterium has not been reported. Here we demonstrate the utility of phiLOV in three species of Clostridium and its application as a marker of real-time protein translation and dynamics through genetic fusion with the cell division protein, FtsZ. Time lapse microscopy of dividing cells suggests that Z ring assembly arises through the extension of the FtsZ arc starting from one point on the circumference. Furthermore, through incorporation of phiLOV into the flagella subunit, FliC, we show the potential of bacterial LOV-based fusion proteins to be successfully exported to the extracellular environment. PMID:26996606

  18. A Dominant Mutation in the Light-Oxygen and Voltage2 Domain Vicinity Impairs Phototropin1 Signaling in Tomato1[C][W][OPEN

    PubMed Central

    Sharma, Sulabha; Kharshiing, Eros; Srinivas, Ankanagari; Zikihara, Kazunori; Tokutomi, Satoru; Nagatani, Akira; Fukayama, Hiroshi; Bodanapu, Reddaiah; Behera, Rajendra K.; Sreelakshmi, Yellamaraju; Sharma, Rameshwar

    2014-01-01

    In higher plants, blue light (BL) phototropism is primarily controlled by the phototropins, which are also involved in stomatal movement and chloroplast relocation. These photoresponses are mediated by two phototropins, phot1 and phot2. Phot1 mediates responses with higher sensitivity than phot2, and phot2 specifically mediates chloroplast avoidance and dark positioning responses. Here, we report the isolation and characterization of a Nonphototropic seedling1 (Nps1) mutant of tomato (Solanum lycopersicum). The mutant is impaired in low-fluence BL responses, including chloroplast accumulation and stomatal opening. Genetic analyses show that the mutant locus is dominant negative in nature. In dark-grown seedlings of the Nps1 mutant, phot1 protein accumulates at a highly reduced level relative to the wild type and lacks BL-induced autophosphorylation. The mutant harbors a single glycine-1484-to-alanine transition in the Hinge1 region of a phot1 homolog, resulting in an arginine-to-histidine substitution (R495H) in a highly conserved A′α helix proximal to the light-oxygen and voltage2 domain of the translated gene product. Significantly, the R495H substitution occurring in the Hinge1 region of PHOT1 abolishes its regulatory activity in Nps1 seedlings, thereby highlighting the functional significance of the A′α helix region in phototropic signaling of tomato. PMID:24515830

  19. Blue light-induced LOV domain dimerization enhances the affinity of Aureochrome 1a for its target DNA sequence

    PubMed Central

    Heintz, Udo; Schlichting, Ilme

    2016-01-01

    The design of synthetic optogenetic tools that allow precise spatiotemporal control of biological processes previously inaccessible to optogenetic control has developed rapidly over the last years. Rational design of such tools requires detailed knowledge of allosteric light signaling in natural photoreceptors. To understand allosteric communication between sensor and effector domains, characterization of all relevant signaling states is required. Here, we describe the mechanism of light-dependent DNA binding of the light-oxygen-voltage (LOV) transcription factor Aureochrome 1a from Phaeodactylum tricornutum (PtAu1a) and present crystal structures of a dark state LOV monomer and a fully light-adapted LOV dimer. In combination with hydrogen/deuterium-exchange, solution scattering data and DNA-binding experiments, our studies reveal a light-sensitive interaction between the LOV and basic region leucine zipper DNA-binding domain that together with LOV dimerization results in modulation of the DNA affinity of PtAu1a. We discuss the implications of these results for the design of synthetic LOV-based photosensors with application in optogenetics. DOI: http://dx.doi.org/10.7554/eLife.11860.001 PMID:26754770

  20. Regulatory mechanism of the light-activable allosteric switch LOV-TAP for the control of DNA binding: a computer simulation study.

    PubMed

    Peter, Emanuel; Dick, Bernhard; Baeurle, Stephan A

    2013-03-01

    The spatio-temporal control of gene expression is fundamental to elucidate cell proliferation and deregulation phenomena in living systems. Novel approaches based on light-sensitive multiprotein complexes have recently been devised, showing promising perspectives for the noninvasive and reversible modulation of the DNA-transcriptional activity in vivo. This has lately been demonstrated in a striking way through the generation of the artificial protein construct light-oxygen-voltage (LOV)-tryptophan-activated protein (TAP), in which the LOV-2-Jα photoswitch of phototropin1 from Avena sativa (AsLOV2-Jα) has been ligated to the tryptophan-repressor (TrpR) protein from Escherichia coli. Although tremendous progress has been achieved on the generation of such protein constructs, a detailed understanding of their functioning as opto-genetical tools is still in its infancy. Here, we elucidate the early stages of the light-induced regulatory mechanism of LOV-TAP at the molecular level, using the noninvasive molecular dynamics simulation technique. More specifically, we find that Cys450-FMN-adduct formation in the AsLOV2-Jα-binding pocket after photoexcitation induces the cleavage of the peripheral Jα-helix from the LOV core, causing a change of its polarity and electrostatic attraction of the photoswitch onto the DNA surface. This goes along with the flexibilization through unfolding of a hairpin-like helix-loop-helix region interlinking the AsLOV2-Jα- and TrpR-domains, ultimately enabling the condensation of LOV-TAP onto the DNA surface. By contrast, in the dark state the AsLOV2-Jα photoswitch remains inactive and exerts a repulsive electrostatic force on the DNA surface. This leads to a distortion of the hairpin region, which finally relieves its tension by causing the disruption of LOV-TAP from the DNA. PMID:23042418

  1. The C-terminal kinase fragment of Arabidopsis phototropin 2 triggers constitutive phototropin responses.

    PubMed

    Kong, Sam-Geun; Kinoshita, Toshinori; Shimazaki, Ken-Ichiro; Mochizuki, Nobuyoshi; Suzuki, Tomomi; Nagatani, Akira

    2007-09-01

    Phototropins mediate various blue-light responses such as phototropism, chloroplast relocation, stomatal opening and leaf flattening in plants. Phototropins are hydrophilic chromoproteins that are mainly bound to the plasma membrane. One of two phototropins in Arabidopsis thaliana, phot2, associates with the Golgi apparatus in a light-dependent manner. In this study, we analyzed the biological activities of the N-terminal photosensory and C-terminal kinase domains of phot2. For this purpose, these domains were fused to green fluorescent protein (GFP) and ectopically expressed in the wild-type and a phot1 phot2 double mutant of Arabidopsis. The kinase domain fused to GFP (P2CG) was localized to the plasma membrane and the Golgi apparatus, whereas the photosensory domain fused to GFP (P2NG) was uniformly localized in the cytosol. Hence, the kinase domain rather than the photosensory domain is responsible for the membrane association. Interestingly, the P2CG plants exhibited constitutive blue-light responses even in dark conditions, i.e. stomata were open and chloroplasts were in the avoidance position. By contrast, P2CG with a mutation that abolishes the kinase activity (P2C[D720/N]G) failed to exhibit these responses. phot2 kinase is therefore suggested to be correctly localized to functional sites in the cell and to trigger light signal transduction through its kinase activity. In contrast to P2CG, P2NG did not affect the phot2 responses, except for partial inhibition of the phototropic response caused by the endogenous phototropins. PMID:17662032

  2. Function, structure, and mechanism in bacterial photosensory LOV proteins

    PubMed Central

    Herrou, Julien; Crosson, Sean

    2012-01-01

    LOV domains are protein photosensors conserved in bacteria, archaea, plants and fungi that detect blue light via a flavin cofactor. In the bacterial kingdom, LOV domains are present in both chemotrophic and phototrophic species, where they are found N-terminally of signaling and regulatory domains such as sensor histidine kinases, diguanylate cyclases/phosphodiesterases, DNA-binding domains, and σ factor regulators. In this review, we describe the current state of knowledge on the function of bacterial LOV proteins, the structural basis of LOV domain-mediated signal transduction, and the use of LOV domains as genetically-encoded photoswitches in synthetic biology. PMID:21822294

  3. The origin and evolution of phototropins.

    PubMed

    Li, Fay-Wei; Rothfels, Carl J; Melkonian, Michael; Villarreal, Juan C; Stevenson, Dennis W; Graham, Sean W; Wong, Gane K-S; Mathews, Sarah; Pryer, Kathleen M

    2015-01-01

    Plant phototropism, the ability to bend toward or away from light, is predominantly controlled by blue-light photoreceptors, the phototropins. Although phototropins have been well-characterized in Arabidopsis thaliana, their evolutionary history is largely unknown. In this study, we complete an in-depth survey of phototropin homologs across land plants and algae using newly available transcriptomic and genomic data. We show that phototropins originated in an ancestor of Viridiplantae (land plants + green algae). Phototropins repeatedly underwent independent duplications in most major land-plant lineages (mosses, lycophytes, ferns, and seed plants), but remained single-copy genes in liverworts and hornworts-an evolutionary pattern shared with another family of photoreceptors, the phytochromes. Following each major duplication event, the phototropins differentiated in parallel, resulting in two specialized, yet partially overlapping, functional forms that primarily mediate either low- or high-light responses. Our detailed phylogeny enables us to not only uncover new phototropin lineages, but also link our understanding of phototropin function in Arabidopsis with what is known in Adiantum and Physcomitrella (the major model organisms outside of flowering plants). We propose that the convergent functional divergences of phototropin paralogs likely contributed to the success of plants through time in adapting to habitats with diverse and heterogeneous light conditions. PMID:26322073

  4. The origin and evolution of phototropins

    PubMed Central

    Li, Fay-Wei; Rothfels, Carl J.; Melkonian, Michael; Villarreal, Juan C.; Stevenson, Dennis W.; Graham, Sean W.; Wong, Gane K.-S.; Mathews, Sarah; Pryer, Kathleen M.

    2015-01-01

    Plant phototropism, the ability to bend toward or away from light, is predominantly controlled by blue-light photoreceptors, the phototropins. Although phototropins have been well-characterized in Arabidopsis thaliana, their evolutionary history is largely unknown. In this study, we complete an in-depth survey of phototropin homologs across land plants and algae using newly available transcriptomic and genomic data. We show that phototropins originated in an ancestor of Viridiplantae (land plants + green algae). Phototropins repeatedly underwent independent duplications in most major land-plant lineages (mosses, lycophytes, ferns, and seed plants), but remained single-copy genes in liverworts and hornworts—an evolutionary pattern shared with another family of photoreceptors, the phytochromes. Following each major duplication event, the phototropins differentiated in parallel, resulting in two specialized, yet partially overlapping, functional forms that primarily mediate either low- or high-light responses. Our detailed phylogeny enables us to not only uncover new phototropin lineages, but also link our understanding of phototropin function in Arabidopsis with what is known in Adiantum and Physcomitrella (the major model organisms outside of flowering plants). We propose that the convergent functional divergences of phototropin paralogs likely contributed to the success of plants through time in adapting to habitats with diverse and heterogeneous light conditions. PMID:26322073

  5. A Native Threonine Coordinates Ordered Water to Tune Light-Oxygen-Voltage (LOV) Domain Photocycle Kinetics and Osmotic Stress Signaling in Trichoderma reesei ENVOY.

    PubMed

    Lokhandwala, Jameela; Silverman Y de la Vega, Rafael I; Hopkins, Hilary C; Britton, Collin W; Rodriguez-Iglesias, Aroa; Bogomolni, Roberto; Schmoll, Monika; Zoltowski, Brian D

    2016-07-01

    Light-oxygen-voltage (LOV) domain-containing proteins function as small light-activated modules capable of imparting blue light control of biological processes. Their small modular nature has made them model proteins for allosteric signal transduction and optogenetic devices. Despite intense research, key aspects of their signal transduction mechanisms and photochemistry remain poorly understood. In particular, ordered water has been identified as a possible key mediator of photocycle kinetics, despite the lack of ordered water in the LOV active site. Herein, we use recent crystal structures of a fungal LOV protein ENVOY to interrogate the role of Thr(101) in recruiting water to the flavin active site where it can function as an intrinsic base to accelerate photocycle kinetics. Kinetic and molecular dynamic simulations confirm a role in solvent recruitment to the active site and identify structural changes that correlate with solvent recruitment. In vivo analysis of T101I indicates a direct role of the Thr(101) position in mediating adaptation to osmotic stress, thereby verifying biological relevance of ordered water in LOV signaling. The combined studies identify position 101 as a mediator of both allostery and photocycle catalysis that can impact organism physiology. PMID:27226624

  6. Essential role of the A'α/Aβ gap in the N-terminal upstream of LOV2 for the blue light signaling from LOV2 to kinase in Arabidopsis photototropin1, a plant blue light receptor.

    PubMed

    Kashojiya, Sachiko; Okajima, Koji; Shimada, Takashi; Tokutomi, Satoru

    2015-01-01

    Phototropin (phot) is a blue light (BL) receptor in plants and is involved in phototropism, chloroplast movement, stomata opening, etc. A phot molecule has two photo-receptive domains named LOV (Light-Oxygen-Voltage) 1 and 2 in its N-terminal region and a serine/threonine kinase (STK) in its C-terminal region. STK activity is regulated mainly by LOV2, which has a cyclic photoreaction, including the transient formation of a flavin mononucleotide (FMN)-cysteinyl adduct (S390). One of the key events for the propagation of the BL signal from LOV2 to STK is conformational changes in a Jα-helix residing downstream of the LOV2 C-terminus. In contrast, we focused on the role of the A'α-helix, which is located upstream of the LOV2 N-terminus and interacts with the Jα-helix. Using LOV2-STK polypeptides from Arabidopsis thaliana phot1, we found that truncation of the A'α-helix and amino acid substitutions at Glu474 and Lys475 in the gap between the A'α and the Aβ strand of LOV2 (A'α/Aβ gap) to Ala impaired the BL-induced activation of the STK, although they did not affect S390 formation. Trypsin digested the LOV2-STK at Lys603 and Lys475 in a light-dependent manner indicating BL-induced structural changes in both the Jα-helix and the gap. The digestion at Lys603 is faster than at Lys475. These BL-induced structural changes were observed with the Glu474Ala and the Lys475Ala substitutes, indicating that the BL signal reached the Jα-helix as well as the A'α/Aβ gap but could not activate STK. The amino acid residues, Glu474 and Lys475, in the gap are conserved among the phots of higher plants and may act as a joint to connect the structural changes in the Jα-helix with the activation of STK. PMID:25886203

  7. Essential Role of the A’α/Aβ Gap in the N-Terminal Upstream of LOV2 for the Blue Light Signaling from LOV2 to Kinase in Arabidopsis Photototropin1, a Plant Blue Light Receptor

    PubMed Central

    Kashojiya, Sachiko; Okajima, Koji; Shimada, Takashi; Tokutomi, Satoru

    2015-01-01

    Phototropin (phot) is a blue light (BL) receptor in plants and is involved in phototropism, chloroplast movement, stomata opening, etc. A phot molecule has two photo-receptive domains named LOV (Light-Oxygen-Voltage) 1 and 2 in its N-terminal region and a serine/threonine kinase (STK) in its C-terminal region. STK activity is regulated mainly by LOV2, which has a cyclic photoreaction, including the transient formation of a flavin mononucleotide (FMN)-cysteinyl adduct (S390). One of the key events for the propagation of the BL signal from LOV2 to STK is conformational changes in a Jα-helix residing downstream of the LOV2 C-terminus. In contrast, we focused on the role of the A’α-helix, which is located upstream of the LOV2 N-terminus and interacts with the Jα-helix. Using LOV2-STK polypeptides from Arabidopsis thaliana phot1, we found that truncation of the A’α-helix and amino acid substitutions at Glu474 and Lys475 in the gap between the A’α and the Aβ strand of LOV2 (A’α/Aβ gap) to Ala impaired the BL-induced activation of the STK, although they did not affect S390 formation. Trypsin digested the LOV2-STK at Lys603 and Lys475 in a light-dependent manner indicating BL-induced structural changes in both the Jα-helix and the gap. The digestion at Lys603 is faster than at Lys475. These BL-induced structural changes were observed with the Glu474Ala and the Lys475Ala substitutes, indicating that the BL signal reached the Jα-helix as well as the A’α/Aβ gap but could not activate STK. The amino acid residues, Glu474 and Lys475, in the gap are conserved among the phots of higher plants and may act as a joint to connect the structural changes in the Jα-helix with the activation of STK. PMID:25886203

  8. Molecular Mechanism of Photozipper, a Light-Regulated Dimerizing Module Consisting of the bZIP and LOV Domains of Aureochrome-1.

    PubMed

    Nakatani, Yoichi; Hisatomi, Osamu

    2015-06-01

    Aureochrome-1 (AUREO1) is a blue light (BL) receptor responsible for the BL-induced blanching of a stramenopile alga, Vaucheria frigida. The AUREO1 protein contains a central basic region/leucine zipper (bZIP) domain, and a C-terminal light-oxygen-voltage-sensing (LOV) domain. BL induces the dimerization of monomeric AUREO1, which subsequently increases the affinity of this transcription factor for its target DNA [Hisatomi, O., et al. (2014) J. Biol. Chem. 289, 17379-17391]. We constructed a synthetic gene encoding N-terminally truncated monomeric AUREO1 (designated Photozipper) to elucidate the molecular mechanism of this BL-regulated transcription factor and to develop it as an optogenetic tool. In this study, four different Photozipper (PZ) protein constructs were prepared comprising different N-terminal truncations. The monomer-dimer equilibria of the PZ constructs were investigated in the dark and light states. Dynamic light scattering and size-exclusion chromatography analyses revealed that the apparent dissociation constants of PZ dimers with and without the ZIP region were ~100 and 30 μM, respectively, indicating that the ZIP region stabilized the monomeric form in the dark state. In the light state, fluorescence resonance energy transfer analyses demonstrated that deletion of the ZIP region increased the dissociation constant from ~0.15 to 0.6 μM, suggesting that intermolecular LOV-LOV and ZIP-ZIP interactions stabilized the dimeric forms. Our results suggest that synergistic interactions between the LOV and bZIP domains stabilize the monomeric form in the dark state and the dimeric form in the light state, which possibly contributes to the function of PZ as a BL-regulated molecular switch. PMID:25932652

  9. Reconstitution of an Initial Step of Phototropin Signaling in Stomatal Guard Cells.

    PubMed

    Takemiya, Atsushi; Doi, Ayaka; Yoshida, Sayumi; Okajima, Koji; Tokutomi, Satoru; Shimazaki, Ken-Ichiro

    2016-01-01

    Phototropins are light-activated receptor kinases that mediate a wide range of blue light responses responsible for the optimization of photosynthesis. Despite the physiological importance of phototropins, it is still unclear how they transduce light signals into physiological responses. Here, we succeeded in reproducing a primary step of phototropin signaling in vitro using a physiological substrate of phototropin, the BLUS1 (BLUE LIGHT SIGNALING1) kinase of guard cells. When PHOT1 and BLUS1 were expressed in Escherichia coli and the resulting recombinant proteins were incubated with ATP, white and blue light induced phosphorylation of BLUS1 but red light and darkness did not. Site-directed mutagenesis of PHOT1 and BLUS1 revealed that the phosphorylation was catalyzed by phot1 kinase. Similar to stomatal blue light responses, the BLUS1 phosphorylation depended on the fluence rate of blue light and was inhibited by protein kinase inhibitors, K-252a and staurosporine. In contrast to the result in vivo, BLUS1 was not dephosphorylated in vitro, suggesting the involvement of a protein phosphatase in the response in vivo. phot1 with a C-terminal kinase domain but devoid of the N-terminal domain, constitutively phosphorylated BLUS1 without blue light, indicating that the N-terminal domain has an autoinhibitory action and prevents substrate phosphorylation. The results provide the first reconstitution of a primary step of phototropin signaling and a clue for understanding the molecular nature of this process. PMID:26707730

  10. Fine tuning chloroplast movements through physical interactions between phototropins

    PubMed Central

    Sztatelman, Olga; Łabuz, Justyna; Hermanowicz, Paweł; Banaś, Agnieszka Katarzyna; Bażant, Aneta; Zgłobicki, Piotr; Aggarwal, Chhavi; Nadzieja, Marcin; Krzeszowiec, Weronika; Strzałka, Wojciech; Gabryś, Halina

    2016-01-01

    Phototropins are plant photoreceptors which regulate numerous responses to blue light, including chloroplast relocation. Weak blue light induces chloroplast accumulation, whereas strong light leads to an avoidance response. Two Arabidopsis phototropins are characterized by different light sensitivities. Under continuous light, both can elicit chloroplast accumulation, but the avoidance response is controlled solely by phot2. As well as continuous light, brief light pulses also induce chloroplast displacements. Pulses of 0.1s and 0.2s of fluence rate saturating the avoidance response lead to transient chloroplast accumulation. Longer pulses (up to 20s) trigger a biphasic response, namely transient avoidance followed by transient accumulation. This work presents a detailed study of transient chloroplast responses in Arabidopsis. Phototropin mutants display altered chloroplast movements as compared with the wild type: phot1 is characterized by weaker responses, while phot2 exhibits enhanced chloroplast accumulation, especially after 0.1s and 0.2s pulses. To determine the cause of these differences, the abundance and phosphorylation levels of both phototropins, as well as the interactions between phototropin molecules are examined. The formation of phototropin homo- and heterocomplexes is the most plausible explanation of the observed phenomena. The physiological consequences of this interplay are discussed, suggesting the universal character of this mechanism that fine-tunes plant reactions to blue light. Additionally, responses in mutants of different protein phosphatase 2A subunits are examined to assess the role of protein phosphorylation in signaling of chloroplast movements. PMID:27406783

  11. PAS/LOV proteins: A proposed new class of plant blue light receptor.

    PubMed

    Ogura, Yasunobu; Tokutomi, Satoru; Wada, Masamitsu; Kiyosue, Tomohiro

    2008-11-01

    The light, oxygen or voltage (LOV) domain belongs to the Per-ARNT-Sim (PAS) superfamily of domains, and functions with the flavin chromophore as a module for sensing blue light in plants and fungi. The Arabidopsis thaliana PAS/LOV proteins (PLPs), of unknown function, possess an N-terminal PAS domain and a C-terminal LOV domain. Our recent analysis using yeast two-hybrid and Escherichia coli protein production systems reveals that the interactions of Arabidopsis PLPs with several proteins diminish under blue light illumination and that the PLP LOV domain may bind to a flavin chromophore. These results suggest that PLP functions as a blue light receptor. Homologs of PLP exist in rice, tomato and moss. The LOV domains of these PLP homologs form a distinct group in phylogenetic analysis. These facts suggest that PLP belongs to a new class of plant blue light receptor. PMID:19704421

  12. Phosphoinositides Play Differential Roles in Regulating Phototropin1- and Phototropin2-Mediated Chloroplast Movements in Arabidopsis

    PubMed Central

    Aggarwal, Chhavi; Łabuz, Justyna; Gabryś, Halina

    2013-01-01

    Phototropins are UVA/blue-light receptors involved in controlling the light-dependent physiological responses which serve to optimize the photosynthetic activity of plants and promote growth. The phototropin-induced phosphoinositide (PI) metabolism has been shown to be essential for stomatal opening and phototropism. However, the role of PIs in phototropin-induced chloroplast movements remains poorly understood. The aim of this work is to determine which PI species are involved in the control of chloroplast movements in Arabidopsis and the nature of their involvement. We present the effects of the inactivation of phospholipase C (PLC), PI3-kinase (PI3K) and PI4-kinase (PI4K) on chloroplast relocations in Arabidopsis. The inhibition of the phosphatidylinositol 4,5-bisphospahte [PI(4,5)P2]-PLC pathway, using neomycin and U73122, suppressed the phot2-mediated chloroplast accumulation and avoidance responses, without affecting movement responses controlled by phot1. On the other hand, PI3K and PI4K activities are more restricted to phot1- and phot2-induced weak-light responses. The inactivation of PI3K and PI4K by wortmannin and LY294002 severely affected the weak blue-light-activated accumulation response but had little effect on the strong blue-light-activated avoidance response. The inhibitory effect observed with PI metabolism inhibitors is, at least partly, due to a disturbance in Ca2+(c) signaling. Using the transgenic aequorin system, we show that the application of these inhibitors suppresses the blue-light-induced transient Ca2+(c) rise. These results demonstrate the importance of PIs in chloroplast movements, with the PI(4,5)P2-PLC pathway involved in phot2 signaling while PI3K and PI4K are required for the phot1- and phot2-induced accumulation response. Our results suggest that these PIs modulate cytosolic Ca2+ signaling during movements. PMID:23405144

  13. An Analysis of the Solution Structure and Signaling Mechanism of LovK, a Sensor Histidine Kinase Integrating Light and Redox Signals

    SciTech Connect

    Purcell, Erin B.; McDonald, Claudia A.; Palfey, Bruce A.; Crosson, Sean

    2010-12-07

    Flavin-binding LOV domains are broadly conserved in plants, fungi, archaea, and bacteria. These {approx}100-residue photosensory modules are generally encoded within larger, multidomain proteins that control a range of blue light-dependent physiologies. The bacterium Caulobacter crescentus encodes a soluble LOV-histidine kinase, LovK, that regulates the adhesive properties of the cell. Full-length LovK is dimeric as are a series of systematically truncated LovK constructs containing only the N-terminal LOV sensory domain. Nonconserved sequence flanking the LOV domain functions to tune the signaling lifetime of the protein. Size exclusion chromatography and small-angle X-ray scattering (SAXS) demonstrate that the LOV sensor domain does not undergo a large conformational change in response to photon absorption. However, limited proteolysis identifies a sequence flanking the C-terminus of the LOV domain as a site of light-induced change in protein conformation and dynamics. On the basis of SAXS envelope reconstruction and bioinformatic prediction, we propose this dynamic region of structure is an extended C-terminal coiled coil that links the LOV domain to the histidine kinase domain. To test the hypothesis that LOV domain signaling is affected by cellular redox state in addition to light, we measured the reduction potential of the LovK FMN cofactor. The measured potential of -258 mV is congruent with the redox potential of Gram-negative cytoplasm during logarithmic growth (-260 to -280 mV). Thus, a fraction of LovK in the cytosol may be in the reduced state under typical growth conditions. Chemical reduction of the FMN cofactor of LovK attenuates the light-dependent ATPase activity of the protein in vitro, demonstrating that LovK can function as a conditional photosensor that is regulated by the oxidative state of the cellular environment.

  14. Crystal Structures of Aureochrome1 LOV Suggest New Design Strategies for Optogenetics

    SciTech Connect

    Mitra, Devrani; Yang, Xiaojing; Moffat, Keith

    2014-10-02

    Aureochrome1, a signaling photoreceptor from a eukaryotic photosynthetic stramenopile, confers blue-light-regulated DNA binding on the organism. Its topology, in which a C-terminal LOV sensor domain is linked to an N-terminal DNA-binding bZIP effector domain, contrasts with the reverse sensor-effector topology in most other known LOV-photoreceptors. How, then, is signal transmitted in Aureochrome1? The dark- and light-state crystal structures of Aureochrome1 LOV domain (AuLOV) show that its helical N- and C-terminal flanking regions are packed against the external surface of the core {beta} sheet, opposite to the FMN chromophore on the internal surface. Light-induced conformational changes occur in the quaternary structure of the AuLOV dimer and in Phe298 of the H{beta} strand in the core. The properties of AuLOV extend the applicability of LOV domains as versatile design modules that permit fusion to effector domains via either the N- or C-termini to confer blue-light sensitivity.

  15. LOV-based optogenetic devices: light-driven modules to impart photoregulated control of cellular signaling

    PubMed Central

    Pudasaini, Ashutosh; El-Arab, Kaley K.; Zoltowski, Brian D.

    2015-01-01

    The Light-Oxygen-Voltage domain family of proteins is widespread in biology where they impart sensory responses to signal transduction domains. The small, light responsive LOV modules offer a novel platform for the construction of optogenetic tools. Currently, the design and implementation of these devices is partially hindered by a lack of understanding of how light drives allosteric changes in protein conformation to activate diverse signal transduction domains. Further, divergent photocycle properties amongst LOV family members complicate construction of highly sensitive devices with fast on/off kinetics. In the present review we discuss the history of LOV domain research with primary emphasis on tuning LOV domain chemistry and signal transduction to allow for improved optogenetic tools. PMID:25988185

  16. Light-induced structural changes in a short light, oxygen, voltage (LOV) protein revealed by molecular dynamics simulations—implications for the understanding of LOV photoactivation

    PubMed Central

    Bocola, Marco; Schwaneberg, Ulrich; Jaeger, Karl-Erich; Krauss, Ulrich

    2015-01-01

    The modularity of light, oxygen, voltage (LOV) blue-light photoreceptors has recently been exploited for the design of LOV-based optogenetic tools, which allow the light-dependent control of biological functions. For the understanding of LOV sensory function and hence the optimal design of LOV-based optogentic tools it is essential to gain an in depth atomic-level understanding of the underlying photoactivation and intramolecular signal-relay mechanisms. To address this question we performed molecular dynamics simulations on both the dark- and light-adapted state of PpSB1-LOV, a short dimeric bacterial LOV-photoreceptor protein, recently crystallized under constant illumination. While LOV dimers remained globally stable during the light-state simulation with regard to the Jα coiled-coil, distinct conformational changes for a glutamine in the vicinity of the FMN chromophore are observed. In contrast, multiple Jα-helix conformations are sampled in the dark-state. These changes coincide with a displacement of the Iβ and Hβ strands relative to the light-state structure and result in a correlated rotation of both LOV core domains in the dimer. These global changes are most likely initiated by the reorientation of the conserved glutamine Q116, whose side chain flips between the Aβ (dark state) and Hβ strand (light state), while maintaining two potential hydrogen bonds to FMN-N5 and FMN-O4, respectively. This local Q116-FMN reorientation impacts on an inter-subunit salt-bridge (K117-E96), which is stabilized in the light state, hence accounting for the observed decreased mobility. Based on these findings we propose an alternative mechanism for dimeric LOV photoactivation and intramolecular signal-relay, assigning a distinct structural role for the conserved “flipping” glutamine. The proposed mechanism is discussed in light of universal applicability and its implications for the understanding of LOV-based optogenetic tools. PMID:26484348

  17. The Drosophila BTB Domain Protein Jim Lovell Has Roles in Multiple Larval and Adult Behaviors

    PubMed Central

    Bjorum, Sonia M.; Simonette, Rebecca A.; Alanis, Raul; Wang, Jennifer E.; Lewis, Benjamin M.; Trejo, Michael H.; Hanson, Keith A.; Beckingham, Kathleen M.

    2013-01-01

    Innate behaviors have their origins in the specification of neural fates during development. Within Drosophila, BTB (Bric-a-brac,Tramtrack, Broad) domain proteins such as Fruitless are known to play key roles in the neural differentiation underlying such responses. We previously identified a gene, which we have termed jim lovell (lov), encoding a BTB protein with a role in gravity responses. To understand more fully the behavioral roles of this gene we have investigated its function through several approaches. Transcript and protein expression patterns have been examined and behavioral phenotypes of new lov mutations have been characterized. Lov is a nuclear protein, suggesting a role as a transcriptional regulator, as for other BTB proteins. In late embryogenesis, Lov is expressed in many CNS and PNS neurons. An examination of the PNS expression indicates that lov functions in the late specification of several classes of sensory neurons. In particular, only two of the five abdominal lateral chordotonal neurons express Lov, predicting functional variation within this highly similar group. Surprisingly, Lov is also expressed very early in embryogenesis in ways that suggests roles in morphogenetic movements, amnioserosa function and head neurogenesis. The phenotypes of two new lov mutations that delete adjacent non-coding DNA regions are strikingly different suggesting removal of different regulatory elements. In lov47, Lov expression is lost in many embryonic neurons including the two lateral chordotonal neurons. lov47 mutant larvae show feeding and locomotor defects including spontaneous backward movement. Adult lov47 males perform aberrant courtship behavior distinguished by courtship displays that are not directed at the female. lov47 adults also show more defective negative gravitaxis than the previously isolated lov91Y mutant. In contrast, lov66 produces largely normal behavior but severe female sterility associated with ectopic lov expression in the ovary. We

  18. Functional Characterization of a LOV-Histidine Kinase Photoreceptor from Xanthomonas citri subsp. citri.

    PubMed

    Kraiselburd, Ivana; Gutt, Alexander; Losi, Aba; Gärtner, Wolfgang; Orellano, Elena G

    2015-01-01

    The blue-light (BL) absorbing protein Xcc-LOV from Xanthomonas citri subsp. citri is composed of a LOV-domain, a histidine kinase (HK) and a response regulator. Spectroscopic characterization of Xcc-LOV identified intermediates and kinetics of the protein's photocycle. Measurements of steady state and time-resolved fluorescence allowed determination of quantum yields for triplet (ΦT  = 0.68 ± 0.03) and photoproduct formation (Φ390  = 0.46 ± 0.05). The lifetime for triplet decay was determined as τT  = 2.4-2.8 μs. Fluorescence of tryptophan and tyrosine residues was unchanged upon light-to-dark conversion, emphasizing the absence of significant conformational changes. Photochemistry was blocked upon cysteine C76 (C76S) mutation, causing a seven-fold longer lifetime of the triplet state (τT  = 16-18.5 μs). Optoacoustic spectroscopy yielded the energy content of the triplet state. Interestingly, Xcc-LOV did not undergo the volume contraction reported for other LOV domains within the observation time window, although the back-conversion into the dark state was accompanied by a volume expansion. A radioactivity-based enzyme function assay revealed a larger HK activity in the lit than in the dark state. The C76S mutant showed a still lower enzyme function, indicating the dark state activity being corrupted by a remaining portion of the long-lived lit state. PMID:26172037

  19. Phototropins do not alter accumulation of evening-phased circadian transcripts under blue light

    PubMed Central

    Litthauer, Suzanne; Battle, Martin W.; Jones, Matthew A.

    2016-01-01

    ABSTRACT The circadian system induces rhythmic variation in a suite of biochemical and physiological processes that serve to optimise plant growth in diel cycles. To be of greatest utility, these rhythmic behaviors are coordinated with regular environmental changes such as the rising and setting of the sun. Photoreceptors, along with metabolites produced during photosynthesis, act to synchronise the internal timing mechanism with lighting cues. We have recently shown that phototropins help maintain robust rhythms of photosynthetic operating efficiency (φPSII or Fq′/Fm′) under blue light, although rhythmic accumulation of morning-phased circadian transcripts in the nucleus was unaffected. Here we report that evening-phased nuclear clock transcripts were also unaffected. We also observe that rhythms of nuclear clock transcript accumulation are maintained in phototropin mutant plants under a fluctuating lighting regime that induced a loss of Fq′/Fm′ rhythms. PMID:26653107

  20. Functional characterization of blue-light-induced responses and PHOTOTROPIN 1 gene in Welwitschia mirabilis.

    PubMed

    Ishishita, Kazuhiro; Suetsugu, Noriyuki; Hirose, Yuki; Higa, Takeshi; Doi, Michio; Wada, Masamitsu; Matsushita, Tomonao; Gotoh, Eiji

    2016-03-01

    The blue light (BL) receptor phototropin (phot) is specifically found in green plants; it regulates various BL-induced responses such as phototropism, chloroplast movement, stomatal opening, and leaf flattening. In Arabidopsis thaliana, two phototropins--phot1 and phot2--respond to blue light in overlapping but distinct ways. These BL-receptor-mediated responses enhance the photosynthetic activity of plants under weak light and minimize photodamage under strong light conditions. Welwitschia mirabilis Hook.f. found in the Namib Desert, and it has adapted to severe environmental stresses such as limiting water and strong sunlight. Although the plant has physiologically and ecologically unique features, it is unknown whether phototropin is functional in this plant. In this study, we assessed the functioning of phot-mediated BL responses in W. mirabilis. BL-dependent phototropism and stomatal opening was observed but light-dependent chloroplast movement was not detected. We performed a functional analysis of the PHOT1 gene of W. mirabilis, WmPHOT1, in Arabidopsis thaliana. We generated transgenic A. thaliana lines expressing WmPHOT1 in a phot1 phot2 double mutant background. Several Wmphot1 transgenic plants showed normal growth, although phot1 phot2 double mutant plants showed stunted growth. Furthermore, Wmphot1 transgenic plants showed normal phot1-mediated responses including phototropism, chloroplast accumulation, stomatal opening, and leaf flattening, but lacked the chloroplast avoidance response that is specifically mediated by phot2. Thus, our findings indicate that W. mirabilis possesses typical phot-mediated BL responses that were at least partially mediated by functional phototropin 1, an ortholog of Atphot1. PMID:26858202

  1. Disruption of ROOT PHOTOTROPISM2 gene does not affect phototropin-mediated stomatal opening.

    PubMed

    Tsutsumi, Toshifumi; Takemiya, Atsushi; Harada, Akiko; Shimazaki, Ken-ichiro

    2013-03-01

    Phototropins (phot1 and phot2), blue light-receptor protein kinases in plants, mediate stomatal opening by activating the plasma membrane H(+)-ATPase in guard cells, but the signaling from phototropins to the H(+)-ATPase remains unknown. A recent study concluded that ROOT PHOTOTROPISM2 (RPT2) is involved in the primary step of this process. However, this conclusion is based solely on the determination of stomatal apertures in the epidermis. We investigated the role of RPT2 in blue light-dependent stomatal opening in more detail. We generated double mutants of rpt2 and phototropins (phot1 or phot2) in the Col ecotype background and obtained the typical phenotypes of rpt2 mutants, including the impairment in phototropism. In contrast, neither blue light-dependent H(+) pumping nor blue light-dependent H(+)-ATPase activation in guard cells was affected in the rpt2 mutants of rpt2, phot1 rpt2, and phot2 rpt2. Stomata in these rpt2 mutants opened widely by blue light in both epidermal peels and intact leaves, and no difference in the responses was found between the wild type and the mutants. From these results, we concluded that RPT2 gene disruption does not affect blue light-dependent stomatal opening. PMID:23352406

  2. Post-translational control of protein function with light using a LOV-intein fusion protein.

    PubMed

    Jones, D C; Mistry, I N; Tavassoli, A

    2016-04-01

    Methods for the post-translational control of protein function with light hold much value as tools in cell biology. To this end, we report a fusion protein that consists of DnaE split-inteins, flanking the light sensitive LOV2 domain of Avena sativa. The resulting chimera combines the activities of these two unrelated proteins to enable controlled formation of a functional protein via upregulation of intein splicing with blue light in bacterial and human cells. PMID:26940144

  3. The blue light receptor Phototropin 1 suppresses lateral root growth by controlling cell elongation.

    PubMed

    Moni, A; Lee, A-Y; Briggs, W R; Han, I-S

    2015-01-01

    We investigated the relationship between the blue light receptor phototropin 1 (phot1) and lateral root growth in Arabidopsis thaliana seedlings. Fluorescence and confocal microscopy images, as well as PHOT1 mRNA expression studies provide evidence that it is highly expressed in the elongation zone of lateral roots where auxin is accumulating. However, treatment with the auxin transport inhibitor N-1-naphthylphthalamic acid significantly reduced PHOT1 expression in this zone. In addition, PHOT1 expression was higher in darkness than in light. The total number of lateral roots was higher in the phot1 mutant than in wild-type Arabidopsis. Cells in the elongation zone of lateral roots of the phot1 mutant were longer than those of wild-type lateral roots. These findings suggest that PHOT1 plays a role(s) in elongation of lateral roots through the control of an auxin-related signalling pathway. PMID:24803136

  4. Optical Control of Peroxisomal Trafficking.

    PubMed

    Spiltoir, Jessica I; Strickland, Devin; Glotzer, Michael; Tucker, Chandra L

    2016-07-15

    The blue-light-responsive LOV2 domain of Avena sativa phototropin1 (AsLOV2) has been used to regulate activity and binding of diverse protein targets with light. Here, we used AsLOV2 to photocage a peroxisomal targeting sequence, allowing light regulation of peroxisomal protein import. We generated a protein tag, LOV-PTS1, that can be appended to proteins of interest to direct their import to the peroxisome with light. This method provides a means to inducibly trigger peroxisomal protein trafficking in specific cells at user-defined times. PMID:26513473

  5. LOV Histidine Kinase Modulates the General Stress Response System and Affects the virB Operon Expression in Brucella abortus

    PubMed Central

    Sycz, Gabriela; Carrica, Mariela Carmen; Tseng, Tong-Seung; Bogomolni, Roberto A.; Briggs, Winslow R.; Goldbaum, Fernando A.; Paris, Gastón

    2015-01-01

    Brucella is the causative agent of the zoonotic disease brucellosis, and its success as an intracellular pathogen relies on its ability to adapt to the harsh environmental conditions that it encounters inside the host. The Brucella genome encodes a sensor histidine kinase containing a LOV domain upstream from the kinase, LOVHK, which plays an important role in light-regulated Brucella virulence. In this report we study the intracellular signaling pathway initiated by the light sensor LOVHK using an integrated biochemical and genetic approach. From results of bacterial two-hybrid assays and phosphotransfer experiments we demonstrate that LOVHK functionally interacts with two response regulators: PhyR and LovR, constituting a functional two-component signal-transduction system. LOVHK contributes to the activation of the General Stress Response (GSR) system in Brucella via PhyR, while LovR is proposed to be a phosphate-sink for LOVHK, decreasing its phosphorylation state. We also show that in the absence of LOVHK the expression of the virB operon is down-regulated. In conclusion, our results suggest that LOVHK positively regulates the GSR system in vivo, and has an effect on the expression of the virB operon. The proposed regulatory network suggests a similar role for LOVHK in other microorganisms. PMID:25993430

  6. The LOV Protein of Xanthomonas citri subsp. citri Plays a Significant Role in the Counteraction of Plant Immune Responses during Citrus Canker

    PubMed Central

    Kraiselburd, Ivana; Daurelio, Lucas D.; Tondo, María Laura; Merelo, Paz; Cortadi, Adriana A.; Talón, Manuel; Tadeo, Francisco R.; Orellano, Elena G.

    2013-01-01

    Pathogens interaction with a host plant starts a set of immune responses that result in complex changes in gene expression and plant physiology. Light is an important modulator of plant defense response and recent studies have evidenced the novel influence of this environmental stimulus in the virulence of several bacterial pathogens. Xanthomonas citri subsp. citri is the bacterium responsible for citrus canker disease, which affects most citrus cultivars. The ability of this bacterium to colonize host plants is influenced by bacterial blue-light sensing through a LOV-domain protein and disease symptoms are considerably altered upon deletion of this protein. In this work we aimed to unravel the role of this photoreceptor during the bacterial counteraction of plant immune responses leading to citrus canker development. We performed a transcriptomic analysis in Citrus sinensis leaves inoculated with the wild type X. citri subsp. citri and with a mutant strain lacking the LOV protein by a cDNA microarray and evaluated the differentially regulated genes corresponding to specific biological processes. A down-regulation of photosynthesis-related genes (together with a corresponding decrease in photosynthesis rates) was observed upon bacterial infection, this effect being more pronounced in plants infected with the lov-mutant bacterial strain. Infection with this strain was also accompanied with the up-regulation of several secondary metabolism- and defense response-related genes. Moreover, we found that relevant plant physiological alterations triggered by pathogen attack such as cell wall fortification and tissue disruption were amplified during the lov-mutant strain infection. These results suggest the participation of the LOV-domain protein from X. citri subsp. citri in the bacterial counteraction of host plant defense response, contributing in this way to disease development. PMID:24260514

  7. Structure of a Light-Activated LOV Protein Dimer That Regulates Transcription

    SciTech Connect

    Vaidya, Anand T.; Chen, Chen-Hui; Dunlap, Jay C.; Loros, Jennifer J.; Crane, Brian R.

    2012-10-25

    Light, oxygen, or voltage (LOV) protein domains are present in many signaling proteins in bacteria, archaea, protists, plants, and fungi. The LOV protein VIVID (VVD) of the filamentous fungus Neurospora crassa enables the organism to adapt to constant or increasing amounts of light and facilitates proper entrainment of circadian rhythms. Here, we determined the crystal structure of the fully light-adapted VVD dimer and reveal the mechanism by which light-driven conformational change alters the oligomeric state of the protein. Light-induced formation of a cysteinyl-flavin adduct generated a new hydrogen bond network that released the amino (N) terminus from the protein core and restructured an acceptor pocket for binding of the N terminus on the opposite subunit of the dimer. Substitution of residues critical for the switch between the monomeric and the dimeric states of the protein had profound effects on light adaptation in Neurospora. The mechanism of dimerization of VVD provides molecular details that explain how members of a large family of photoreceptors convert light responses to alterations in protein-protein interactions.

  8. Phototropin encoded by a single-copy gene mediates chloroplast photorelocation movements in the liverwort Marchantia polymorpha.

    PubMed

    Komatsu, Aino; Terai, Mika; Ishizaki, Kimitsune; Suetsugu, Noriyuki; Tsuboi, Hidenori; Nishihama, Ryuichi; Yamato, Katsuyuki T; Wada, Masamitsu; Kohchi, Takayuki

    2014-09-01

    Blue-light-induced chloroplast photorelocation movement is observed in most land plants. Chloroplasts move toward weak-light-irradiated areas to efficiently absorb light (the accumulation response) and escape from strong-light-irradiated areas to avoid photodamage (the avoidance response). The plant-specific kinase phototropin (phot) is the blue-light receptor for chloroplast movements. Although the molecular mechanisms for chloroplast photorelocation movement have been analyzed, the overall aspects of signal transduction common to land plants are still unknown. Here, we show that the liverwort Marchantia polymorpha exhibits the accumulation and avoidance responses exclusively induced by blue light as well as specific chloroplast positioning in the dark. Moreover, in silico and Southern-blot analyses revealed that the M. polymorpha genome encodes a single PHOT gene, MpPHOT, and its knockout line displayed none of the chloroplast photorelocation movements, indicating that the sole MpPHOT gene mediates all types of movement. Mpphot was localized on the plasma membrane and exhibited blue-light-dependent autophosphorylation both in vitro and in vivo. Heterologous expression of MpPHOT rescued the defects in chloroplast movement of phot mutants in the fern Adiantum capillus-veneris and the seed plant Arabidopsis (Arabidopsis thaliana). These results indicate that Mpphot possesses evolutionarily conserved regulatory activities for chloroplast photorelocation movement. M. polymorpha offers a simple and versatile platform for analyzing the fundamental processes of phototropin-mediated chloroplast photorelocation movement common to land plants. PMID:25096976

  9. Photophysics of the LOV-Based Fluorescent Protein Variant iLOV-Q489K Determined by Simulation and Experiment.

    PubMed

    Davari, Mehdi D; Kopka, Benita; Wingen, Marcus; Bocola, Marco; Drepper, Thomas; Jaeger, Karl-Erich; Schwaneberg, Ulrich; Krauss, Ulrich

    2016-04-01

    Light, oxygen, voltage (LOV) based fluorescent proteins (FPs) represent a promising alternative to fluorescent reporters of the green fluorescent protein family. For certain applications like multicolor imaging or the design of FRET-based biosensors, the generation of spectrally shifted LOV-based FPs would be required. In a recent theoretical study ( Khrenova J. Phys. Chem. B 2015 , 119 ( 16 ), pp 5176 - 5183 ), the photophysical properties of a variant of the LOV-based fluorescent protein iLOV were predicted using quantum mechanics/molecular mechanics (QM/MM) approaches. The variant contained a lysine residue at the position of a highly conserved glutamine residue (Q489K), which directly interacts with the O4 and N5 atom of the flavin mononucleotide (FMN) chromophore. On the basis of QM/MM calculations, iLOV-Q489K was suggested to possess substantially red-shifted absorption and fluorescence-emission maxima with respect to parental iLOV. Here, we describe the experimental characterization of this variant, which, surprisingly contrary to the theoretical prediction, shows blue-shifted absorption and fluorescence-emission maxima. Using molecular dynamics (MD) simulations and QM/MM calculations, the molecular basis for the contradictory theoretical and experimental results is presented. Essentially, our computational analysis suggests that, in the Q489K variant, two possible side-chain conformers exist: (i) a least populated conformer K489in forming a hydrogen bond with the O4 atom of FMN chromophore and (ii) a most populated conformer K489out with the side-chain amino group flipped away from the FMN chromophore forming a new hydrogen bond with the backbone oxygen of G487. QM/MM calculated spectra of the K489out conformer are blue-shifted compared to the calculated spectra of parental iLOV, which is in accordance with experimental data. This suggests that the change in the conformation of K489 from K498in to K489out accounts for the change in the direction of the

  10. Phototropins Function in High-Intensity Blue Light-Induced Hypocotyl Phototropism in Arabidopsis by Altering Cytosolic Calcium1[C][W][OA

    PubMed Central

    Zhao, Xiang; Wang, Yan-Liang; Qiao, Xin-Rong; Wang, Jin; Wang, Lin-Dan; Xu, Chang-Shui; Zhang, Xiao

    2013-01-01

    Phototropins (phot1 and phot2), the blue light receptors in plants, regulate hypocotyl phototropism in a fluence-dependent manner. Especially under high fluence rates of blue light (HBL), the redundant function mediated by both phot1 and phot2 drastically restricts the understanding of the roles of phot2. Here, systematic analysis of phototropin-related mutants and overexpression transgenic lines revealed that HBL specifically induced a transient increase in cytosolic Ca2+ concentration ([Ca2+]cyt) in Arabidopsis (Arabidopsis thaliana) hypocotyls and that the increase in [Ca2+]cyt was primarily attributed to phot2. Pharmacological and genetic experiments illustrated that HBL-induced Ca2+ increases were modulated differently by phot1 and phot2. Phot2 mediated the HBL-induced increase in [Ca2+]cyt mainly by an inner store-dependent Ca2+-release pathway, not by activating plasma membrane Ca2+ channels. Further analysis showed that the increase in [Ca2+]cyt was possibly responsible for HBL-induced hypocotyl phototropism. An inhibitor of auxin efflux carrier exhibited significant inhibitions of both phototropism and increases in [Ca2+]cyt, which indicates that polar auxin transport is possibly involved in HBL-induced responses. Moreover, PHYTOCHROME KINASE SUBSTRATE1 (PKS1), the phototropin-related signaling element identified, interacted physically with phototropins, auxin efflux carrier PIN-FORMED1 and calcium-binding protein CALMODULIN4, in vitro and in vivo, respectively, and HBL-induced phototropism was impaired in pks multiple mutants, indicating the role of the PKS family in HBL-induced phototropism. Together, these results provide new insights into the functions of phototropins and highlight a potential integration point through which Ca2+ signaling-related HBL modulates hypocotyl phototropic responses. PMID:23674105

  11. Arabidopsis NPH1: a protein kinase with a putative redox-sensing domain.

    PubMed

    Huala, E; Oeller, P W; Liscum, E; Han, I S; Larsen, E; Briggs, W R

    1997-12-19

    The NPH1 (nonphototropic hypocotyl 1) gene encodes an essential component acting very early in the signal-transduction chain for phototropism. Arabidopsis NPH1 contains a serine-threonine kinase domain and LOV1 and LOV2 repeats that share similarity (36 to 56 percent) with Halobacterium salinarium Bat, Azotobacter vinelandii NIFL, Neurospora crassa White Collar-1, Escherichia coli Aer, and the Eag family of potassium-channel proteins from Drosophila and mammals. Sequence similarity with a known (NIFL) and a suspected (Aer) flavoprotein suggests that NPH1 LOV1 and LOV2 may be flavin-binding domains that regulate kinase activity in response to blue light-induced redox changes. PMID:9405347

  12. The Role of Distant Mutations and Allosteric Regulation on LovD Active Site Dynamics

    PubMed Central

    Jiménez-Osés, Gonzalo; Osuna, Sílvia; Gao, Xue; Sawaya, Michael R.; Gilson, Lynne; Collier, Steven J.; Huisman, Gjalt W.; Yeates, Todd O.; Tang, Yi; Houk, K. N.

    2014-01-01

    Natural enzymes have evolved to perform their cellular functions under complex selective pressures, which often require their catalytic activities to be regulated by other proteins. We contrasted a natural enzyme, LovD, which acts on a protein-bound (LovF) acyl substrate, with a laboratory-generated variant that was transformed by directed evolution to accept instead a small free acyl thioester, and no longer requires the acyl carrier protein. The resulting 29-mutant variant is 1000-fold more efficient in the synthesis of the drug simvastatin than the wild-type LovD. This is the first non-patent report of the enzyme currently used for the manufacture of simvastatin, as well as the intermediate evolved variants. Crystal structures and microsecond molecular dynamics simulations revealed the mechanism by which the laboratory-generated mutations free LovD from dependence on protein-protein interactions. Mutations dramatically altered conformational dynamics of the catalytic residues, obviating the need for allosteric modulation by the acyl carrier LovF. PMID:24727900

  13. Light Regulation of Swarming Motility in Pseudomonas syringae Integrates Signaling Pathways Mediated by a Bacteriophytochrome and a LOV Protein

    PubMed Central

    Wu, Liang; McGrane, Regina S.; Beattie, Gwyn A.

    2013-01-01

    ABSTRACT The biological and regulatory roles of photosensory proteins are poorly understood for nonphotosynthetic bacteria. The foliar bacterial pathogen Pseudomonas syringae has three photosensory protein-encoding genes that are predicted to encode the blue-light-sensing LOV (light, oxygen, or voltage) histidine kinase (LOV-HK) and two red/far-red-light-sensing bacteriophytochromes, BphP1 and BphP2. We provide evidence that LOV-HK and BphP1 form an integrated network that regulates swarming motility in response to multiple light wavelengths. The swarming motility of P. syringae B728a deletion mutants indicated that LOV-HK positively regulates swarming motility in response to blue light and BphP1 negatively regulates swarming motility in response to red and far-red light. BphP2 does not detectably regulate swarming motility. The histidine kinase activity of each LOV-HK and BphP1 is required for this regulation based on the loss of complementation upon mutation of residues key to their kinase activity. Surprisingly, mutants lacking both lov and bphP1 were similar in motility to a bphP1 single mutant in blue light, indicating that the loss of bphP1 is epistatic to the loss of lov and also that BphP1 unexpectedly responds to blue light. Moreover, whereas expression of bphP1 did not alter motility under blue light in a bphP1 mutant, it reduced motility in a mutant lacking lov and bphP1, demonstrating that LOV-HK positively regulates motility by suppressing negative regulation by BphP1. These results are the first to show cross talk between the LOV protein and phytochrome signaling pathways in bacteria, and the similarity of this regulatory network to that of photoreceptors in plants suggests a possible common ancestry. PMID:23760465

  14. Light-induced nuclear export reveals rapid dynamics of epigenetic modifications.

    PubMed

    Yumerefendi, Hayretin; Lerner, Andrew Michael; Zimmerman, Seth Parker; Hahn, Klaus; Bear, James E; Strahl, Brian D; Kuhlman, Brian

    2016-06-01

    We engineered a photoactivatable system for rapidly and reversibly exporting proteins from the nucleus by embedding a nuclear export signal in the LOV2 domain from phototropin 1. Fusing the chromatin modifier Bre1 to the photoswitch, we achieved light-dependent control of histone H2B monoubiquitylation in yeast, revealing fast turnover of the ubiquitin mark. Moreover, this inducible system allowed us to dynamically monitor the status of epigenetic modifications dependent on H2B ubiquitylation. PMID:27089030

  15. Listening to Others' Voices (LOV) Project: An Empowering Strategy Incorporating Marginalized Perspectives

    ERIC Educational Resources Information Center

    Kim, Minsung; Ryu, Jae-Myong

    2014-01-01

    This study introduces the Listening to Others' Voices (LOV) project, an empowering strategy in geography education. This research aims to create a dataset detailing the perspectives of negatively stereotyped countries with respect to how their countries are portrayed in geography textbooks and to investigate the pedagogical effects of the LOV…

  16. Optogenetics: optical control of a photoactivatable Rac in living cells.

    PubMed

    Yin, Taofei; Wu, Yi I

    2015-01-01

    Recent developments in optogenetics have extended optical control of signaling to intracellular proteins, including Rac, a small G protein in the Rho family. A blue light-sensing LOV (light, oxygen, or voltage) domain derived from Avena sativa (oat) phototropin was fused to the N-terminus of a constitutively active mutant of Rac, via an α-helix (Jα) that is conserved among plant phototropins. The fused LOV domain occluded binding of downstream effectors to Rac in the dark. Exposure to blue light caused a conformational change of the LOV domain and unwinding of the Jα helix, relieving steric inhibition. The LOV domain incorporates a flavin as the photon-absorbing cofactor and can be activated by light in a reversible and repeatable fashion. In cultured cells, global illumination with blue light rapidly activated Rac and led to cell spreading and membrane ruffling. Localized and pulsed illumination generated a gradient of Rac activity and induced directional migration. In this chapter, we will describe the techniques in detail and present some examples of applications of using photoactivatable Rac (PA-Rac) in living cells. PMID:25391805

  17. Overexpression of AtLOV1 in Switchgrass Alters Plant Architecture, Lignin Content, and Flowering Time

    PubMed Central

    Xu, Bin; Sathitsuksanoh, Noppadon; Tang, Yuhong; Udvardi, Michael K.; Zhang, Ji-Yi; Shen, Zhengxing; Balota, Maria; Harich, Kim; Zhang, Percival Y.-H.; Zhao, Bingyu

    2012-01-01

    Background Switchgrass (Panicum virgatum L.) is a prime candidate crop for biofuel feedstock production in the United States. As it is a self-incompatible polyploid perennial species, breeding elite and stable switchgrass cultivars with traditional breeding methods is very challenging. Translational genomics may contribute significantly to the genetic improvement of switchgrass, especially for the incorporation of elite traits that are absent in natural switchgrass populations. Methodology/Principal Findings In this study, we constitutively expressed an Arabidopsis NAC transcriptional factor gene, LONG VEGETATIVE PHASE ONE (AtLOV1), in switchgrass. Overexpression of AtLOV1 in switchgrass caused the plants to have a smaller leaf angle by changing the morphology and organization of epidermal cells in the leaf collar region. Also, overexpression of AtLOV1 altered the lignin content and the monolignol composition of cell walls, and caused delayed flowering time. Global gene-expression analysis of the transgenic plants revealed an array of responding genes with predicted functions in plant development, cell wall biosynthesis, and flowering. Conclusions/Significance To our knowledge, this is the first report of a single ectopically expressed transcription factor altering the leaf angle, cell wall composition, and flowering time of switchgrass, therefore demonstrating the potential advantage of translational genomics for the genetic improvement of this crop. PMID:23300513

  18. On the midpoint potential of the FAD chromophore in a BLUF-domain containing photoreceptor protein.

    PubMed

    Arents, Jos C; Perez, Marcela Avila; Hendriks, Johnny; Hellingwerf, Klaas J

    2011-01-01

    The redox-midpoint potential of the FAD chromophore in the BLUF domain of anti-transcriptional regulator AppA from Rhodobacter sphaeroides equals ∼-260mV relative to the calomel electrode. Altering the structure of its chromophore-binding pocket through site-directed mutagenesis brings this midpoint potential closer to that of free flavin in aqueous solution. The redox-midpoint potential of this BLUF domain is intermediate between those of LOV domains and Cryptochromes, which may rationalize the primary photochemistry observed in these three flavin-containing photoreceptor families. These results also imply that LOV domains, among the flavin-containing photosensory receptors, are least sensitive to intracellular chemical reduction in the dark. PMID:21110976

  19. Phototropins But Not Cryptochromes Mediate the Blue Light-Specific Promotion of Stomatal Conductance, While Both Enhance Photosynthesis and Transpiration under Full Sunlight12[C][W][OA

    PubMed Central

    Boccalandro, Hernán E.; Giordano, Carla V.; Ploschuk, Edmundo L.; Piccoli, Patricia N.; Bottini, Rubén; Casal, Jorge J.

    2012-01-01

    Leaf epidermal peels of Arabidopsis (Arabidopsis thaliana) mutants lacking either phototropins 1 and 2 (phot1 and phot2) or cryptochromes 1 and 2 (cry1 and cry2) exposed to a background of red light show severely impaired stomatal opening responses to blue light. Since phot and cry are UV-A/blue light photoreceptors, they may be involved in the perception of the blue light-specific signal that induces the aperture of the stomatal pores. In leaf epidermal peels, the blue light-specific effect saturates at low irradiances; therefore, it is considered to operate mainly under the low irradiance of dawn, dusk, or deep canopies. Conversely, we show that both phot1 phot2 and cry1 cry2 have reduced stomatal conductance, transpiration, and photosynthesis, particularly under the high irradiance of full sunlight at midday. These mutants show compromised responses of stomatal conductance to irradiance. However, the effects of phot and cry on photosynthesis were largely nonstomatic. While the stomatal conductance phenotype of phot1 phot2 was blue light specific, cry1 cry2 showed reduced stomatal conductance not only in response to blue light, but also in response to red light. The levels of abscisic acid were elevated in cry1 cry2. We conclude that considering their effects at high irradiances cry and phot are critical for the control of transpiration and photosynthesis rates in the field. The effects of cry on stomatal conductance are largely indirect and involve the control of abscisic acid levels. PMID:22147516

  20. The signal transducer NPH3 integrates the phototropin1 photosensor with PIN2-based polar auxin transport in Arabidopsis root phototropism.

    PubMed

    Wan, Yinglang; Jasik, Jan; Wang, Li; Hao, Huaiqing; Volkmann, Dieter; Menzel, Diedrik; Mancuso, Stefano; Baluška, František; Lin, Jinxing

    2012-02-01

    Under blue light (BL) illumination, Arabidopsis thaliana roots grow away from the light source, showing a negative phototropic response. However, the mechanism of root phototropism is still unclear. Using a noninvasive microelectrode system, we showed that the BL sensor phototropin1 (phot1), the signal transducer NONPHOTOTROPIC HYPOCOTYL3 (NPH3), and the auxin efflux transporter PIN2 were essential for BL-induced auxin flux in the root apex transition zone. We also found that PIN2-green fluorescent protein (GFP) localized to vacuole-like compartments (VLCs) in dark-grown root epidermal and cortical cells, and phot1/NPH3 mediated a BL-initiated pathway that caused PIN2 redistribution to the plasma membrane. When dark-grown roots were exposed to brefeldin A (BFA), PIN2-GFP remained in VLCs in darkness, and BL caused PIN2-GFP disappearance from VLCs and induced PIN2-GFP-FM4-64 colocalization within enlarged compartments. In the nph3 mutant, both dark and BL BFA treatments caused the disappearance of PIN2-GFP from VLCs. However, in the phot1 mutant, PIN2-GFP remained within VLCs under both dark and BL BFA treatments, suggesting that phot1 and NPH3 play different roles in PIN2 localization. In conclusion, BL-induced root phototropism is based on the phot1/NPH3 signaling pathway, which stimulates the shootward auxin flux by modifying the subcellular targeting of PIN2 in the root apex transition zone. PMID:22374399

  1. The Signal Transducer NPH3 Integrates the Phototropin1 Photosensor with PIN2-Based Polar Auxin Transport in Arabidopsis Root Phototropism[C][W

    PubMed Central

    Wan, Yinglang; Jasik, Jan; Wang, Li; Hao, Huaiqing; Volkmann, Dieter; Menzel, Diedrik; Mancuso, Stefano; Baluška, František; Lin, Jinxing

    2012-01-01

    Under blue light (BL) illumination, Arabidopsis thaliana roots grow away from the light source, showing a negative phototropic response. However, the mechanism of root phototropism is still unclear. Using a noninvasive microelectrode system, we showed that the BL sensor phototropin1 (phot1), the signal transducer NONPHOTOTROPIC HYPOCOTYL3 (NPH3), and the auxin efflux transporter PIN2 were essential for BL-induced auxin flux in the root apex transition zone. We also found that PIN2-green fluorescent protein (GFP) localized to vacuole-like compartments (VLCs) in dark-grown root epidermal and cortical cells, and phot1/NPH3 mediated a BL-initiated pathway that caused PIN2 redistribution to the plasma membrane. When dark-grown roots were exposed to brefeldin A (BFA), PIN2-GFP remained in VLCs in darkness, and BL caused PIN2-GFP disappearance from VLCs and induced PIN2-GFP-FM4-64 colocalization within enlarged compartments. In the nph3 mutant, both dark and BL BFA treatments caused the disappearance of PIN2-GFP from VLCs. However, in the phot1 mutant, PIN2-GFP remained within VLCs under both dark and BL BFA treatments, suggesting that phot1 and NPH3 play different roles in PIN2 localization. In conclusion, BL-induced root phototropism is based on the phot1/NPH3 signaling pathway, which stimulates the shootward auxin flux by modifying the subcellular targeting of PIN2 in the root apex transition zone. PMID:22374399

  2. A LOV protein modulates the physiological attributes of Xanthomonas axonopodis pv. citri relevant for host plant colonization.

    PubMed

    Kraiselburd, Ivana; Alet, Analía I; Tondo, María Laura; Petrocelli, Silvana; Daurelio, Lucas D; Monzón, Jesica; Ruiz, Oscar A; Losi, Aba; Orellano, Elena G

    2012-01-01

    Recent studies have demonstrated that an appropriate light environment is required for the establishment of efficient vegetal resistance responses in several plant-pathogen interactions. The photoreceptors implicated in such responses are mainly those belonging to the phytochrome family. Data obtained from bacterial genome sequences revealed the presence of photosensory proteins of the BLUF (Blue Light sensing Using FAD), LOV (Light, Oxygen, Voltage) and phytochrome families with no known functions. Xanthomonas axonopodis pv. citri is a Gram-negative bacterium responsible for citrus canker. The in silico analysis of the X. axonopodis pv. citri genome sequence revealed the presence of a gene encoding a putative LOV photoreceptor, in addition to two genes encoding BLUF proteins. This suggests that blue light sensing could play a role in X. axonopodis pv. citri physiology. We obtained the recombinant Xac-LOV protein by expression in Escherichia coli and performed a spectroscopic analysis of the purified protein, which demonstrated that it has a canonical LOV photochemistry. We also constructed a mutant strain of X. axonopodis pv. citri lacking the LOV protein and found that the loss of this protein altered bacterial motility, exopolysaccharide production and biofilm formation. Moreover, we observed that the adhesion of the mutant strain to abiotic and biotic surfaces was significantly diminished compared to the wild-type. Finally, inoculation of orange (Citrus sinensis) leaves with the mutant strain of X. axonopodis pv. citri resulted in marked differences in the development of symptoms in plant tissues relative to the wild-type, suggesting a role for the Xac-LOV protein in the pathogenic process. Altogether, these results suggest the novel involvement of a photosensory system in the regulation of physiological attributes of a phytopathogenic bacterium. A functional blue light receptor in Xanthomonas spp. has been described for the first time, showing an important

  3. A LOV Protein Modulates the Physiological Attributes of Xanthomonas axonopodis pv. citri Relevant for Host Plant Colonization

    PubMed Central

    Kraiselburd, Ivana; Alet, Analía I.; Tondo, María Laura; Petrocelli, Silvana; Daurelio, Lucas D.; Monzón, Jesica; Ruiz, Oscar A.; Losi, Aba; Orellano, Elena G.

    2012-01-01

    Recent studies have demonstrated that an appropriate light environment is required for the establishment of efficient vegetal resistance responses in several plant-pathogen interactions. The photoreceptors implicated in such responses are mainly those belonging to the phytochrome family. Data obtained from bacterial genome sequences revealed the presence of photosensory proteins of the BLUF (Blue Light sensing Using FAD), LOV (Light, Oxygen, Voltage) and phytochrome families with no known functions. Xanthomonas axonopodis pv. citri is a Gram-negative bacterium responsible for citrus canker. The in silico analysis of the X. axonopodis pv. citri genome sequence revealed the presence of a gene encoding a putative LOV photoreceptor, in addition to two genes encoding BLUF proteins. This suggests that blue light sensing could play a role in X. axonopodis pv. citri physiology. We obtained the recombinant Xac-LOV protein by expression in Escherichia coli and performed a spectroscopic analysis of the purified protein, which demonstrated that it has a canonical LOV photochemistry. We also constructed a mutant strain of X. axonopodis pv. citri lacking the LOV protein and found that the loss of this protein altered bacterial motility, exopolysaccharide production and biofilm formation. Moreover, we observed that the adhesion of the mutant strain to abiotic and biotic surfaces was significantly diminished compared to the wild-type. Finally, inoculation of orange (Citrus sinensis) leaves with the mutant strain of X. axonopodis pv. citri resulted in marked differences in the development of symptoms in plant tissues relative to the wild-type, suggesting a role for the Xac-LOV protein in the pathogenic process. Altogether, these results suggest the novel involvement of a photosensory system in the regulation of physiological attributes of a phytopathogenic bacterium. A functional blue light receptor in Xanthomonas spp. has been described for the first time, showing an important

  4. Allosteric communication between DNA-binding and light-responsive domains of diatom class I aureochromes

    PubMed Central

    Banerjee, Ankan; Herman, Elena; Serif, Manuel; Maestre-Reyna, Manuel; Hepp, Sebastian; Pokorny, Richard; Kroth, Peter G.; Essen, Lars-Oliver; Kottke, Tilman

    2016-01-01

    The modular architecture of aureochrome blue light receptors, found in several algal groups including diatoms, is unique by having the LOV-type photoreceptor domain fused to the C-terminus of its putative effector, an N-terminal DNA-binding bZIP module. The structural and functional understanding of aureochromes’ light-dependent signaling mechanism is limited, despite their promise as an optogenetic tool. We show that class I aureochromes 1a and 1c from the diatom Phaeodactylum tricornutum are regulated in a light-independent circadian rhythm. These aureochromes are capable to form functional homo- and heterodimers, which recognize the ACGT core sequence within the canonical ‘aureo box’, TGACGT, in a light-independent manner. The bZIP domain holds a more folded and less flexible but extended conformation in the duplex DNA-bound state. FT-IR spectroscopy in the absence and the presence of DNA shows light-dependent helix unfolding in the LOV domain, which leads to conformational changes in the bZIP region. The solution structure of DNA bound to aureochrome points to a tilted orientation that was further validated by molecular dynamics simulations. We propose that aureochrome signaling relies on an allosteric pathway from LOV to bZIP that results in conformational changes near the bZIP-DNA interface without major effects on the binding affinity. PMID:27179025

  5. Allosteric communication between DNA-binding and light-responsive domains of diatom class I aureochromes.

    PubMed

    Banerjee, Ankan; Herman, Elena; Serif, Manuel; Maestre-Reyna, Manuel; Hepp, Sebastian; Pokorny, Richard; Kroth, Peter G; Essen, Lars-Oliver; Kottke, Tilman

    2016-07-01

    The modular architecture of aureochrome blue light receptors, found in several algal groups including diatoms, is unique by having the LOV-type photoreceptor domain fused to the C-terminus of its putative effector, an N-terminal DNA-binding bZIP module. The structural and functional understanding of aureochromes' light-dependent signaling mechanism is limited, despite their promise as an optogenetic tool. We show that class I aureochromes 1a and 1c from the diatom Phaeodactylum tricornutum are regulated in a light-independent circadian rhythm. These aureochromes are capable to form functional homo- and heterodimers, which recognize the ACGT core sequence within the canonical 'aureo box', TGACGT, in a light-independent manner. The bZIP domain holds a more folded and less flexible but extended conformation in the duplex DNA-bound state. FT-IR spectroscopy in the absence and the presence of DNA shows light-dependent helix unfolding in the LOV domain, which leads to conformational changes in the bZIP region. The solution structure of DNA bound to aureochrome points to a tilted orientation that was further validated by molecular dynamics simulations. We propose that aureochrome signaling relies on an allosteric pathway from LOV to bZIP that results in conformational changes near the bZIP-DNA interface without major effects on the binding affinity. PMID:27179025

  6. Engineering light-inducible nuclear localization signals for precise spatiotemporal control of protein dynamics in living cells

    PubMed Central

    Niopek, Dominik; Benzinger, Dirk; Roensch, Julia; Draebing, Thomas; Wehler, Pierre; Eils, Roland; Di Ventura, Barbara

    2014-01-01

    The function of many eukaryotic proteins is regulated by highly dynamic changes in their nucleocytoplasmic distribution. The ability to precisely and reversibly control nuclear translocation would, therefore, allow dissecting and engineering cellular networks. Here we develop a genetically encoded, light-inducible nuclear localization signal (LINuS) based on the LOV2 domain of Avena sativa phototropin 1. LINuS is a small, versatile tag, customizable for different proteins and cell types. LINuS-mediated nuclear import is fast and reversible, and can be tuned at different levels, for instance, by introducing mutations that alter AsLOV2 domain photo-caging properties or by selecting nuclear localization signals (NLSs) of various strengths. We demonstrate the utility of LINuS in mammalian cells by controlling gene expression and entry into mitosis with blue light. PMID:25019686

  7. Recalculated mass balance record for Midre Lovénbreen, Svalbard

    NASA Astrophysics Data System (ADS)

    Kohler, J.

    2013-12-01

    Glacier mass balance has been measured since 1968 on Midre Lovénbreen, Svalbard, one of the longest high Arctic records. Available data includes areally-averaged winter, summer, and net balances. Balances by elevation, however, were not consistently reported. Here we derive a time-series of the balances as a function of elevation using original stake data from archived field notebooks and maps, graphs of balance as a function of elevation taken from old reports. We recalculate areally-averaged balances using a different fits to the data, rather than hand-drawn curves from earlier years, and adjust for changes in hypsometry. There is good agreement between in situ mass balance and geodetic changes obtained by differencing digital elevation models (DEMs) from different dates (1936, 1962, 1969, 1977, 1995, 2003, 2005). The main long-term trends over the length of the 44-yr record are that winter and net balance are decreasing overall, and that summer and net balance elevational gradients increase, the result of increasing ice loss at lower elevations.

  8. Automation of ⁹⁹Tc extraction by LOV prior ICP-MS detection: application to environmental samples.

    PubMed

    Rodríguez, Rogelio; Leal, Luz; Miranda, Silvia; Ferrer, Laura; Avivar, Jessica; García, Ariel; Cerdà, Víctor

    2015-02-01

    A new, fast, automated and inexpensive sample pre-treatment method for (99)Tc determination by inductively coupled plasma-mass spectrometry (ICP-MS) detection is presented. The miniaturized approach is based on a lab-on-valve (LOV) system, allowing automatic separation and preconcentration of (99)Tc. Selectivity is provided by the solid phase extraction system used (TEVA resin) which retains selectively pertechnetate ion in diluted nitric acid solution. The proposed system has some advantages such as minimization of sample handling, reduction of reagents volume, improvement of intermediate precision and sample throughput, offering a significant decrease of both time and cost per analysis in comparison to other flow techniques and batch methods. The proposed LOV system has been successfully applied to different samples of environmental interest (water and soil) with satisfactory recoveries, between 94% and 98%. The detection limit (LOD) of the developed method is 0.005 ng. The high durability of the resin and its low amount (32 mg), its good intermediate precision (RSD 3.8%) and repeatability (RSD 2%) and its high extraction frequency (up to 5 h(-1)) makes this method an inexpensive, high precision and fast tool for monitoring (99)Tc in environmental samples. PMID:25435232

  9. Structural Insights into the HWE Histidine Kinase Family: The Brucella Blue Light-Activated Histidine Kinase Domain.

    PubMed

    Rinaldi, Jimena; Arrar, Mehrnoosh; Sycz, Gabriela; Cerutti, María Laura; Berguer, Paula M; Paris, Gastón; Estrín, Darío Ariel; Martí, Marcelo Adrián; Klinke, Sebastián; Goldbaum, Fernando Alberto

    2016-03-27

    In response to light, as part of a two-component system, the Brucella blue light-activated histidine kinase (LOV-HK) increases its autophosphorylation, modulating the virulence of this microorganism. The Brucella histidine kinase (HK) domain belongs to the HWE family, for which there is no structural information. The HWE family is exclusively present in proteobacteria and usually coupled to a wide diversity of light sensor domains. This work reports the crystal structure of the Brucella HK domain, which presents two different dimeric assemblies in the asymmetric unit: one similar to the already described canonical parallel homodimers (C) and the other, an antiparallel non-canonical (NC) dimer, each with distinct relative subdomain orientations and dimerization interfaces. Contrary to these crystallographic structures and unlike other HKs, in solution, the Brucella HK domain is monomeric and still active, showing an astonishing instability of the dimeric interface. Despite this instability, using cross-linking experiments, we show that the C dimer is the functionally relevant species. Mutational analysis demonstrates that the autophosphorylation activity occurs in cis. The different relative subdomain orientations observed for the NC and C states highlight the large conformational flexibility of the HK domain. Through the analysis of these alternative conformations by means of molecular dynamics simulations, we also propose a catalytic mechanism for Brucella LOV-HK. PMID:26851072

  10. MSFIA-LOV system for (226)Ra isolation and pre-concentration from water samples previous radiometric detection.

    PubMed

    Rodríguez, Rogelio; Borràs, Antoni; Leal, Luz; Cerdà, Víctor; Ferrer, Laura

    2016-03-10

    An automatic system based on multisyringe flow injection analysis (MSFIA) and lab-on-valve (LOV) flow techniques for separation and pre-concentration of (226)Ra from drinking and natural water samples has been developed. The analytical protocol combines two different procedures: the Ra adsorption on MnO2 and the BaSO4 co-precipitation, achieving more selectivity especially in water samples with low radium levels. Radium is adsorbed on MnO2 deposited on macroporous of bead cellulose. Then, it is eluted with hydroxylamine to transform insoluble MnO2 to soluble Mn(II) thus freeing Ra, which is then coprecipitated with BaSO4. The (226)Ra can be directly detected in off-line mode using a low background proportional counter (LBPC) or through a liquid scintillation counter (LSC), after performing an on-line coprecipitate dissolution. Thus, the versatility of the proposed system allows the selection of the radiometric detection technique depending on the detector availability or the required response efficiency (sample number vs. response time and limit of detection). The MSFIA-LOV system improves the precision (1.7% RSD), and the extraction frequency (up to 3 h(-1)). Besides, it has been satisfactorily applied to different types of water matrices (tap, mineral, well and sea water). The (226)Ra minimum detectable activities (LSC: 0.004 Bq L(-1); LBPC: 0.02 Bq L(-1)) attained by this system allow to reach the guidance values proposed by the relevant international agencies e.g. WHO, EPA and EC. PMID:26893088

  11. Domain Engineering

    NASA Astrophysics Data System (ADS)

    Bjørner, Dines

    Before software can be designed we must know its requirements. Before requirements can be expressed we must understand the domain. So it follows, from our dogma, that we must first establish precise descriptions of domains; then, from such descriptions, “derive” at least domain and interface requirements; and from those and machine requirements design the software, or, more generally, the computing systems.

  12. Exploiting the bead injection LOV approach to carry out spectrophotometric assays in wine: application to the determination of iron.

    PubMed

    Vidigal, Susana S M P; Tóth, Ildikó V; Rangel, António O S S

    2011-06-15

    A sequential injection lab-on-valve (SI-LOV) system was used to develop a new methodology for the determination of iron in wine samples exploiting the bead injection (BI) concept for solid phase extraction and spectrophotometric measurement. Nitrilotriacetic Acid (NTA) Superflow resin was used to build the bead column of the flow through sensor. The iron (III) ions were retained by the bead column and react with SCN(-) producing an intense red colour. The change in absorbance was monitored spectrophotometrically on the optosensor at 480 nm. It was possible to achieve a linear range of 0.09-5.0 mg L(-1) of iron, with low sample and reagent consumption; 500 μL of sample, 15 μmol of SCN(-), and 9 μmol of H(2)O(2), per assay. The proposed method was successfully applied to the determination of iron in wine, with no previous treatment other than dilution, and to other food samples. PMID:21641441

  13. Light-activated DNA binding in a designed allosteric protein

    SciTech Connect

    Strickland, Devin; Moffat, Keith; Sosnick, Tobin R.

    2008-09-03

    An understanding of how allostery, the conformational coupling of distant functional sites, arises in highly evolvable systems is of considerable interest in areas ranging from cell biology to protein design and signaling networks. We reasoned that the rigidity and defined geometry of an {alpha}-helical domain linker would make it effective as a conduit for allosteric signals. To test this idea, we rationally designed 12 fusions between the naturally photoactive LOV2 domain from Avena sativa phototropin 1 and the Escherichia coli trp repressor. When illuminated, one of the fusions selectively binds operator DNA and protects it from nuclease digestion. The ready success of our rational design strategy suggests that the helical 'allosteric lever arm' is a general scheme for coupling the function of two proteins.

  14. Structural details of light activation of the LOV2-based photoswitch PA-Rac1.

    PubMed

    Winkler, Andreas; Barends, Thomas R M; Udvarhelyi, Anikó; Lenherr-Frey, Daniel; Lomb, Lukas; Menzel, Andreas; Schlichting, Ilme

    2015-02-20

    Optical control of cellular processes is an emerging approach for studying biological systems, affording control with high spatial and temporal resolution. Specifically designed artificial photoswitches add an interesting extension to naturally occurring light-regulated functionalities. However, despite a great deal of structural information, the generation of new tools cannot be based fully on rational design yet; in many cases design is limited by our understanding of molecular details of light activation and signal transduction. Our biochemical and biophysical studies on the established optogenetic tool PA-Rac1, the photoactivatable small GTPase Rac1, reveal how unexpected details of the sensor-effector interface, such as metal coordination, significantly affect functionally important structural elements of this photoswitch. Together with solution scattering experiments, our results favor differences in the population of pre-existing conformations as the underlying allosteric activation mechanism of PA-Rac1, rather than the assumed release of the Rac1 domain from the caging photoreceptor domain. These results have implications for the design of new optogenetic tools and highlight the importance of including molecular details of the sensor-effector interface, which is however difficult to assess during the initial design of novel artificial photoswitches. PMID:25368973

  15. Structure and changing dynamics of a polythermal valley glacier on a centennial timescale: Midre Lovénbreen, Svalbard

    NASA Astrophysics Data System (ADS)

    Hambrey, Michael J.; Murray, Tavi; Glasser, Neil F.; Hubbard, Alun; Hubbard, Bryn; Stuart, Graham; Hansen, Siri; Kohler, Jack

    2005-03-01

    Most polythermal glaciers in Svalbard, other than those of surge type, have receded steadily since the early 20th century. Midre Lovénbreen, a slow-moving, 4-km-long valley glacier terminating on land, is a typical example, and its internal structures reflect changing dynamics over this period. The three-dimensional structural style of this glacier and the sequential development of structures have been determined from surface mapping, ground-penetrating radar, and numerical flow modeling. In order of formation the structures observed today at the glacier surface are (1) primary stratification that has become folded about flow-parallel axes; (2) axial plane longitudinal foliation associated with this folding; (3) several sets of intersecting crevasse traces; (4) arcuate upglacier-dipping fractures developed as part of a thrust complex near the snout; and (5) longitudinal splaying fractures in the snout area. The long-term evolution and dynamic significance of these structures can be ascertained from historical ground and aerial photographs. Modeling indicates that stratification and foliation continue to evolve today as a result of internal deformation, especially in zones of converging flow, where simple shear is most pronounced, but within the tongue are carried passively toward the snout. Crevasse traces appear to be no longer actively forming but are interpreted as relict structures when the ice was more dynamic and mostly wet based. The interpretation of arcuate fractures near the snout as thrusts is supported by the matching orientations of modeled strain ellipses, which illustrate the importance of longitudinal compression.

  16. Gene expression profile of zeitlupe/lov kelch protein1 T-DNA insertion mutants in Arabidopsis thaliana: Downregulation of auxin-inducible genes in hypocotyls

    PubMed Central

    Saitoh, Aya; Takase, Tomoyuki; Kitaki, Hiroyuki; Miyazaki, Yuji; Kiyosue, Tomohiro

    2015-01-01

    Elongation of hypocotyl cells has been studied as a model for elucidating the contribution of cellular expansion to plant organ growth. ZEITLUPE (ZTL) or LOV KELCH PROTEIN1 (LKP1) is a positive regulator of warmth-induced hypocotyl elongation under white light in Arabidopsis, although the molecular mechanisms by which it promotes hypocotyl cell elongation remain unknown. Microarray analysis showed that 134 genes were upregulated and 204 genes including 15 auxin-inducible genes were downregulated in the seedlings of 2 ztl T-DNA insertion mutants grown under warm conditions with continuous white light. Application of a polar auxin transport inhibitor, an auxin antagonist or an auxin biosynthesis inhibitor inhibited hypocotyl elongation of control seedlings to the level observed with the ztl mutant. Our data suggest the involvement of auxin and auxin-inducible genes in ZTL-mediated hypocotyl elongation. PMID:26237185

  17. Control of Protein Activity and Cell Fate Specification via Light-Mediated Nuclear Translocation

    PubMed Central

    Zimmerman, Seth P.; Bear, James E.; Goldstein, Bob; Hahn, Klaus; Kuhlman, Brian

    2015-01-01

    Light-activatable proteins allow precise spatial and temporal control of biological processes in living cells and animals. Several approaches have been developed for controlling protein localization with light, including the conditional inhibition of a nuclear localization signal (NLS) with the Light Oxygen Voltage (AsLOV2) domain of phototropin 1 from Avena sativa. In the dark, the switch adopts a closed conformation that sterically blocks the NLS motif. Upon activation with blue light the C-terminus of the protein unfolds, freeing the NLS to direct the protein to the nucleus. A previous study showed that this approach can be used to control the localization and activity of proteins in mammalian tissue culture cells. Here, we extend this result by characterizing the binding properties of a LOV/NLS switch and demonstrating that it can be used to control gene transcription in yeast. Additionally, we show that the switch, referred to as LANS (light-activated nuclear shuttle), functions in the C. elegans embryo and allows for control of nuclear localization in individual cells. By inserting LANS into the C. elegans lin-1 locus using Cas9-triggered homologous recombination, we demonstrated control of cell fate via light-dependent manipulation of a native transcription factor. We conclude that LANS can be a valuable experimental method for spatial and temporal control of nuclear localization in vivo. PMID:26083500

  18. Impacts of recent paraglacial dynamics on plant colonization: A case study on Midtre Lovénbreen foreland, Spitsbergen (79°N)

    NASA Astrophysics Data System (ADS)

    Moreau, Myrtille; Mercier, Denis; Laffly, Dominique; Roussel, Erwan

    2008-03-01

    Climatic changes since the end of the Little Ice Age have considerably disturbed environmental balances of plant colonization in high latitudes. Within one century on Spitsbergen, valley glaciers have retreated up to 1 km from their original terminus as of 1918, affecting several hundred hectares of two types of landscape processes: plant colonization and paraglacial morphogenesis. Since these processes are limited to the chronological position of the old ice front, it is possible to know the rate of plant colonization by both qualitative and quantitative means, as well as speculate on the processes involved, such as the effects of runoff. The present study is limited to the Midtre Lovénbreen forefield (latitude 79°N, longitude 12°E), where geomorphologic and floristic samples were collected in 2003. On stable deposits in this area, the settlement and the evolution of floristic groups have been documented. During this time of period of colonization, the plain areas are reworked by runoff at a kilometric scale and are characterized similar to their surrounding biogeographic landscapes. Thus, a relationship can be observed between the paraglacial process occurring in the proglacial forelands and surrounding stable surfaces in till deposits. These features that occur as spatial discontinuities across the landscape are perceptible through either plant colonization or disturbance to vegetation caused by hydrological processes. Ultimately, however, runoff dynamics maintain pioneer vegetation groups which are superimposed on plant colonization that are driven by temporal periods of deglaciation. Differences in the rates and the nature of plant colonization are biomarkers of paraglacial dynamics.

  19. A genetically-encoded photoactivatable Rac controls the motility of living cells

    PubMed Central

    Wu, Yi I.; Frey, Daniel; Lungu, Oana I.; Jaehrig, Angelika; Schlichting, Ilme; Kuhlman, Brian; Hahn, Klaus M.

    2009-01-01

    The precise spatio-temporal dynamics of protein activity are often critical in determining cell behaviour, yet for most proteins they remain poorly understood; it remains difficult to manipulate protein activity at precise times and places within living cells. Protein activity has been controlled by light, through protein derivatization with photocleavable moieties1 or using photoreactive small molecule ligands2. However, this requires use of toxic UV wavelengths, activation is irreversible, and/or cell loading is accomplished via disruption of the cell membrane (i.e. through microinjection). We have developed a new approach to produce genetically-encoded photo-activatable derivatives of Rac1, a key GTPase regulating actin cytoskeletal dynamics3,4. Rac1 mutants were fused to the photoreactive LOV (light oxygen voltage) domain from phototropin5,6, sterically blocking Rac1 interactions until irradiation unwound a helix linking LOV to Rac1. Photoactivatable Rac1 (PA-Rac1) could be reversibly and repeatedly activated using 458 or 473 nm light to generate precisely localized cell protrusions and ruffling. Localized Rac activation or inactivation was sufficient to produce cell motility and control the direction of cell movement. Myosin was involved in Rac control of directionality but not in Rac-induced protrusion, while PAK was required for Rac-induced protrusion. PA-Rac1 was used to elucidate Rac regulation of RhoA in cell motility. Rac and Rho coordinate cytoskeletal behaviours with seconds and submicron precision7,8. Their mutual regulation remains controversial9, with data indicating that Rac inhibits and/or activates Rho10,11. Rac was shown to inhibit RhoA in living cells, with inhibition modulated at protrusions and ruffles. A PA-Rac crystal structure and modelling revealed LOV-Rac interactions that will facilitate extension of this photoactivation approach to other proteins. PMID:19693014

  20. Domains and Naive Theories

    PubMed Central

    Gelman, Susan A.; Noles, Nicholaus S.

    2013-01-01

    Human cognition entails domain-specific cognitive processes that influence memory, attention, categorization, problem-solving, reasoning, and knowledge organization. This review examines domain-specific causal theories, which are of particular interest for permitting an examination of how knowledge structures change over time. We first describe the properties of commonsense theories, and how commonsense theories differ from scientific theories, illustrating with children’s classification of biological and non-biological kinds. We next consider the implications of domain-specificity for broader issues regarding cognitive development and conceptual change. We then examine the extent to which domain-specific theories interact, and how people reconcile competing causal frameworks. Future directions for research include examining how different content domains interact, the nature of theory change, the role of context (including culture, language, and social interaction) in inducing different frameworks, and the neural bases for domain-specific reasoning. PMID:24187603

  1. Learning and Domain Adaptation

    NASA Astrophysics Data System (ADS)

    Mansour, Yishay

    Domain adaptation is a fundamental learning problem where one wishes to use labeled data from one or several source domains to learn a hypothesis performing well on a different, yet related, domain for which no labeled data is available. This generalization across domains is a very significant challenge for many machine learning applications and arises in a variety of natural settings, including NLP tasks (document classification, sentiment analysis, etc.), speech recognition (speakers and noise or environment adaptation) and face recognition (different lighting conditions, different population composition).

  2. Causal Learning Across Domains

    ERIC Educational Resources Information Center

    Schulz, Laura E.; Gopnik, Alison

    2004-01-01

    Five studies investigated (a) children's ability to use the dependent and independent probabilities of events to make causal inferences and (b) the interaction between such inferences and domain-specific knowledge. In Experiment 1, preschoolers used patterns of dependence and independence to make accurate causal inferences in the domains of…

  3. Modeling Protein Domain Function

    ERIC Educational Resources Information Center

    Baker, William P.; Jones, Carleton "Buck"; Hull, Elizabeth

    2007-01-01

    This simple but effective laboratory exercise helps students understand the concept of protein domain function. They use foam beads, Styrofoam craft balls, and pipe cleaners to explore how domains within protein active sites interact to form a functional protein. The activity allows students to gain content mastery and an understanding of the…

  4. Domain wall filters

    SciTech Connect

    Baer, Oliver; Narayanan, Rajamani; Neuberger, Herbert; Witzel, Oliver

    2007-03-15

    We propose using the extra dimension separating the domain walls carrying lattice quarks of opposite handedness to gradually filter out the ultraviolet fluctuations of the gauge fields that are felt by the fermionic excitations living in the bulk. This generalization of the homogeneous domain wall construction has some theoretical features that seem nontrivial.

  5. Optical Frequency Domain Imaging

    NASA Astrophysics Data System (ADS)

    Bouma, Brett E.; Tearney, Guillermo J.; Vakoc, Benjamin; Yun, Seok Hyun

    In this chapter, we discuss a frequency-domain approach, optical frequency-domain imaging (OFDI), which is based on optical frequency-domain reflectometry and uses a wavelength-swept laser and standard single-element photodetectors. The chapter begins with an overview of the fundamental aspects of the technology, including the detected signal, sensitivity, depth range, and resolution, and then goes on to discuss specific component technologies including the light source, interferometer and acquisition electronics, and image processing. The final section of the chapter provides a brief glimpse at some of the biomedical applications that most directly take advantage of the improved speed and sensitivity of OFDI.

  6. Visualizing Knowledge Domains.

    ERIC Educational Resources Information Center

    Borner, Katy; Chen, Chaomei; Boyack, Kevin W.

    2003-01-01

    Reviews visualization techniques for scientific disciplines and information retrieval and classification. Highlights include historical background of scientometrics, bibliometrics, and citation analysis; map generation; process flow of visualizing knowledge domains; measures and similarity calculations; vector space model; factor analysis;…

  7. Oscillons and domain walls

    SciTech Connect

    Hindmarsh, Mark; Salmi, Petja

    2008-05-15

    Oscillons, extremely long-lived localized oscillations of a scalar field, are shown to be produced by evolving domain wall networks in {phi}{sup 4} theory in two spatial dimensions. We study the oscillons in frequency space using the classical spectral function at zero momentum, and obtain that the velocity distribution is suppressed as {gamma}{sup -2} at large Lorentz factor {gamma}, with oscillons produced up to at least {gamma}{approx}10. This leads us to speculate that oscillons are produced at cusps, regions of the domain wall travelling near the speed of light. In order to gain some insight onto the dilute oscillon 'gas' produced by the domain walls, we prepare a denser gas by filling the simulation volume with oscillons boosted in random directions. We finish the study by revisiting collisions between oscillons and between an oscillon and a domain wall, showing that in the latter case they can pass straight through with minimal distortion.

  8. Tandem BRCT Domains

    PubMed Central

    Mesquita, Rafael D.; Woods, Nicholas T.; Seabra-Junior, Eloy S.; Monteiro, Alvaro N.A.

    2010-01-01

    The cell’s ability to sense and respond to specific stimuli is a complex system derived from precisely regulated protein-protein interactions. Some of these protein-protein interactions are mediated by the recognition of linear peptide motifs by protein modular domains. BRCT (BRCA1 C-terminal) domains and their linear motif counterparts, which contain phosphoserines, are one such pair-wise interaction system that seems to have evolved to serve as a surveillance system to monitor threats to the cell’s genetic integrity. Evidence indicates that BRCT domains found in tandem can cooperate to provide sequence-specific binding of phosphorylated peptides as is the case for the breast and ovarian cancer susceptibility gene BRCA1 and the PAX transcription factor–interacting protein PAXIP1. Particular interest has been paid to tandem BRCT domains as “readers” of signaling events in the form of phosphorylated serine moieties induced by the activation of DNA damage response kinases ATM, ATR, and DNA-PK. However, given the diversity of tandem BRCT-containing proteins, questions remain as to the origin and evolution of this domain. Here, we discuss emerging views of the origin and evolving roles of tandem BRCT domain repeats in the DNA damage response. PMID:21533002

  9. Domains in Ferroelectric Nanostructures

    NASA Astrophysics Data System (ADS)

    Gregg, Marty

    2010-03-01

    Ferroelectric materials have great potential in influencing the future of small scale electronics. At a basic level, this is because ferroelectric surfaces are charged, and so interact strongly with charge-carrying metals and semiconductors - the building blocks for all electronic systems. Since the electrical polarity of the ferroelectric can be reversed, surfaces can both attract and repel charges in nearby materials, and can thereby exert complete control over both charge distribution and movement. It should be no surprise, therefore, that microelectronics industries have already looked very seriously at harnessing ferroelectric materials in a variety of applications, from solid state memory chips (FeRAMs) to field effect transistors (FeFETs). In all such applications, switching the direction of the polarity of the ferroelectric is a key aspect of functional behavior. The mechanism for switching involves the field-induced nucleation and growth of domains. Domain coarsening, through domain wall propagation, eventually causes the entire ferroelectric to switch its polar direction. It is thus the existence and behavior of domains that determine the switching response, and ultimately the performance of the ferroelectric device. A major issue, associated with the integration of ferroelectrics into microelectronic devices, has been that the fundamental properties associated with ferroelectrics, when in bulk form, appear to change quite dramatically and unpredictably when at the nanoscale: new modes of behaviour, and different functional characteristics from those seen in bulk appear. For domains, in particular, the proximity of surfaces and boundaries have a dramatic effect: surface tension and depolarizing fields both serve to increase the equilibrium density of domains, such that minor changes in scale or morphology can have major ramifications for domain redistribution. Given the importance of domains in dictating the overall switching characteristics of a device

  10. Axion domain wall baryogenesis

    SciTech Connect

    Daido, Ryuji; Kitajima, Naoya; Takahashi, Fuminobu

    2015-07-28

    We propose a new scenario of baryogenesis, in which annihilation of axion domain walls generates a sizable baryon asymmetry. Successful baryogenesis is possible for a wide range of the axion mass and decay constant, m≃10{sup 8}–10{sup 13} GeV and f≃10{sup 13}–10{sup 16} GeV. Baryonic isocurvature perturbations are significantly suppressed in our model, in contrast to various spontaneous baryogenesis scenarios in the slow-roll regime. In particular, the axion domain wall baryogenesis is consistent with high-scale inflation which generates a large tensor-to-scalar ratio within the reach of future CMB B-mode experiments. We also discuss the gravitational waves produced by the domain wall annihilation and its implications for the future gravitational wave experiments.

  11. Predicting domain-domain interactions using a parsimony approach

    PubMed Central

    Guimarães, Katia S; Jothi, Raja; Zotenko, Elena; Przytycka, Teresa M

    2006-01-01

    We propose a novel approach to predict domain-domain interactions from a protein-protein interaction network. In our method we apply a parsimony-driven explanation of the network, where the domain interactions are inferred using linear programming optimization, and false positives in the protein network are handled by a probabilistic construction. This method outperforms previous approaches by a considerable margin. The results indicate that the parsimony principle provides a correct approach for detecting domain-domain contacts. PMID:17094802

  12. Time-domain imaging

    NASA Technical Reports Server (NTRS)

    Tolliver, C. L.

    1989-01-01

    The quest for the highest resolution microwave imaging and principle of time-domain imaging has been the primary motivation for recent developments in time-domain techniques. With the present technology, fast time varying signals can now be measured and recorded both in magnitude and in-phase. It has also enhanced our ability to extract relevant details concerning the scattering object. In the past, the interface of object geometry or shape for scattered signals has received substantial attention in radar technology. Various scattering theories were proposed to develop analytical solutions to this problem. Furthermore, the random inversion, frequency swept holography, and the synthetic radar imaging, have two things in common: (1) the physical optic far-field approximation, and (2) the utilization of channels as an extra physical dimension, were also advanced. Despite the inherent vectorial nature of electromagnetic waves, these scalar treatments have brought forth some promising results in practice with notable examples in subsurface and structure sounding. The development of time-domain techniques are studied through the theoretical aspects as well as experimental verification. The use of time-domain imaging for space robotic vision applications has been suggested.

  13. Cellulose binding domain proteins

    DOEpatents

    Shoseyov, O.; Shpiegl, I.; Goldstein, M.; Doi, R.

    1998-11-17

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

  14. Cellulose binding domain proteins

    DOEpatents

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc; Doi, Roy

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  15. Simplified Parallel Domain Traversal

    SciTech Connect

    Erickson III, David J

    2011-01-01

    Many data-intensive scientific analysis techniques require global domain traversal, which over the years has been a bottleneck for efficient parallelization across distributed-memory architectures. Inspired by MapReduce and other simplified parallel programming approaches, we have designed DStep, a flexible system that greatly simplifies efficient parallelization of domain traversal techniques at scale. In order to deliver both simplicity to users as well as scalability on HPC platforms, we introduce a novel two-tiered communication architecture for managing and exploiting asynchronous communication loads. We also integrate our design with advanced parallel I/O techniques that operate directly on native simulation output. We demonstrate DStep by performing teleconnection analysis across ensemble runs of terascale atmospheric CO{sub 2} and climate data, and we show scalability results on up to 65,536 IBM BlueGene/P cores.

  16. Magnetic bubble domain memories

    NASA Technical Reports Server (NTRS)

    Ypma, J. E.

    1974-01-01

    Some attractive features of Bubble Domain Memory and its relation to existing technologies are discussed. Two promising applications are block access mass memory and tape recorder replacement. The required chip capabilities for these uses are listed, and the specifications for a block access mass memory designed to fit between core and HPT disk are presented. A feasibility model for a tape recorder replacement is introduced.

  17. Domain Specific vs Domain General: Implications for Dynamic Assessment

    ERIC Educational Resources Information Center

    Kaniel, Shlomo

    2010-01-01

    The article responds to the need for evidence-based dynamic assessment. The article is divided into two sections: In Part 1 we examine the scientific answer to the question of how far human mental activities and capabilities are domain general (DG) / domain specific (DS). A highly complex answer emerges from the literature review of domains such…

  18. Frequency domain nonlinear optics

    NASA Astrophysics Data System (ADS)

    Legare, Francois

    2016-05-01

    The universal dilemma of gain narrowing occurring in fs amplifiers prevents ultra-high power lasers from delivering few-cycle pulses. This problem is overcome by a new amplification concept: Frequency domain Optical Parametric Amplification - FOPA. It enables simultaneous up-scaling of peak power and amplified spectral bandwidth and can be performed at any wavelength range of conventional amplification schemes, however, with the capability to amplify single cycles of light. The key idea for amplification of octave-spanning spectra without loss of spectral bandwidth is to amplify the broad spectrum ``slice by slice'' in the frequency domain, i.e. in the Fourier plane of a 4f-setup. The striking advantages of this scheme, are its capability to amplify (more than) one octave of bandwidth without shorting the corresponding pulse duration. This is because ultrabroadband phase matching is not defined by the properties of the nonlinear crystal employed but the number of crystals employed. In the same manner, to increase the output energy one simply has to increase the spectral extension in the Fourier plane and to add one more crystal. Thus, increasing pulse energy and shortening its duration accompany each other. A proof of principle experiment was carried out at ALLS on the sub-two cycle IR beam line and yielded record breaking performance in the field of few-cycle IR lasers. 100 μJ two-cycle pulses from a hollow core fibre compression setup were amplified to 1.43mJ without distorting spatial or temporal properties. Pulse duration at the input of FOPA and after FOPA remains the same. Recently, we have started upgrading this system to be pumped by 250 mJ to reach 40 mJ two-cycle IR few-cycle pulses and latest results will be presented at the conference. Furthermore, the extension of the concept of FOPA to other nonlinear optical processes will be discussed. Frequency domain nonlinear optics.

  19. On Probability Domains III

    NASA Astrophysics Data System (ADS)

    Frič, Roman; Papčo, Martin

    2015-12-01

    Domains of generalized probability have been introduced in order to provide a general construction of random events, observables and states. It is based on the notion of a cogenerator and the properties of product. We continue our previous study and show how some other quantum structures fit our categorical approach. We discuss how various epireflections implicitly used in the classical probability theory are related to the transition to fuzzy probability theory and describe the latter probability theory as a genuine categorical extension of the former. We show that the IF-probability can be studied via the fuzzy probability theory. We outline a "tensor modification" of the fuzzy probability theory.

  20. Transfer of high domain knowledge to a similar domain.

    PubMed

    Jessup, Ryan K

    2009-01-01

    Researchers have widely examined domain knowledge yet rarely investigate the transfer of knowledge from one domain to another. This study sought to fill in the literature gap concerning the impact of domain knowledge on memory in a similar situation. Specifically, this study examined whether high knowledge of baseball could enhance memory for the similar yet unknown domain of cricket, using a 2 (knowledge) x 2 (prime) design. An interaction occurred, indicating that when primed, baseball knowledge improves memory for cricket events in participants with high baseball knowledge but reduces memory in their low-knowledge counterparts. These results suggest that extensive knowledge in one domain allows it to serve as an organizational framework for incoming information in a similar domain; conversely, priming poorly understood domain knowledge results in negative transfer. PMID:19353932

  1. STAS Domain Structure and Function

    PubMed Central

    Sharma, Alok K.; Rigby, Alan C.; Alper, Seth L.

    2011-01-01

    Pendrin shares with nearly all SLC26/SulP anion transporters a carboxy-terminal cytoplasmic segment organized around a Sulfate Transporter and Anti-Sigma factor antagonist (STAS) domain. STAS domains of divergent amino acid sequence exhibit a conserved fold of 4 β strands interspersed among 5 α helices. The first STAS domain proteins studied were single-domain anti-sigma factor antagonists (anti-anti-σ). These anti-anti-σ indirectly stimulate bacterial RNA polymerase by inactivating inhibitory anti-σ kinases, liberating σ factors to direct specific transcription of target genes or operons. Some STAS domains are nucleotide-binding phosphoproteins or nucleotidases. Others are interaction/transduction modules within multidomain sensors of light, oxygen and other gasotransmitters, cyclic nucleotides, inositol phosphates, and G proteins. Additional multidomain STAS protein sequences suggest functions in sensing, metabolism, or transport of nutrients such as sugars, amino acids, lipids, anions, vitamins, or hydrocarbons. Still other multidomain STAS polypeptides include histidine and serine/threonine kinase domains and ligand-activated transcription factor domains. SulP/SLC26 STAS domains and adjacent sequences interact with other transporters, cytoskeletal scaffolds, and with enzymes metabolizing transported anion substrates, forming putative metabolons. STAS domains are central to membrane targeting of many SulP/SLC26 anion transporters, and STAS domain mutations are associated with at least three human recessive diseases. This review summarizes STAS domain structure and function. PMID:22116355

  2. Beyond the Number Domain

    PubMed Central

    Cantlon, Jessica F.; Platt, Michael L.; Brannon, Elizabeth M.

    2009-01-01

    In a world without numbers, we would be unable to build a skyscraper, hold a national election, plan a wedding, or pay for a chicken at the market. The numerical symbols used in all these behaviors build on the approximate number system (ANS) which represents the number of discrete objects or events as a continuous mental magnitude. In this review, we first discuss evidence that the ANS bears a set of behavioral and brain signatures that are universally displayed across animal species, human cultures, and development. We then turn to the question of whether the ANS constitutes a specialized cognitive and neural domain--a question central to understanding how this system works, the nature of its evolutionary and developmental trajectory, and its physical instantiation in the brain. PMID:19131268

  3. Crystallization of PTP Domains.

    PubMed

    Levy, Colin; Adams, James; Tabernero, Lydia

    2016-01-01

    Protein crystallography is the most powerful method to obtain atomic resolution information on the three-dimensional structure of proteins. An essential step towards determining the crystallographic structure of a protein is to produce good quality crystals from a concentrated sample of purified protein. These crystals are then used to obtain X-ray diffraction data necessary to determine the 3D structure by direct phasing or molecular replacement if the model of a homologous protein is available. Here, we describe the main approaches and techniques to obtain suitable crystals for X-ray diffraction. We include tools and guidance on how to evaluate and design the protein construct, how to prepare Se-methionine derivatized protein, how to assess the stability and quality of the sample, and how to crystallize and prepare crystals for diffraction experiments. While general strategies for protein crystallization are summarized, specific examples of the application of these strategies to the crystallization of PTP domains are discussed. PMID:27514806

  4. Multifunctionalities driven by ferroic domains

    SciTech Connect

    Yang, J. C.; Huang, Y. L.; Chu, Y. H.; He, Q.

    2014-08-14

    Considerable attention has been paid to ferroic systems in pursuit of advanced applications in past decades. Most recently, the emergence and development of multiferroics, which exhibit the coexistence of different ferroic natures, has offered a new route to create functionalities in the system. In this manuscript, we step from domain engineering to explore a roadmap for discovering intriguing phenomena and multifunctionalities driven by periodic domain patters. As-grown periodic domains, offering exotic order parameters, periodic local perturbations and the capability of tailoring local spin, charge, orbital and lattice degrees of freedom, are introduced as modeling templates for fundamental studies and novel applications. We discuss related significant findings on ferroic domain, nanoscopic domain walls, and conjunct heterostructures based on the well-organized domain patterns, and end with future prospects and challenges in the field.

  5. Dynamical domain wall and localization

    NASA Astrophysics Data System (ADS)

    Toyozato, Yuta; Higuchi, Masafumi; Nojiri, Shin'ichi

    2016-03-01

    Based on the previous works (Toyozato et al., 2013 [24]; Higuchi and Nojiri, 2014 [25]), we investigate the localization of the fields on the dynamical domain wall, where the four-dimensional FRW universe is realized on the domain wall in the five-dimensional space-time. Especially we show that the chiral spinor can localize on the domain wall, which has not been succeeded in the past works as the seminal work in George et al. (2009) [23].

  6. Domain transfer multiple kernel learning.

    PubMed

    Duan, Lixin; Tsang, Ivor W; Xu, Dong

    2012-03-01

    Cross-domain learning methods have shown promising results by leveraging labeled patterns from the auxiliary domain to learn a robust classifier for the target domain which has only a limited number of labeled samples. To cope with the considerable change between feature distributions of different domains, we propose a new cross-domain kernel learning framework into which many existing kernel methods can be readily incorporated. Our framework, referred to as Domain Transfer Multiple Kernel Learning (DTMKL), simultaneously learns a kernel function and a robust classifier by minimizing both the structural risk functional and the distribution mismatch between the labeled and unlabeled samples from the auxiliary and target domains. Under the DTMKL framework, we also propose two novel methods by using SVM and prelearned classifiers, respectively. Comprehensive experiments on three domain adaptation data sets (i.e., TRECVID, 20 Newsgroups, and email spam data sets) demonstrate that DTMKL-based methods outperform existing cross-domain learning and multiple kernel learning methods. PMID:21646679

  7. Hydrophilic Domains Enhance Nanobubble Stability.

    PubMed

    Nishiyama, Takashi; Takahashi, Koji; Ikuta, Tatsuya; Yamada, Yutaka; Takata, Yasuyuki

    2016-05-18

    Highly stable nanoscale gas states at solid/liquid interfaces, referred to as nanobubbles, have been widely studied for over a decade. In this study, nanobubbles generated on a hydrophobic Teflon amorphous fluoroplastic thin film in the presence and absence of hydrophilic carbon domains are investigated by peak force quantitative nanomechanics. On the hydrophobic surface without hydrophilic domains, a small number of nanobubbles are generated and then rapidly decrease in size. On the hydrophobic surface with hydrophilic domains, the hydrophilic domains have a significant effect on the generation and stability of nanobubbles, with bubbles remaining on the surface for up to three days. PMID:26864857

  8. Mapping the Moral Domain

    PubMed Central

    Graham, Jesse; Nosek, Brian A.; Haidt, Jonathan; Iyer, Ravi; Koleva, Spassena; Ditto, Peter H.

    2010-01-01

    The moral domain is broader than the empathy and justice concerns assessed by existing measures of moral competence, and it is not just a subset of the values assessed by value inventories. To fill the need for reliable and theoretically-grounded measurement of the full range of moral concerns, we developed the Moral Foundations Questionnaire (MFQ) based on a theoretical model of five universally available (but variably developed) sets of moral intuitions: Harm/care, Fairness/reciprocity, Ingroup/loyalty, Authority/respect, and Purity/sanctity. We present evidence for the internal and external validity of the scale and the model, and in doing so present new findings about morality: 1. Comparative model fitting of confirmatory factor analyses provides empirical justification for a five-factor structure of moral concerns. 2. Convergent/discriminant validity evidence suggests that moral concerns predict personality features and social group attitudes not previously considered morally relevant. 3. We establish pragmatic validity of the measure in providing new knowledge and research opportunities concerning demographic and cultural differences in moral intuitions. These analyses provide evidence for the usefulness of Moral Foundations Theory in simultaneously increasing the scope and sharpening the resolution of psychological views of morality. PMID:21244182

  9. Ontology development for Sufism domain

    NASA Astrophysics Data System (ADS)

    Iqbal, Rizwan

    2012-01-01

    Domain ontology is a descriptive representation of any particular domain which in detail describes the concepts in a domain, the relationships among those concepts and organizes them in a hierarchal manner. It is also defined as a structure of knowledge, used as a means of knowledge sharing to the community. An Important aspect of using ontologies is to make information retrieval more accurate and efficient. Thousands of domain ontologies from all around the world are available online on ontology repositories. Ontology repositories like SWOOGLE currently have over 1000 ontologies covering a wide range of domains. It was found that up to date there was no ontology available covering the domain of "Sufism". This unavailability of "Sufism" domain ontology became a motivation factor for this research. This research came up with a working "Sufism" domain ontology as well a framework, design of the proposed framework focuses on the resolution to problems which were experienced while creating the "Sufism" ontology. The development and working of the "Sufism" domain ontology are covered in detail in this research. The word "Sufism" is a term which refers to Islamic mysticism. One of the reasons to choose "Sufism" for ontology creation is its global curiosity. This research has also managed to create some individuals which inherit the concepts from the "Sufism" ontology. The creation of individuals helps to demonstrate the efficient and precise retrieval of data from the "Sufism" domain ontology. The experiment of creating the "Sufism" domain ontology was carried out on a tool called Protégé. Protégé is a tool which is used for ontology creation, editing and it is open source.

  10. Ontology development for Sufism domain

    NASA Astrophysics Data System (ADS)

    Iqbal, Rizwan

    2011-12-01

    Domain ontology is a descriptive representation of any particular domain which in detail describes the concepts in a domain, the relationships among those concepts and organizes them in a hierarchal manner. It is also defined as a structure of knowledge, used as a means of knowledge sharing to the community. An Important aspect of using ontologies is to make information retrieval more accurate and efficient. Thousands of domain ontologies from all around the world are available online on ontology repositories. Ontology repositories like SWOOGLE currently have over 1000 ontologies covering a wide range of domains. It was found that up to date there was no ontology available covering the domain of "Sufism". This unavailability of "Sufism" domain ontology became a motivation factor for this research. This research came up with a working "Sufism" domain ontology as well a framework, design of the proposed framework focuses on the resolution to problems which were experienced while creating the "Sufism" ontology. The development and working of the "Sufism" domain ontology are covered in detail in this research. The word "Sufism" is a term which refers to Islamic mysticism. One of the reasons to choose "Sufism" for ontology creation is its global curiosity. This research has also managed to create some individuals which inherit the concepts from the "Sufism" ontology. The creation of individuals helps to demonstrate the efficient and precise retrieval of data from the "Sufism" domain ontology. The experiment of creating the "Sufism" domain ontology was carried out on a tool called Protégé. Protégé is a tool which is used for ontology creation, editing and it is open source.

  11. Taxonomic characterization, adaptation strategies and biotechnological potential of cryophilic yeasts from ice cores of Midre Lovénbreen glacier, Svalbard, Arctic.

    PubMed

    Singh, Purnima; Tsuji, Masaharu; Singh, Shiv Mohan; Roy, Utpal; Hoshino, Tamotsu

    2013-04-01

    Ten strains of cryophilic yeast were studied from glacier ice cores of Svalbard, Arctic. The ice melt samples contained about 3×10(3) - 1×10(4) colony forming unit (CFUs) per ml. Sequence analysis of the isolates, using D1/D2 domain identified five species of yeasts: Cryptococcus adeliensis (MLB-18 JX192655), Cryptococcus albidosimilis (MLB-19 JX192656), Cryptococcus saitoi (MLB-22 JX192659), Rhodosporidium lusitaniae (MLB-20 JX192657), and Rhodotorula mucilaginosa (MLB-27 JX192664). Effect of temperature on growth of these isolates was studied. The strains are able to grow at temperatures ranging between 1 and 20°C. Screening of the cultures for amylase, cellulase, protease, lipase, urease and catalase activity were carried out indicating varying amounts of enzyme production at different temperatures. Characterization of lipase in strain Cryptococcus sp. MLB-24 was performed. Fatty acid methyl ester (FAME) analysis of the cultures grown at four different temperatures (1, 4, 15, and 20°C) was also done. Decrease in temperature was reported to cause increase in concentration of unsaturated fatty acids. High amount of oleic acid accumulated with increase in temperature. These fatty acids possibly help the strains to survive in glacial ice core cold environment. The extracellular and intracellular filtrate of the cultures showed negative antifreeze protein (AFP) activity. The observations indicate that probably the isolates in the present undertaking adapt to low temperatures, by enzyme and PUFA secretion rather than by antifreeze protein secretion. PMID:23353800

  12. Fractional diffusion on bounded domains

    DOE PAGESBeta

    Defterli, Ozlem; D'Elia, Marta; Du, Qiang; Gunzburger, Max Donald; Lehoucq, Richard B.; Meerschaert, Mark M.

    2015-03-13

    We found that the mathematically correct specification of a fractional differential equation on a bounded domain requires specification of appropriate boundary conditions, or their fractional analogue. In this paper we discuss the application of nonlocal diffusion theory to specify well-posed fractional diffusion equations on bounded domains.

  13. Polarized domains of myelinated axons.

    PubMed

    Salzer, James L

    2003-10-01

    The entire length of myelinated axons is organized into a series of polarized domains that center around nodes of Ranvier. These domains, which are crucial for normal saltatory conduction, consist of distinct multiprotein complexes of cell adhesion molecules, ion channels, and scaffolding molecules; they also differ in their diameter, organelle content, and rates of axonal transport. Juxtacrine signals from myelinating glia direct their sequential assembly. The composition, mechanisms of assembly, and function of these molecular domains will be reviewed. I also discuss similarities of this domain organization to that of polarized epithelia and present emerging evidence that disorders of domain organization and function contribute to the axonopathies of myelin and other neurologic disorders. PMID:14556710

  14. The monocyte binding domain(s) on human immunoglobulin G.

    PubMed

    Woof, J M; Nik Jaafar, M I; Jefferis, R; Burton, D R

    1984-06-01

    Monocyte binding has previously been assigned to the C gamma 3 domain of human immunoglobulin G (IgG) largely on the ability of the pFc' fragment to inhibit the monocyte-IgG interaction. This ability is markedly reduced compared to the intact parent IgG. We find this result with a conventional pFc' preparation but this preparation is found to contain trace contamination of parent IgG as demonstrated by reactivity with monoclonal antibodies directed against C gamma 2 domain and light-chain epitopes of human IgG. Extensive immunoaffinity purification of the pFc' preparation removes its inhibitory ability indicating that this originates in the trace contamination of parent IgG (or Fc). Neither of the human IgG1 paraproteins TIM, lacking the C gamma 2 domain, or SIZ, lacking the C gamma 3 domain, are found to inhibit the monocyte-IgG interaction. The hinge-deleted IgG1 Dob protein shows little or no inhibitory ability. Indirect evidence for the involvement of the C gamma 2 domain in monocyte binding is considered. We suggest finally that the site of interaction is found either on the C gamma 2 domain alone or between the C gamma 2 and C gamma 3 domains. PMID:6235444

  15. Domain walls riding the wave.

    SciTech Connect

    Karapetrov, G.; Novosad, V.; Materials Science Division

    2010-11-01

    Recent years have witnessed a rapid proliferation of electronic gadgets around the world. These devices are used for both communication and entertainment, and it is a fact that they account for a growing portion of household energy consumption and overall world consumption of electricity. Increasing the energy efficiency of these devices could have a far greater and immediate impact than a gradual switch to renewable energy sources. The advances in the area of spintronics are therefore very important, as gadgets are mostly comprised of memory and logic elements. Recent developments in controlled manipulation of magnetic domains in ferromagnet nanostructures have opened opportunities for novel device architectures. This new class of memories and logic gates could soon power millions of consumer electronic devices. The attractiveness of using domain-wall motion in electronics is due to its inherent reliability (no mechanical moving parts), scalability (3D scalable architectures such as in racetrack memory), and nonvolatility (retains information in the absence of power). The remaining obstacles in widespread use of 'racetrack-type' elements are the speed and the energy dissipation during the manipulation of domain walls. In their recent contribution to Physical Review Letters, Oleg Tretiakov, Yang Liu, and Artem Abanov from Texas A&M University in College Station, provide a theoretical description of domain-wall motion in nanoscale ferromagnets due to the spin-polarized currents. They find exact conditions for time-dependent resonant domain-wall movement, which could speed up the motion of domain walls while minimizing Ohmic losses. Movement of domain walls in ferromagnetic nanowires can be achieved by application of external magnetic fields or by passing a spin-polarized current through the nanowire itself. On the other hand, the readout of the domain state is done by measuring the resistance of the wire. Therefore, passing current through the ferromagnetic wire is

  16. Modeling software systems by domains

    NASA Technical Reports Server (NTRS)

    Dippolito, Richard; Lee, Kenneth

    1992-01-01

    The Software Architectures Engineering (SAE) Project at the Software Engineering Institute (SEI) has developed engineering modeling techniques that both reduce the complexity of software for domain-specific computer systems and result in systems that are easier to build and maintain. These techniques allow maximum freedom for system developers to apply their domain expertise to software. We have applied these techniques to several types of applications, including training simulators operating in real time, engineering simulators operating in non-real time, and real-time embedded computer systems. Our modeling techniques result in software that mirrors both the complexity of the application and the domain knowledge requirements. We submit that the proper measure of software complexity reflects neither the number of software component units nor the code count, but the locus of and amount of domain knowledge. As a result of using these techniques, domain knowledge is isolated by fields of engineering expertise and removed from the concern of the software engineer. In this paper, we will describe kinds of domain expertise, describe engineering by domains, and provide relevant examples of software developed for simulator applications using the techniques.

  17. Information Fusion: Moving from domain independent to domain literate approaches

    NASA Astrophysics Data System (ADS)

    McGuinness, D.

    2008-12-01

    Information Fusion has been a focus of research within the field of computer science for a number of years. Numerous environments aimed at general schema evaluation, diagnosis, and evolution have evolved within those communities including for example the Chimaera Ontology Evolution Environment and the Prompt environment for mapping schema alignment. General (domain independent) efforts have produced useful research results and numerous tools, however these results have predominantly been generated and used by computer scientists and have been focused largely on information schema integration and diagnosis. More recently semantically-enabled web-centric approaches have emerged that utilize domain knowledge to provide tools and services aimed at natural scientists needs for data fusion. In this talk, we will introduce some foundations for information fusion and provide deployed examples of how these foundations and evolving tools have been and are being used today in natural science domains by domain scientists. Some examples will be provided from deployed virtual observatory settings.

  18. Matching Recommendation Technologies and Domains

    NASA Astrophysics Data System (ADS)

    Burke, Robin; Ramezani, Maryam

    Recommender systems form an extremely diverse body of technologies and approaches. The chapter aims to assist researchers and developers to identify the recommendation technologies that are most likely to be applicable to different domains of recommendation. Unlike other taxonomies of recommender systems, our approach is centered on the question of knowledge: what knowledge does a recommender system need in order to function, and where does that knowledge come from? Different recommendation domains (books vs condominiums, for example) provide different opportunities for the gathering and application of knowledge. These considerations give rise to a mapping between domain characteristics and recommendation technologies.

  19. Lung-protective ventilation initiated in the emergency department (LOV-ED): a study protocol for a quasi-experimental, before-after trial aimed at reducing pulmonary complications

    PubMed Central

    Fuller, Brian M; Ferguson, Ian; Mohr, Nicholas M; Stephens, Robert J; Briscoe, Cristopher C; Kolomiets, Angelina A; Hotchkiss, Richard S; Kollef, Marin H

    2016-01-01

    Introduction In critically ill patients, acute respiratory distress syndrome (ARDS) and ventilator-associated conditions (VACs) are associated with increased mortality, survivor morbidity and healthcare resource utilisation. Studies conclusively demonstrate that initial ventilator settings in patients with ARDS, and at risk for it, impact outcome. No studies have been conducted in the emergency department (ED) to determine if lung-protective ventilation in patients at risk for ARDS can reduce its incidence. Since the ED is the entry point to the intensive care unit for hundreds of thousands of mechanically ventilated patients annually in the USA, this represents a knowledge gap in this arena. A lung-protective ventilation strategy was instituted in our ED in 2014. It aims to address the parameters in need of quality improvement, as demonstrated by our previous research: (1) prevention of volutrauma; (2) appropriate positive end-expiratory pressure setting; (3) prevention of hyperoxia; and (4) aspiration precautions. Methods and analysis The lung-protective ventilation initiated in the emergency department (LOV-ED) trial is a single-centre, quasi-experimental before-after study testing the hypothesis that lung-protective ventilation, initiated in the ED, is associated with reduced pulmonary complications. An intervention cohort of 513 mechanically ventilated adult ED patients will be compared with over 1000 preintervention control patients. The primary outcome is a composite outcome of pulmonary complications after admission (ARDS and VACs). Multivariable logistic regression with propensity score adjustment will test the hypothesis that ED lung-protective ventilation decreases the incidence of pulmonary complications. Ethics and dissemination Approval of the study was obtained prior to data collection on the first patient. As the study is a before-after observational study, examining the effect of treatment changes over time, it is being conducted with waiver of

  20. Dobson, Brewer, ERA-40 and ERA-Interim original and assimilated total ozone data sets - evaluation of differences: a case study, Hradec Králové (Czech), 1961-2010

    NASA Astrophysics Data System (ADS)

    Vaníček, K.; Metelka, L.; Skřivánková, P.; Staněk, M.

    2012-05-01

    Homogenized data series of total ozone measurements taken by the regularly and well calibrated Dobson and Brewer spectrophotometers at Hradec Králové (Czech) and the data from the re-analyses ERA-40 and ERA-Interim were assimilated and combined to investigate differences between the particular data sets over Central Europe, the NH mid-latitudes. The Dobson-to-Brewer transfer function and the algorithm for approximation of the data from the re-analyses were developed, tested and applied for creation of instrumentally consistent and completed total ozone data series of the 50-yr period 1961-2010 of observations. The assimilation has reduced the well-known seasonal differences between Dobson and Brewer data below the 1% calibration limit of the spectrophotometers. Incorporation of the ERA-40 and ERA-Interim total ozone data on days with missing measurements significantly improved completeness and reliability of the data series mainly in the first two decades of the period concerned. Consistent behaviour of the original and assimilated data sets was found in the pre-ozone-hole period (1961-1985). In the post-Pinatubo (1994-2010) era the data series show seasonal differences that can introduce uncertainty in estimation of ozone recovery mainly in the winter-spring season when the effect of the Montreal Protocol and its Amendments is expected. All the data sets confirm substantial depletion of ozone also in the summer months that gives rise to the question about its origin. The assimilated and completed data series of total ozone will be further analyzed to quantify chemical ozone losses and contribution of natural atmospheric processes to the ozone depletion over the region. This case study points out importance of selection and evaluation of the quality and consistency of the input data sets used in estimation of long-term ozone changes including recovery of the ozone layer over the selected areas. Data are available from the PANGAEA database at

  1. Dobson, Brewer, ERA-40 and ERA-Interim original and merged total ozone data sets - evaluation of differences: a case study, Hradec Králové (Czech), 1961-2010

    NASA Astrophysics Data System (ADS)

    Vaníček, K.; Metelka, L.; Skřivánková, P.; Staněk, M.

    2012-09-01

    Homogenized data series of total ozone measurements taken by the regularly and well calibrated Dobson and Brewer spectrophotometers at Hradec Králové (Czech) and the data from the re-analyses ERA-40 and ERA-Interim were merged and compared to investigate differences between the particular data sets originated in Central Europe, the Northern Hemisphere (NH) mid-latitudes. The Dobson-to-Brewer transfer function and the algorithm for approximation of the data from the re-analyses were developed, tested and applied for creation of instrumentally consistent and completed total ozone data series of the 50-yr period 1961-2010 of observations. This correction has reduced the well-known seasonal differences between Dobson and Brewer data below the 1% calibration limit of the spectrophotometers. Incorporation of the ERA-40 and ERA-Interim total ozone data on days with missing measurements significantly improved completeness and reliability of the data series mainly in the first two decades of the period concerned. Consistent behaviour of the original and corrected/merged data sets was found in the pre-ozone-hole period (1961-1985). In the post-Pinatubo (1994-2010) era the data series show seasonal differences that can introduce uncertainty in estimation of ozone recovery mainly in the winter-spring season when the effect of the Montreal Protocol and its Amendments is expected. All the data sets confirm substantial depletion of ozone also in the summer months that gives rise to the question about its origin. The merged and completed data series of total ozone will be further analyzed to quantify chemical ozone losses and contribution of natural atmospheric processes to the ozone depletion over the region. This case study points out the importance of selection and evaluation of the quality and consistency of the input data sets used in estimation of long-term ozone changes including recovery of the ozone layer over the selected areas. Data are available from the PANGAEA

  2. Engineered CH2 domains (nanoantibodies).

    PubMed

    Dimitrov, Dimiter S

    2009-01-01

    Currently, almost all FDA approved therapeutic antibodies (except ReoPro, Lucentis and Cimzia which are Fabs), and the vast majority of those in clinical trials are full-size antibodies mostly in IgG1 format of about 150 kDa size. A fundamental problem for such large molecules is their poor penetration into tissues (e.g., solid tumors) and poor or absent binding to regions on the surface of some molecules (e.g., on the HIV envelope glycoprotein) which are fully accessible only by molecules of smaller size. Therefore, much work especially during the last decade has been aimed at developing novel scaffolds of much smaller size and high stability. Here I briefly describe a proposition to use the immunoglobulin (Ig) constant CH2 domain (CH3 for IgE and IgM) as a scaffold. CH2 is critical for the Ig effector functions. Isolated CH2 is stable monomer in contrast to all other constant domains and most of the variable domains. CH2 and engineered CH2 domains with improved stability can be used as scaffolds for construction of libraries containing diverse binders to various antigens. Such binders based on a CH2 scaffold could also confer some effector functions. Because the CH2 domains are the smallest independently folded antibody domains that can be engineered to contain simultaneously antigen-binding sites and binding sites mediating effector and stability functions, and to distinguish them from domain antibodies which are used to denote engineered VH or VL domains or nanobodies which are used to denote camelid VHH, I termed them nanoantibodies (nAbs). PMID:20046570

  3. Domain Walls with Strings Attached

    SciTech Connect

    Shmakova, Marina

    2001-08-20

    We have constructed a bulk and brane action of IIA theory which describes a pair of BPS domain walls on S{sub 1}/Z{sub 2}, with strings attached. The walls are given by two orientifold O8-planes with coincident D8-branes and F1-D0-strings are stretched between the walls. This static configuration satisfies all matching conditions for the string and domain wall sources and has 1/4 of unbroken supersymmetry.

  4. Domain and Specification Models for Software Engineering

    NASA Technical Reports Server (NTRS)

    Iscoe, Neil; Liu, Zheng-Yang; Feng, Guohui

    1992-01-01

    This paper discusses our approach to representing application domain knowledge for specific software engineering tasks. Application domain knowledge is embodied in a domain model. Domain models are used to assist in the creation of specification models. Although many different specification models can be created from any particular domain model, each specification model is consistent and correct with respect to the domain model. One aspect of the system-hierarchical organization is described in detail.

  5. Localization of resistive domains in inhomogeneous superconductors

    SciTech Connect

    Gurevich, A.V.; Mints, R.G.

    1981-01-01

    The properties of resistive domains due to the Joule heating in inhomogeneous superconductors with transport currents are studied. The equilibrium of a domain at an inhomogeneity of arbitrary type and with dimensions much smaller than the dimensions of the domain is investigated. It is shown that resistive domains can become localized at inhomogeneities. The temperature distribution in a domain and the current--voltage characteristic of the domain are determined. The stability of localized domains is discussed. It is shown that such domains give rise to a hysteresis in the destruction (recovery) of the superconductivity by the transport current.

  6. Functional domain walls in multiferroics

    NASA Astrophysics Data System (ADS)

    Meier, Dennis

    2015-11-01

    During the last decade a wide variety of novel and fascinating correlation phenomena has been discovered at domain walls in multiferroic bulk systems, ranging from unusual electronic conductance to inseparably entangled spin and charge degrees of freedom. The domain walls represent quasi-2D functional objects that can be induced, positioned, and erased on demand, bearing considerable technological potential for future nanoelectronics. Most of the challenges that remain to be solved before turning related device paradigms into reality, however, still fall in the field of fundamental condensed matter physics and materials science. In this topical review seminal experimental findings gained on electric and magnetic domain walls in multiferroic bulk materials are addressed. A special focus is put on the physical properties that emerge at so-called charged domain walls and the added functionality that arises from coexisting magnetic order. The research presented in this review highlights that we are just entering a whole new world of intriguing nanoscale physics that is yet to be explored in all its details. The goal is to draw attention to the persistent challenges and identify future key directions for the research on functional domain walls in multiferroics.

  7. Functional domain walls in multiferroics.

    PubMed

    Meier, Dennis

    2015-11-25

    During the last decade a wide variety of novel and fascinating correlation phenomena has been discovered at domain walls in multiferroic bulk systems, ranging from unusual electronic conductance to inseparably entangled spin and charge degrees of freedom. The domain walls represent quasi-2D functional objects that can be induced, positioned, and erased on demand, bearing considerable technological potential for future nanoelectronics. Most of the challenges that remain to be solved before turning related device paradigms into reality, however, still fall in the field of fundamental condensed matter physics and materials science. In this topical review seminal experimental findings gained on electric and magnetic domain walls in multiferroic bulk materials are addressed. A special focus is put on the physical properties that emerge at so-called charged domain walls and the added functionality that arises from coexisting magnetic order. The research presented in this review highlights that we are just entering a whole new world of intriguing nanoscale physics that is yet to be explored in all its details. The goal is to draw attention to the persistent challenges and identify future key directions for the research on functional domain walls in multiferroics. PMID:26523728

  8. Predicting cognitive change within domains

    PubMed Central

    Duff, Kevin; Beglinger, Leigh J.; Moser, David J.; Paulsen, Jane S.

    2010-01-01

    Standardized regression based (SRB) formulas, a method for predicting cognitive change across time, traditionally use baseline performance on a neuropsychological measure to predict future performance on that same measure. However, there are instances in which the same tests may not be given at follow-up assessments (e.g., lack of continuity of provider, avoiding practice effects). The current study sought to expand this methodology by developing SRBs to predict performance on different tests within the same cognitive domain. Using a sample of 127 non-demented community-dwelling older adults assessed at baseline and after one year, two sets of SRBs were developed: 1. those predicting performance on the same test, and 2. those predicting performance on a different test within the same cognitive domain. The domains examined were learning and memory, processing speed, and language. Across both sets of SRBs, one year scores were significantly predicted by baseline scores, especially for the learning and memory and processing speed measures. Although SRBs developed for the same test were comparable to those developed for different tests within the same domain, less variance was accounted for as tests became less similar. The current results lend preliminary support for additional development of SRBs, both for same- and different-tests, as well as beginning to examine domain-based SRBs. PMID:20358479

  9. Faraday instability in deformable domains

    NASA Astrophysics Data System (ADS)

    Pucci, Giuseppe; Ben Amar, Martine; Couder, Yves

    2014-11-01

    We investigate the Faraday instability in floating liquid lenses, as an example of hydrodynamic instability that develops in a domain with flexible boundaries. We show that a mutual adaptation of the instability pattern and the domain shape occurs, as a result of the competition between the wave radiation pressure and the capillary response of the lens border. Two archetypes of behaviour are observed. In the first, stable shapes are obtained experimentally and predicted theoretically as the exact solutions of a Riccati equation, and they result from the equilibrium between wave radiation pressure and capillarity. In the second, the radiation pressure exceeds the capillary response of the lens border and leads to non-equilibrium behaviours, with breaking into smaller domains that have a complex dynamics including spontaneous propagation. The authors are grateful to Université Franco-Italienne (UFI) for financial support.

  10. Domain walls inside localised orientifolds

    NASA Astrophysics Data System (ADS)

    Blåbäck, J.; van der Woerd, E.; Van Riet, T.; Williams, M.

    2015-12-01

    The equations of motion of toroidal orientifold compactifications with fluxes are in one-to-one correspondence with gauged supergravity if the orientifold (and D-brane) sources are smeared over the compact space. This smeared limit is identical to the approximation that ignores warping. It is therefore relevant to compare quantities obtained from the gauged supergravity with the true 10d solution with localised sources. In this paper we find the correspondence between BPS domain walls in gauged SUGRA and 10D SUGRA with localised sources. Our model is the simplest orientifold with fluxes we are aware of: an O6/D6 compactification on {T}^3/{Z}_2 in massive IIA with H 3-flux. The BPS domain walls correspond to a O6/D6/NS5/D8 bound state. Our analysis reveals that the domain wall energy computed in gauged SUGRA is unaffected by the localisation of the O6/D6 sources.

  11. Inferring Domain-Domain Interactions from Protein-Protein Interactions with Formal Concept Analysis

    PubMed Central

    Khor, Susan

    2014-01-01

    Identifying reliable domain-domain interactions will increase our ability to predict novel protein-protein interactions, to unravel interactions in protein complexes, and thus gain more information about the function and behavior of genes. One of the challenges of identifying reliable domain-domain interactions is domain promiscuity. Promiscuous domains are domains that can occur in many domain architectures and are therefore found in many proteins. This becomes a problem for a method where the score of a domain-pair is the ratio between observed and expected frequencies because the protein-protein interaction network is sparse. As such, many protein-pairs will be non-interacting and domain-pairs with promiscuous domains will be penalized. This domain promiscuity challenge to the problem of inferring reliable domain-domain interactions from protein-protein interactions has been recognized, and a number of work-arounds have been proposed. This paper reports on an application of Formal Concept Analysis to this problem. It is found that the relationship between formal concepts provides a natural way for rare domains to elevate the rank of promiscuous domain-pairs and enrich highly ranked domain-pairs with reliable domain-domain interactions. This piggybacking of promiscuous domain-pairs onto less promiscuous domain-pairs is possible only with concept lattices whose attribute-labels are not reduced and is enhanced by the presence of proteins that comprise both promiscuous and rare domains. PMID:24586450

  12. A Method to Examine Content Domain Structures

    ERIC Educational Resources Information Center

    D'Agostino, Jerome; Karpinski, Aryn; Welsh, Megan

    2011-01-01

    After a test is developed, most content validation analyses shift from ascertaining domain definition to studying domain representation and relevance because the domain is assumed to be set once a test exists. We present an approach that allows for the examination of alternative domain structures based on extant test items. In our example based on…

  13. Tensor distinction of domains in ferroic crystals

    NASA Astrophysics Data System (ADS)

    Litvin, D. B.

    2009-10-01

    Ferroic crystals contain two or more domains and may be distinguished by the values of components of tensorial physical properties of the domains. We have extended Aizu’s global tensor distinction by magnetization, polarization, and strain of all domains which arise in a ferroic phase transition to include distinction by toroidal moment, and from phases invariant under time reversal to domains which arise in transitions from all magnetic and non-magnetic phases. For determining possible switching of domains, a domain pair tensor distinction is also considered for all pairs of domains which arise in each ferroic phase transition.

  14. Protein structural domains: definition and prediction.

    PubMed

    Ezkurdia, Iakes; Tress, Michael L

    2011-11-01

    Recognition and prediction of structural domains in proteins is an important part of structure and function prediction. This unit lists the range of tools available for domain prediction, and describes sequence and structural analysis tools that complement domain prediction methods. Also detailed are the basic domain prediction steps, along with suggested strategies for different protein sequences and potential pitfalls in domain boundary prediction. The difficult problem of domain orientation prediction is also discussed. All the resources necessary for domain boundary prediction are accessible via publicly available Web servers and databases and do not require computational expertise. PMID:22045561

  15. Development in the Food Domain.

    ERIC Educational Resources Information Center

    Rozin, Paul

    1990-01-01

    Discusses problems of general interest in developmental psychology that can be successfully studied in the domain of food; these include (1) development of food likes and dislikes; (2) establishment of the edible/inedible distinction; (3) disgust and contagion; (4) transgenerational communication of preferences; and (5) transition to food…

  16. Cellulose binding domain fusion proteins

    DOEpatents

    Shoseyov, O.; Yosef, K.; Shpiegl, I.; Goldstein, M.A.; Doi, R.H.

    1998-02-17

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

  17. Cellulose binding domain fusion proteins

    DOEpatents

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc A.; Doi, Roy H.

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  18. Enabling Interoperability in Heliophysical Domains

    NASA Astrophysics Data System (ADS)

    Bentley, Robert

    2013-04-01

    There are many aspects of science in the Solar System that are overlapping - phenomena observed in one domain can have effects in other domains. However, there are many problems related to exploiting the data in cross-disciplinary studies because of lack of interoperability of the data and services. The CASSIS project is a Coordination Action funded under FP7 that has the objective of improving the interoperability of data and services related Solar System science. CASSIS has been investigating how the data could be made more accessible with some relatively minor changes to the observational metadata. The project has been looking at the services that are used within the domain and determining whether they are interoperable with each other and if not what would be required make them so. It has also been examining all types of metadata that are used when identifying and using observations and trying to make them more compliant with techniques and standards developed by bodies such as the International Virtual Observatory Alliance (IVOA). Many of the lessons that are being learnt in the study are applicable to domains that go beyond those directly involved in heliophysics. Adopting some simple standards related to the design of the services interfaces and metadata that are used would make it much easier to investigate interdisciplinary science topics. We will report on our finding and describe a roadmap for the future. For more information about CASSIS, please visit the project Web site on cassis-vo.eu

  19. Identification of alternative topological domains in chromatin

    PubMed Central

    2014-01-01

    Chromosome conformation capture experiments have led to the discovery of dense, contiguous, megabase-sized topological domains that are similar across cell types and conserved across species. These domains are strongly correlated with a number of chromatin markers and have since been included in a number of analyses. However, functionally-relevant domains may exist at multiple length scales. We introduce a new and efficient algorithm that is able to capture persistent domains across various resolutions by adjusting a single scale parameter. The ensemble of domains we identify allows us to quantify the degree to which the domain structure is hierarchical as opposed to overlapping, and our analysis reveals a pronounced hierarchical structure in which larger stable domains tend to completely contain smaller domains. The identified novel domains are substantially different from domains reported previously and are highly enriched for insulating factor CTCF binding and histone marks at the boundaries. PMID:24868242

  20. Diversity in protein recognition by PTB domains.

    PubMed

    Forman-Kay, J D; Pawson, T

    1999-12-01

    Phosphotyrosine-binding (PTB) domains were originally identified as modular domains that recognize phosphorylated Asn-Pro-Xxx-p Tyr-containing proteins. Recent binding and structural studies of PTB domain complexes with target peptides have revealed a number of deviations from the previously described mode of interaction, with respect to both the sequences of possible targets and their structures within the complexes. This diversity of recognition by PTB domains extends and strengthens our general understanding of modular binding domain recognition. PMID:10607674

  1. Analysis of multi-domain protein dynamics

    PubMed Central

    Roy, Amitava; Hua, Duy P; Post, Carol Beth

    2016-01-01

    Proteins with a modular architecture of multiple domains connected by linkers often exhibit diversity in the relative positions of domains while the domain tertiary structure remains unchanged. The biological function of these modular proteins, or the regulation of their activity depends on the variation in domain orientation and separation. Accordingly, careful characterization of inter-domain motion and correlated fluctuations of multi-domain systems is relevant for understanding the functional behavior of modular proteins. Molecular dynamics (MD) simulations provides a powerful approach to study these motions in atomic detail. Nevertheless, the common procedure for analyzing fluctuations from MD simulations after overall rigid-body alignment fails for multi-domain proteins; it greatly overestimates correlated positional fluctuations in the presence of relative domain motion. We show here that expressing the atomic motions of a multi-domain protein as a combination of displacement within the domain reference frame and motion of the relative domains correctly separates the internal motions to allow a useful description of correlated fluctuations. We illustrate the methodology of separating the domain fluctuations and local fluctuations by application to the tandem SH2 domains of human Syk protein kinase and by characterizing an effect of phosphorylation on the dynamics. Correlated motions are assessed from a distance covariance rather than the more common vector-coordinate covariance. The approach makes it possible to calculate the proper correlations in fluctuations internal to a domain as well as between domains. PMID:26675644

  2. Gabor domain optical coherence microscopy

    NASA Astrophysics Data System (ADS)

    Murali, Supraja

    Time domain Optical Coherence Tomography (TD-OCT), first reported in 1991, makes use of the low temporal coherence properties of a NIR broadband laser to create depth sectioning of up to 2mm under the surface using optical interferometry and point to point scanning. Prior and ongoing work in OCT in the research community has concentrated on improving axial resolution through the development of broadband sources and speed of image acquisition through new techniques such as Spectral domain OCT (SD-OCT). In SD-OCT, an entire depth scan is acquired at once with a low numerical aperture (NA) objective lens focused at a fixed point within the sample. In this imaging geometry, a longer depth of focus is achieved at the expense of lateral resolution, which is typically limited to 10 to 20 mum. Optical Coherence Microscopy (OCM), introduced in 1994, combined the advantages of high axial resolution obtained in OCT with high lateral resolution obtained by increasing the NA of the microscope placed in the sample arm. However, OCM presented trade-offs caused by the inverse quadratic relationship between the NA and the DOF of the optics used. For applications requiring high lateral resolution, such as cancer diagnostics, several solutions have been proposed including the periodic manual re-focusing of the objective lens in the time domain as well as the spectral domain C-mode configuration in order to overcome the loss in lateral resolution outside the DOF. In this research, we report for the first time, high speed, sub-cellular imaging (lateral resolution of 2 mum) in OCM using a Gabor domain image processing algorithm with a custom designed and fabricated dynamic focus microscope interfaced to a Ti:Sa femtosecond laser centered at 800 nm within an SD-OCM configuration. It is envisioned that this technology will provide a non-invasive replacement for the current practice of multiple biopsies for skin cancer diagnosis. The research reported here presents three important advances

  3. Spline interpolation on unbounded domains

    NASA Astrophysics Data System (ADS)

    Skeel, Robert D.

    2016-06-01

    Spline interpolation is a splendid tool for multiscale approximation on unbounded domains. In particular, it is well suited for use by the multilevel summation method (MSM) for calculating a sum of pairwise interactions for a large set of particles in linear time. Outlined here is an algorithm for spline interpolation on unbounded domains that is efficient and elegant though not so simple. Further gains in efficiency are possible via quasi-interpolation, which compromises collocation but with minimal loss of accuracy. The MSM, which may also be of value for continuum models, embodies most of the best features of both hierarchical clustering methods (tree methods, fast multipole methods, hierarchical matrix methods) and FFT-based 2-level methods (particle-particle particle-mesh methods, particle-mesh Ewald methods).

  4. Certifying Domain-Specific Policies

    NASA Technical Reports Server (NTRS)

    Lowry, Michael; Pressburger, Thomas; Rosu, Grigore; Koga, Dennis (Technical Monitor)

    2001-01-01

    Proof-checking code for compliance to safety policies potentially enables a product-oriented approach to certain aspects of software certification. To date, previous research has focused on generic, low-level programming-language properties such as memory type safety. In this paper we consider proof-checking higher-level domain -specific properties for compliance to safety policies. The paper first describes a framework related to abstract interpretation in which compliance to a class of certification policies can be efficiently calculated Membership equational logic is shown to provide a rich logic for carrying out such calculations, including partiality, for certification. The architecture for a domain-specific certifier is described, followed by an implemented case study. The case study considers consistency of abstract variable attributes in code that performs geometric calculations in Aerospace systems.

  5. Frequency domain optical parametric amplification

    PubMed Central

    Schmidt, Bruno E.; Thiré, Nicolas; Boivin, Maxime; Laramée, Antoine; Poitras, François; Lebrun, Guy; Ozaki, Tsuneyuki; Ibrahim, Heide; Légaré, François

    2014-01-01

    Today’s ultrafast lasers operate at the physical limits of optical materials to reach extreme performances. Amplification of single-cycle laser pulses with their corresponding octave-spanning spectra still remains a formidable challenge since the universal dilemma of gain narrowing sets limits for both real level pumped amplifiers as well as parametric amplifiers. We demonstrate that employing parametric amplification in the frequency domain rather than in time domain opens up new design opportunities for ultrafast laser science, with the potential to generate single-cycle multi-terawatt pulses. Fundamental restrictions arising from phase mismatch and damage threshold of nonlinear laser crystals are not only circumvented but also exploited to produce a synergy between increased seed spectrum and increased pump energy. This concept was successfully demonstrated by generating carrier envelope phase stable, 1.43 mJ two-cycle pulses at 1.8 μm wavelength. PMID:24805968

  6. Pyramidal inversion domain boundaries revisited

    SciTech Connect

    Remmele, T.; Albrecht, M.; Irmscher, K.; Fornari, R.; Strassburg, M.

    2011-10-03

    The structure of pyramidal inversion domain boundaries in GaN:Mg was investigated by aberration corrected transmission electron microscopy. The analysis shows the upper (0001) boundary to consist of a single Mg layer inserted between polarity inverted GaN layers in an abcab stacking. The Mg bound in these defects is at least one order of magnitude lower than the chemical Mg concentration. Temperature dependent Hall effect measurements show that up to 27% of the Mg acceptors is electrically compensated.

  7. System time-domain simulation

    NASA Technical Reports Server (NTRS)

    Dawson, C. T.; Eggleston, T. W.; Goris, A. C.; Fashano, M.; Paynter, D.; Tranter, W. H.

    1980-01-01

    Complex systems are simulated by engineers without extensive computer experience. Analyst uses free-form engineering-oriented language to input "black box" description. System Time Domain (SYSTID) Simulation Program generates appropriate algorithms and proceeds with simulation. Program is easily linked to postprocessing routines. SYSTID program is written in FORTRAN IV for batch execution and has been implemented on UNIVAC 1110 under control of EXEC 8, Level 31.

  8. Flexible time domain averaging technique

    NASA Astrophysics Data System (ADS)

    Zhao, Ming; Lin, Jing; Lei, Yaguo; Wang, Xiufeng

    2013-09-01

    Time domain averaging(TDA) is essentially a comb filter, it cannot extract the specified harmonics which may be caused by some faults, such as gear eccentric. Meanwhile, TDA always suffers from period cutting error(PCE) to different extent. Several improved TDA methods have been proposed, however they cannot completely eliminate the waveform reconstruction error caused by PCE. In order to overcome the shortcomings of conventional methods, a flexible time domain averaging(FTDA) technique is established, which adapts to the analyzed signal through adjusting each harmonic of the comb filter. In this technique, the explicit form of FTDA is first constructed by frequency domain sampling. Subsequently, chirp Z-transform(CZT) is employed in the algorithm of FTDA, which can improve the calculating efficiency significantly. Since the signal is reconstructed in the continuous time domain, there is no PCE in the FTDA. To validate the effectiveness of FTDA in the signal de-noising, interpolation and harmonic reconstruction, a simulated multi-components periodic signal that corrupted by noise is processed by FTDA. The simulation results show that the FTDA is capable of recovering the periodic components from the background noise effectively. Moreover, it can improve the signal-to-noise ratio by 7.9 dB compared with conventional ones. Experiments are also carried out on gearbox test rigs with chipped tooth and eccentricity gear, respectively. It is shown that the FTDA can identify the direction and severity of the eccentricity gear, and further enhances the amplitudes of impulses by 35%. The proposed technique not only solves the problem of PCE, but also provides a useful tool for the fault symptom extraction of rotating machinery.

  9. Subharmonic Fourier domain mode locking.

    PubMed

    Eigenwillig, Christoph M; Wieser, Wolfgang; Biedermann, Benjamin R; Huber, Robert

    2009-03-15

    We demonstrate a subharmonically Fourier domain mode-locked wavelength-swept laser source with a substantially reduced cavity fiber length. In contrast to a standard Fourier domain mode-locked configuration, light is recirculated repetitively in the delay line with the optical bandpass filter used as switch. The laser has a fundamental optical round trip frequency of 285 kHz and can be operated at integer fractions thereof (subharmonics). Sweep ranges up to 95 nm full width centred at 1317 nm are achieved at the 1/5th subharmonic. A maximum sensitivity of 116 dB and an axial resolution of 12 microm in air are measured at an average sweep power of 12 mW. A sensitivity roll-off of 11 dB over 4 mm and 25 dB over 10 mm is observed and optical coherence tomography imaging is demonstrated. Besides the advantage of a reduced fiber length, subharmonic Fourier domain mode locking (shFDML) enables simple scaling of the sweep speed by extracting light from the delay part of the resonator. A sweep rate of 570 kHz is achieved. Characteristic features of shFDML operation, such as power leakage during fly-back and cw breakthrough, are investigated. PMID:19282912

  10. Mapping knowledge domains: Characterizing PNAS

    PubMed Central

    Boyack, Kevin W.

    2004-01-01

    A review of data mining and analysis techniques that can be used for the mapping of knowledge domains is given. Literature mapping techniques can be based on authors, documents, journals, words, and/or indicators. Most mapping questions are related to research assessment or to the structure and dynamics of disciplines or networks. Several mapping techniques are demonstrated on a data set comprising 20 years of papers published in PNAS. Data from a variety of sources are merged to provide unique indicators of the domain bounded by PNAS. By using funding source information and citation counts, it is shown that, on an aggregate basis, papers funded jointly by the U.S. Public Health Service (which includes the National Institutes of Health) and non-U.S. government sources outperform papers funded by other sources, including by the U.S. Public Health Service alone. Grant data from the National Institute on Aging show that, on average, papers from large grants are cited more than those from small grants, with performance increasing with grant amount. A map of the highest performing papers over the 20-year period was generated by using citation analysis. Changes and trends in the subjects of highest impact within the PNAS domain are described. Interactions between topics over the most recent 5-year period are also detailed. PMID:14963238

  11. Elastic Domain Architectures in Constrained Layers

    NASA Astrophysics Data System (ADS)

    Slutsker, J.; Artemev, A.; Roytburd, A. L.

    2002-08-01

    The formation of elastic domains in transforming constrained films is a mechanism of relaxation of internal stresses caused by the misfit between a film and a substrate. The formation and evolution of polydomain microstructure as a result of the cubic-tetragonal transformation in a constrained layer are investigated by phase-field simulation. It has been shown that the three-domain hierarchical structure can be formed in the epitaxial films. With changing a fraction of out-of-plane domain there are two types of morphological transitions: from the three-domain structure to the two-domain one and from the hierarchical three-domain structure to the cellular three-domain structure. The results of the phase-field simulation are compared with available experimental data on 90deg domain structures in epitaxial ferroelectric films.

  12. Characterization of lipid domains in erythrocyte membranes.

    PubMed Central

    Rodgers, W; Glaser, M

    1991-01-01

    Fluorescence digital imaging microscopy was used to study the lateral distribution of the lipid components in erythrocyte membranes. Intact erythrocytes labeled with phospholipids containing a fluorophore attached to one fatty acid chain showed an uneven distribution of the phospholipids in the membrane thereby demonstrating the presence of membrane domains. The enrichment of the lipotropic compound chlor-promazine in domains in intact erythrocytes also suggested that the domains are lipid-enriched regions. Similar membrane domains were present in erythrocyte ghosts. The phospholipid enrichment was increased in the domains by inducing membrane protein aggregation. Double-labeling experiments were done to determine the relative distributions of different phospholipids in the membrane. Vesicles made from extracted lipids did not show the presence of domains consistent with the conclusion that membrane proteins were responsible for creating the domains. Overall, it was found that large domains exist in the red blood cell membrane with unequal enrichment of the different phospholipid species. Images PMID:1996337

  13. Generic domain models in software engineering

    NASA Technical Reports Server (NTRS)

    Maiden, Neil

    1992-01-01

    This paper outlines three research directions related to domain-specific software development: (1) reuse of generic models for domain-specific software development; (2) empirical evidence to determine these generic models, namely elicitation of mental knowledge schema possessed by expert software developers; and (3) exploitation of generic domain models to assist modelling of specific applications. It focuses on knowledge acquisition for domain-specific software development, with emphasis on tool support for the most important phases of software development.

  14. Frequency domain photoacoustic and fluorescence microscopy

    PubMed Central

    Langer, Gregor; Buchegger, Bianca; Jacak, Jaroslaw; Klar, Thomas A.; Berer, Thomas

    2016-01-01

    We report on simultaneous frequency domain optical-resolution photoacoustic and fluorescence microscopy with sub-µm lateral resolution. With the help of a blood smear, we show that photoacoustic and fluorescence images provide complementary information. Furthermore, we compare theoretically predicted signal-to-noise ratios of sinusoidal modulation in frequency domain with pulsed excitation in time domain. PMID:27446698

  15. Frequency domain photoacoustic and fluorescence microscopy.

    PubMed

    Langer, Gregor; Buchegger, Bianca; Jacak, Jaroslaw; Klar, Thomas A; Berer, Thomas

    2016-07-01

    We report on simultaneous frequency domain optical-resolution photoacoustic and fluorescence microscopy with sub-µm lateral resolution. With the help of a blood smear, we show that photoacoustic and fluorescence images provide complementary information. Furthermore, we compare theoretically predicted signal-to-noise ratios of sinusoidal modulation in frequency domain with pulsed excitation in time domain. PMID:27446698

  16. Pectin Homogalacturonans: Nanostructural Characterization of Methylesterified Domains

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Functionality of pectic hydrocolloids is largely dependent on the two major domains commonly found in their homogalacturonan (HG) regions, i.e., methylester protected domains (MPDs)and non methylesterified domains (NMDs). MPDs can participate in hydrogen bonding and hydrophobic interactions but unli...

  17. 22 CFR 120.11 - Public domain.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Public domain. 120.11 Section 120.11 Foreign... Public domain. (a) Public domain means information which is published and which is generally accessible or available to the public: (1) Through sales at newsstands and bookstores; (2) Through...

  18. The Promise of Domain Adaptation

    NASA Astrophysics Data System (ADS)

    Mahabal, Ashish A.; Li, Jingling; Vaijanapurkar, Samarth; Bue, Brian; Miller, Adam; Donalek, Ciro; Djorgovski, Stanislav G.; Drake, Andrew J.; Graham, Matthew; CRTS, iPTF

    2016-01-01

    Most new surveys spend an appreciable time in collecting data on which to train classifiers before they can be used on future observations from the same dataset. The result generating phase can start much earlier if the training could incorporate data accumulated from older surveys enhanced with a small set from the new survey. This is exactly what Domain Adaptation (DA) allows us to do. The main idea behind DAs can be summarized thus: if we have two classes of separable objects in some feature space of a Source survey (S), we can define a hyperplane to separate the two types. In a second Target survey (T), for the same features the hyperplane would be inclined differently. DA methods get the mapping between the two hyperplanes using a small fraction of data from the Target (T) survey and can then be used to predict the classes of the remaining majority of data in T. We discuss the parameters that need to be tuned, the difficulties involved, and ways to improve the results. As we move towards bigger, and deeper surveys, being able to use existing labelled information to conduct classification in future surveys will be more cost-effective and promote time efficiency as well. Starting with the light curve data of 50,000 periodic objects from Catalina Real-Time Transient Survey (CRTS), we have applied domain adaptation techniques such as Geodesic Flow Kernel (GFK) with Random forest classifier and Co-training for domain adaptation (CODA) to the CRTS data which has 35,000 points overlapping with Palomar Transient Factory (PTF), and 12,000 with Lincoln Near-Earth Asteroid Research (LINEAR). The results suggest that domain adaptation is an area worth exploring as the knowledge between these surveys is transferable and the approaches to find the mappings between these surveys can be applied to the remaining data as well as for near future surveys such as CRTS-II, Zwicky Transient Facility (ZTF) and the Large Synoptic Survey Telescope (LSST) to name a few at the optical

  19. AIDA: ab initio domain assembly for automated multi-domain protein structure prediction and domain–domain interaction prediction

    PubMed Central

    Xu, Dong; Jaroszewski, Lukasz; Li, Zhanwen; Godzik, Adam

    2015-01-01

    Motivation: Most proteins consist of multiple domains, independent structural and evolutionary units that are often reshuffled in genomic rearrangements to form new protein architectures. Template-based modeling methods can often detect homologous templates for individual domains, but templates that could be used to model the entire query protein are often not available. Results: We have developed a fast docking algorithm ab initio domain assembly (AIDA) for assembling multi-domain protein structures, guided by the ab initio folding potential. This approach can be extended to discontinuous domains (i.e. domains with ‘inserted’ domains). When tested on experimentally solved structures of multi-domain proteins, the relative domain positions were accurately found among top 5000 models in 86% of cases. AIDA server can use domain assignments provided by the user or predict them from the provided sequence. The latter approach is particularly useful for automated protein structure prediction servers. The blind test consisting of 95 CASP10 targets shows that domain boundaries could be successfully determined for 97% of targets. Availability and implementation: The AIDA package as well as the benchmark sets used here are available for download at http://ffas.burnham.org/AIDA/. Contact: adam@sanfordburnham.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25701568

  20. Domain wall fermion quenched spectroscopy

    NASA Astrophysics Data System (ADS)

    Malureanu, Catalin Ionut

    We measure y and the hadron spectrum on quenched ensembles using the domain wall fermion formulation. For the first time a 1/mf behavior of y for small valence masses has been observed. Our measurements of y on two different volumes of 83 x 32 and 163 x 32 at β = 5.85 suggest the behavior goes away on large enough volumes. Extensive spectrum calculations were done on 8 3 x 32 lattices at β = 5.7 and 5.85 corresponding roughly to a box size of 1.6 fm and 1.0 fm respectively. We have investigated five values of the extent of the fifth dimension Ls = 10, 16, 24, 32 and 48 with valence masses in the range 0.02 to 0.2 for the β = 5.7 ensemble and two values of Ls = 10 and 16 with valence masses in the range 0.02 to 0.08 for the β = 5.85 ensemble. Our pion remains massive in the infinite Ls extrapolation. This may be a finite volume effect. The nucleon to rho mass ratio stays constant at 1.4(1). Scaling violations for domain wall fermions are smaller roughly by a factor of four compared to the scaling violations in similar calculations done with staggered fermions.

  1. Frequency-domain Hadamard spectroscopy

    NASA Astrophysics Data System (ADS)

    Kupče, Ēriks; Freeman, Ray

    2003-05-01

    A new technique is proposed for multichannel excitation and detection of NMR signals in the frequency domain, an alternative to the widely used pulse-excited Fourier transform method. An extensive array of N radiofrequency irradiation channels covers the spectrum of interest. A selective radiofrequency pulse sequence is applied to each channel, generating a steady-state NMR response acquired one-point-at-a-time in the intervals between pulses. The excitation pattern is repeated N times, phase-encoded according to a Hadamard matrix, and the corresponding N composite responses are decoded by reference to the same matrix. This multiplex technique offers the same sensitivity advantage as conventional Fourier transform spectroscopy. The irradiation pattern may be tailored to concentrate on interesting spectral regions, to facilitate homonuclear double resonance, or to avoid exciting strong solvent peaks. As no free induction decay is involved, the new method avoids problems of pulse breakthrough or lineshape distortion by premature termination of the time-domain signal.

  2. Interfaces between Block Copolymer Domains

    NASA Astrophysics Data System (ADS)

    Kim, Jaeup; Jeong, Seong-Jun; Kim, Sang Ouk

    2011-03-01

    Block copolymers naturally form nanometer scale structures which repeat their geometry on a larger scale. Such a small scale periodic pattern can be used for various applications such as storage media, nano-circuits and optical filters. However, perfect alignment of block copolymer domains in the macroscopic scale is still a distant dream. The nanostructure formation usually occurs with spontaneously broken symmetry; hence it is easily infected by topological defects which sneak in due to entropic fluctuation and incomplete annealing. Careful annealing can gradually reduce the number of defects, but once kinetically trapped, it is extremely difficult to remove all the defects. One of the main reasons is that the defect finds a locally metastable morphology whose potential depth is large enough to prohibit further morphology evolution. In this work, the domain boundaries between differently oriented lamellar structures in thin film are studied. For the first time, it became possible to quantitatively study the block copolymer morphology in the transitional region, and it was shown that the twisted grain boundary is energetically favorable compared to the T-junction grain boundary. [Nano Letters, 9, 2300 (2010)]. This theoretical method successfully explained the experimental results.

  3. Word Domain Disambiguation via Word Sense Disambiguation

    SciTech Connect

    Sanfilippo, Antonio P.; Tratz, Stephen C.; Gregory, Michelle L.

    2006-06-04

    Word subject domains have been widely used to improve the perform-ance of word sense disambiguation al-gorithms. However, comparatively little effort has been devoted so far to the disambiguation of word subject do-mains. The few existing approaches have focused on the development of al-gorithms specific to word domain dis-ambiguation. In this paper we explore an alternative approach where word domain disambiguation is achieved via word sense disambiguation. Our study shows that this approach yields very strong results, suggesting that word domain disambiguation can be ad-dressed in terms of word sense disam-biguation with no need for special purpose algorithms.

  4. Single-domain antibodies for biomedical applications.

    PubMed

    Krah, Simon; Schröter, Christian; Zielonka, Stefan; Empting, Martin; Valldorf, Bernhard; Kolmar, Harald

    2016-01-01

    Single-domain antibodies are the smallest antigen-binding units of antibodies, consisting either only of one variable domain or one engineered constant domain that solely facilitates target binding. This class of antibody derivatives comprises naturally occurring variable domains derived from camelids and sharks as well as engineered human variable or constant antibody domains of the heavy or light chain. Because of their high affinity and specificity as well as stability, small size and benefit of multiple re-formatting opportunities, those molecules emerged as promising candidates for biomedical applications and some of these entities have already proven to be successful in clinical development. PMID:26551147

  5. Domain swapping: entangling alliances between proteins.

    PubMed Central

    Bennett, M J; Choe, S; Eisenberg, D

    1994-01-01

    The comparison of monomeric and dimeric diphtheria toxin (DT) reveals a mode for protein association which we call domain swapping. The structure of dimeric DT has been extensively refined against data to 2.0-A resolution and a three-residue loop has been corrected as compared with our published 2.5-A-resolution structure. The monomeric DT structure has also been determined, at 2.3-A resolution. Monomeric DT is a Y-shaped molecule with three domains: catalytic (C), transmembrane (T), and receptor binding (R). Upon freezing in phosphate buffer, DT forms a long-lived, metastable dimer. The protein chain tracing discloses that upon dimerization an unprecedented conformational rearrangement occurs: the entire R domain from each molecule of the dimer is exchanged for the R domain from the other. This involves breaking the noncovalent interactions between the R domain and the C and T domains, rotating the R domain by 180 degrees with atomic movements up to 65 A, and re-forming the same noncovalent interactions between the R domain and the C and T domains of the other chain of the dimer. This conformational transition explains the long life and metastability of the DT dimer. Several other intertwined, dimeric protein structures satisfy our definition of domain swapping and suggest that domain swapping may be the molecular mechanism for evolution of these oligomers and possibly of oligomeric proteins in general. Images PMID:8159715

  6. Enhanced protein domain discovery using taxonomy

    PubMed Central

    Coin, Lachlan; Bateman, Alex; Durbin, Richard

    2004-01-01

    Background It is well known that different species have different protein domain repertoires, and indeed that some protein domains are kingdom specific. This information has not yet been incorporated into statistical methods for finding domains in sequences of amino acids. Results We show that by incorporating our understanding of the taxonomic distribution of specific protein domains, we can enhance domain recognition in protein sequences. We identify 4447 new instances of Pfam domains in the SP-TREMBL database using this technique, equivalent to the coverage increase given by the last 8.3% of Pfam families and to a 0.7% increase in the number of domain predictions. We use PSI-BLAST to cross-validate our new predictions. We also benchmark our approach using a SCOP test set of proteins of known structure, and demonstrate improvements relative to standard Hidden Markov model techniques. Conclusions Explicitly including knowledge about the taxonomic distribution of protein domains can enhance protein domain recognition. Our method can also incorporate other context-specific domain distributions – such as domain co-occurrence and protein localisation. PMID:15137915

  7. Domain adaptive boosting method and its applications

    NASA Astrophysics Data System (ADS)

    Geng, Jie; Miao, Zhenjiang

    2015-03-01

    Differences of data distributions widely exist among datasets, i.e., domains. For many pattern recognition, nature language processing, and content-based analysis systems, a decrease in performance caused by the domain differences between the training and testing datasets is still a notable problem. We propose a domain adaptation method called domain adaptive boosting (DAB). It is based on the AdaBoost approach with extensions to cover the domain differences between the source and target domains. Two main stages are contained in this approach: source-domain clustering and source-domain sample selection. By iteratively adding the selected training samples from the source domain, the discrimination model is able to achieve better domain adaptation performance based on a small validation set. The DAB algorithm is suitable for the domains with large scale samples and easy to extend for multisource adaptation. We implement this method on three computer vision systems: the skin detection model in single images, the video concept detection model, and the object classification model. In the experiments, we compare the performances of several commonly used methods and the proposed DAB. Under most situations, the DAB is superior.

  8. Domain wall conduction in multiaxial ferroelectrics

    SciTech Connect

    Eliseev, E. A.; Morozovska, A. N.; Svechnikov, S. V.; Maksymovych, Petro; Kalinin, Sergei V

    2012-01-01

    The conductance of domain wall structures consisting of either stripes or cylindrical domains in multiaxial ferroelectric-semiconductors is analyzed. The effects of the flexoelectric coupling, domain size, wall tilt, and curvature on charge accumulation are analyzed using the Landau-Ginsburg Devonshire theory for polarization vector combined with the Poisson equation for charge distributions. The proximity and size effect of the electron and donor accumulation/depletion by thin stripe domains and cylindrical nanodomains are revealed. In contrast to thick domain stripes and wider cylindrical domains, in which the carrier accumulation (and so the static conductivity) sharply increases at the domain walls only, small nanodomains of radii less than 5-10 correlation lengths appeared conducting across the entire cross-section. Implications of such conductive nanosized channels may be promising for nanoelectronics.

  9. Functional innovation from changes in protein domains and their combinations.

    PubMed

    Lees, Jonathan G; Dawson, Natalie L; Sillitoe, Ian; Orengo, Christine A

    2016-06-01

    Domains are the functional building blocks of proteins. In this work we discuss how domains can contribute to the evolution of new functions. Domains themselves can evolve through various mechanisms, altering their intrinsic function. Domains can also facilitate functional innovations by combining with other domains to make novel proteins. We discuss the mechanisms by which domain and domain combinations support functional innovations. We highlight interesting examples where changes in domain combination promote changes at the domain level. PMID:27309309

  10. Structure and Function of KH Domains

    SciTech Connect

    Valverde, R.; Regan, E

    2008-01-01

    The hnRNP K homology (KH) domain was first identified in the protein human heterogeneous nuclear ribonucleoprotein K (hnRNP K) 14 years ago. Since then, KH domains have been identified as nucleic acid recognition motifs in proteins that perform a wide range of cellular functions. KH domains bind RNA or ssDNA, and are found in proteins associated with transcriptional and translational regulation, along with other cellular processes. Several diseases, e.g. fragile X mental retardation syndrome and paraneoplastic disease, are associated with the loss of function of a particular KH domain. Here we discuss the progress made towards understanding both general and specific features of the molecular recognition of nucleic acids by KH domains. The typical binding surface of KH domains is a cleft that is versatile but that can typically accommodate only four unpaired bases. Van der Waals forces and hydrophobic interactions and, to a lesser extent, electrostatic interactions, contribute to the nucleic acid binding affinity. 'Augmented' KH domains or multiple copies of KH domains within a protein are two strategies that are used to achieve greater affinity and specificity of nucleic acid binding. Isolated KH domains have been seen to crystallize as monomers, dimers and tetramers, but no published data support the formation of noncovalent higher-order oligomers by KH domains in solution. Much attention has been given in the literature to a conserved hydrophobic residue (typically Ile or Leu) that is present in most KH domains. The interest derives from the observation that an individual with this Ile mutated to Asn, in the KH2 domain of fragile X mental retardation protein, exhibits a particularly severe form of the syndrome. The structural effects of this mutation in the fragile X mental retardation protein KH2 domain have recently been reported. We discuss the use of analogous point mutations at this position in other KH domains to dissect both structure and function.

  11. Listening natively across perceptual domains?

    PubMed

    Langus, Alan; Seyed-Allaei, Shima; Uysal, Ertuğrul; Pirmoradian, Sahar; Marino, Caterina; Asaadi, Sina; Eren, Ömer; Toro, Juan M; Peña, Marcela; Bion, Ricardo A H; Nespor, Marina

    2016-07-01

    Our native tongue influences the way we perceive other languages. But does it also determine the way we perceive nonlinguistic sounds? The authors investigated how speakers of Italian, Turkish, and Persian group sequences of syllables, tones, or visual shapes alternating in either frequency or duration. We found strong native listening effects with linguistic stimuli. Speakers of Italian grouped the linguistic stimuli differently from speakers of Turkish and Persian. However, speakers of all languages showed the same perceptual biases when grouping the nonlinguistic auditory and the visual stimuli. The shared perceptual biases appear to be determined by universal grouping principles, and the linguistic differences caused by prosodic differences between the languages. Although previous findings suggest that acquired linguistic knowledge can either enhance or diminish the perception of both linguistic and nonlinguistic auditory stimuli, we found no transfer of native listening effects across auditory domains or perceptual modalities. (PsycINFO Database Record PMID:26820498

  12. Analysis of DCC domain structure

    SciTech Connect

    Randrup, J.; Thews, R.L.

    1997-10-01

    Wavelet-type methods are employed for the analysis of pion field configurations that have been obtained by dynamical simulations in idealized scenarios relevant to the formation of disoriented chiral condensates. It is illustrated how the measurement of the isospin domain structure depends on the ability to zoom in on limited parts of the phase space, due to the interplay between the pion correlation length and the effective source geometry. The need for advanced analysis methods is underscored by the fact that the extracted neutral-fraction distribution would differ significantly from the ideal form, even under perfect experimental conditions, and, moreover, by the circumstance that thermal sources with suitably adjusted temperatures can lead to distributions that may be practically indistinguishable from those arising from DCC-type nonequilibrium evolutions. {copyright} {ital 1997} {ital The American Physical Society}

  13. Analysis of DCC domain structure

    SciTech Connect

    Randrup, J.; Thews, R.L.

    1997-05-07

    Wavelet-type methods are employed for the analysis of pion field configurations that have been obtained by dynamical simulations in idealized scenarios relevant to the formation of disoriented chiral condensates. It is illustrated how the measurement of the isospin domain structure depends on the ability to zoom in on limited parts of the phase space, due to the interplay between the pion correlation length and the effective source geometry. The need for advanced analysis methods is underscored by the fact that the extracted neutral-fraction distribution would differ significantly from the ideal form, even under perfect experimental conditions, and, moreover, by the circumstance that thermal sources with suitably adjusted temperatures can lead to distributions that may be practically indistinguishable from those arising from DCC-type nonequilibrium evolutions.

  14. Time domain electromagnetic metal detectors

    SciTech Connect

    Hoekstra, P.

    1996-04-01

    This presentation focuses on illustrating by case histories the range of applications and limitations of time domain electromagnetic (TDEM) systems for buried metal detection. Advantages claimed for TDEM metal detectors are: independent of instrument response (Geonics EM61) to surrounding soil and rock type; simple anomaly shape; mitigation of interference by ambient electromagnetic noise; and responsive to both ferrous and non-ferrous metallic targets. The data in all case histories to be presented were acquired with the Geonics EM61 TDEM system. Case histories are a test bed site on Molokai, Hawaii; Fort Monroe, Virginia; and USDOE, Rocky Flats Plant. The present limitations of this technology are: discrimination capabilities in terms of type of ordnance, and depth of burial is limited, and ability of resolving targets with small metallic ambient needs to be improved.

  15. Frequency domain modelling of wind turbine structures

    SciTech Connect

    Soerensen, P.; Larsen, G.C.; Christensen, C.J.

    1995-09-01

    The present paper describes a frequency domain model of the structure of an operating horizontal axis wind turbine. The frequency domain model is implemented along with an analogous time domain modeling the Risoe PC code Design Basis 2, and a more detailed description of the model is offered in a Risoe report by Soerensen (1994). The structure of an operating wind turbine is affected by essential non-linearities between structural variables on blades and tower respectively. These non-linearities are caused by the rotation of the blades. The transformations between the blade coordinate systems and the tower coordinate system will depend on the instantaneous azimuth positions of the blades as they rotate. Frequency domain analysis are much faster than time simulations and in some respects they give more insight into the dynamics of the structure. However, the non-linear terms in the dynamic equations for a complex wind turbine structure are usually thought to preclude the use of frequency domain methods. Design Basis 2 is used to verify the frequency domain model comparing loads on the structure calculated with the frequency domain model both to loads calculated with the time domain model and to measured loads. Examples show that frequency and time domain calculations of typical PSD`s of loads are in very good agreement. Also the agreement between the calculated and measured PSD`s is good. Moreover, Design Basis 2 has shown that the frequency domain model results in an extremely fast calculation method.

  16. Imaging Ferroelectric Domains and Domain Walls Using Charge Gradient Microscopy: Role of Screening Charges.

    PubMed

    Tong, Sheng; Jung, Il Woong; Choi, Yoon-Young; Hong, Seungbum; Roelofs, Andreas

    2016-02-23

    Advanced scanning probe microscopies (SPMs) open up the possibilities of the next-generation ferroic devices that utilize both domains and domain walls as active elements. However, current SPMs lack the capability of dynamically monitoring the motion of domains and domain walls in conjunction with the transport of the screening charges that lower the total electrostatic energy of both domains and domain walls. Charge gradient microscopy (CGM) is a strong candidate to overcome these shortcomings because it can map domains and domain walls at high speed and mechanically remove the screening charges. Yet the underlying mechanism of the CGM signals is not fully understood due to the complexity of the electrostatic interactions. Here, we designed a semiconductor-metal CGM tip, which can separate and quantify the ferroelectric domain and domain wall signals by simply changing its scanning direction. Our investigation reveals that the domain wall signals are due to the spatial change of polarization charges, while the domain signals are due to continuous removal and supply of screening charges at the CGM tip. In addition, we observed asymmetric CGM domain currents from the up and down domains, which are originated from the different debonding energies and the amount of the screening charges on positive and negative bound charges. We believe that our findings can help design CGM with high spatial resolution and lead to breakthroughs in information storage and energy-harvesting devices. PMID:26751281

  17. Is the myonuclear domain size fixed?

    PubMed

    Van der Meer, S F T; Jaspers, R T; Degens, H

    2011-12-01

    It has been suggested that the number of myonuclei in a muscle fibre changes in proportion to the change in fibre size, resulting in a constant myonuclear domain size, defined as the cytoplasmic volume per myonucleus. The myonuclear domain size varies, however, between fibre types and is inversely related with the oxidative capacity of a fibre. Overall, the observations of an increase in myonuclear domain size during both maturational growth and overload-induced hypertrophy, and the decrease in myonuclear domain size during disuse- and ageing-associated muscle atrophy suggest that the concept of a constant myonuclear domain size needs to be treated cautiously. It also suggests that only when the myonuclear domain size exceeds a certain threshold during growth or overload-induced hypertrophy acquisition of new myonuclei is required for further fibre hypertrophy. PMID:22130137

  18. Failure to Burrow and Tunnel Reveals Roles for jim lovell in the Growth and Endoreplication of the Drosophila Larval Tracheae

    PubMed Central

    Qiang, Karen M.; Beckingham, Kathleen M.

    2016-01-01

    The Drosophila protein Jim Lovell (Lov) is a putative transcription factor of the BTB/POZ (Bric- a-Brac/Tramtrack/Broad/ Pox virus and Zinc finger) domain class that is expressed in many elements of the developing larval nervous system. It has roles in innate behaviors such as larval locomotion and adult courtship. In performing tissue-specific knockdown with the Gal4-UAS system we identified a new behavioral phenotype for lov: larvae failed to burrow into their food during their growth phase and then failed to tunnel into an agarose substratum during their wandering phase. We determined that these phenotypes originate in a previously unrecognized role for lov in the tracheae. By using tracheal-specific Gal4 lines, Lov immunolocalization and a lov enhancer trap line, we established that lov is normally expressed in the tracheae from late in embryogenesis through larval life. Using an assay that monitors food burrowing, substrate tunneling and death we showed that lov tracheal knockdown results in tracheal fluid-filling, producing hypoxia that activates the aberrant behaviors and inhibits development. We investigated the role of lov in the tracheae that initiates this sequence of events. We discovered that when lov levels are reduced, the tracheal cells are smaller, more numerous and show lower levels of endopolyploidization. Together our findings indicate that Lov is necessary for tracheal endoreplicative growth and that its loss in this tissue causes loss of tracheal integrity resulting in chronic hypoxia and abnormal burrowing and tunneling behavior. PMID:27494251

  19. Protein Domain Decomposition Using a Graph-Theoretic Approach

    SciTech Connect

    Xu, Y.; Xu, D.; Gabow, H.N.

    2000-08-20

    This paper presents a new algorithm for the decomposition of a multi-domain protein into individual structural domains. The underlying principle used is that residue-residue contacts are denser within a domain than between domains.

  20. Domain Transfer Learning for MCI Conversion Prediction

    PubMed Central

    Cheng, Bo; Liu, Mingxia; Zhang, Daoqiang; Munsell, Brent C.; Shen, Dinggang

    2015-01-01

    Machine learning methods have been increasingly used to predict the conversion of mild cognitive impairment (MCI) to Alzheimer's disease (AD), by classifying MCI converters (MCI-C) from MCI non-converters (MCI-NC). However, most of existing methods construct classifiers using only data from one particular target domain (e.g., MCI), and ignore data in the other related domains (e.g., AD and normal control (NC)) that could provide valuable information to promote the performance of MCI conversion prediction. To this end, we develop a novel domain transfer learning method for MCI conversion prediction, which can use data from both the target domain (i.e., MCI) and the auxiliary domains (i.e., AD and NC). Specifically, the proposed method consists of three key components: 1) a domain transfer feature selection (DTFS) component that selects the most informative feature-subset from both target domain and auxiliary domains with different imaging modalities, 2) a domain transfer sample selection (DTSS) component that selects the most informative sample-subset from the same target and auxiliary domains with different data modalities, and 3) a domain transfer support vector machine (DTSVM) classification component that fuses the selected features and samples to separate MCI-C and MCI-NC patients. We evaluate our method on 202 subjects from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) with MRI, FDG-PET and CSF data. The experimental results show that the proposed method can classify MCI-C patients from MCI-NC patients with an accuracy of 79.4%, with the aid of additional domain knowledge learned from AD and NC. PMID:25751861

  1. Domain decomposition for the SPN solver MINOS

    SciTech Connect

    Jamelot, Erell; Baudron, Anne-Marie; Lautard, Jean-Jacques

    2012-07-01

    In this article we present a domain decomposition method for the mixed SPN equations, discretized with Raviart-Thomas-Nedelec finite elements. This domain decomposition is based on the iterative Schwarz algorithm with Robin interface conditions to handle communications. After having described this method, we give details on how to optimize the convergence. Finally, we give some numerical results computed in a realistic 3D domain. The computations are done with the MINOS solver of the APOLLO3 (R) code. (authors)

  2. Domain Transfer Learning for MCI Conversion Prediction.

    PubMed

    Cheng, Bo; Liu, Mingxia; Zhang, Daoqiang; Munsell, Brent C; Shen, Dinggang

    2015-07-01

    Machine learning methods have successfully been used to predict the conversion of mild cognitive impairment (MCI) to Alzheimer's disease (AD), by classifying MCI converters (MCI-C) from MCI nonconverters (MCI-NC). However, most existing methods construct classifiers using data from one particular target domain (e.g., MCI), and ignore data in other related domains (e.g., AD and normal control (NC)) that may provide valuable information to improve MCI conversion prediction performance. To address is limitation, we develop a novel domain transfer learning method for MCI conversion prediction, which can use data from both the target domain (i.e., MCI) and auxiliary domains (i.e., AD and NC). Specifically, the proposed method consists of three key components: 1) a domain transfer feature selection component that selects the most informative feature-subset from both target domain and auxiliary domains from different imaging modalities; 2) a domain transfer sample selection component that selects the most informative sample-subset from the same target and auxiliary domains from different data modalities; and 3) a domain transfer support vector machine classification component that fuses the selected features and samples to separate MCI-C and MCI-NC patients. We evaluate our method on 202 subjects from the Alzheimer's Disease Neuroimaging Initiative (ADNI) that have MRI, FDG-PET, and CSF data. The experimental results show the proposed method can classify MCI-C patients from MCI-NC patients with an accuracy of 79.4%, with the aid of additional domain knowledge learned from AD and NC. PMID:25751861

  3. Domain wall dynamics in cylindrical nanomagnet

    NASA Astrophysics Data System (ADS)

    Mukhopadhyay, Soumik; Singh, Amrita; Ghosh, Arindam

    2011-06-01

    The stochasticity associated with domain wall nucleation and propagation in a cylinderical nanowire has been studied using time resolved resistance measurement in presence of magnetic field. We have shown that the propagation stochasticity of domain wall in a cylindrical nanowire is reflected in the magnetic field dependent velocity distribution whereas the stochasticity involved in the domain wall nucleation can be effectively tuned by varying the angle between the direction of applied magnetic field and the long axis of the cylinder.

  4. Spread spectrum time domain reflectometry

    NASA Astrophysics Data System (ADS)

    Smith, Paul Samuel

    For many years, wiring has been treated as a system that could be installed and expected to work for the life of the aircraft. As aircraft age far beyond their original expected life span, this attitude is rapidly changing. Wiring problems have recently been identified as the cause of several tragic mishaps and hundreds of thousands of lost mission hours. Intermittent wiring faults have been and continue to be difficult to resolve. Test methods that pinpoint faults on the ground can miss intermittent failures. New test methods involving spread spectrum signals are investigated that could be used in flight to locate intermittent failures, including open circuits, short circuits, and arcs. Spread spectrum time domain reflectometry (SSTDR) and sequence time domain reflectometry (STDR) are analyzed in light of the signals commonly present on aircraft wiring. Pseudo noise codes used for the generation of STDR and SSTDR signals are analyzed for application in a STDR/SSTDR test system in the presence of noise. The effects of Mil-Std 1553 and white noise on the STDR and SSTDR signals are discussed analytically, through simulations, and with the use of test hardware. A test system using STDR and SSTDR is designed, built, and used to collect STDR and SSTDR test data. The data collected with the STDR/SSTDR test hardware is analyzed and compared to the theoretical results. Experimental data for open and short circuits collected using SSTDR and a curve fitting algorithm shows a maximum range estimation error of +/-0.2 ft for 75O coaxial cable up to 100ft, and +/-0.6ft for a sample 32.5ft non-controlled impedance aircraft cable. Mil-Std 1553 is specified to operate reliably with a signal-to-noise ratio of 17.5dB, and the SSTDR test system was able to locate an open circuit on a cable also carrying simulated Mil-Std 1553 data where the SSTDR signal was 50dB below the Mil-Std 1553 signal. STDR and SSTDR are shown to be effective in detecting and locating dry and wet arcs on wires.

  5. Cross-domain human action recognition.

    PubMed

    Bian, Wei; Tao, Dacheng; Rui, Yong

    2012-04-01

    Conventional human action recognition algorithms cannot work well when the amount of training videos is insufficient. We solve this problem by proposing a transfer topic model (TTM), which utilizes information extracted from videos in the auxiliary domain to assist recognition tasks in the target domain. The TTM is well characterized by two aspects: 1) it uses the bag-of-words model trained from the auxiliary domain to represent videos in the target domain; and 2) it assumes each human action is a mixture of a set of topics and uses the topics learned from the auxiliary domain to regularize the topic estimation in the target domain, wherein the regularization is the summation of Kullback-Leibler divergences between topic pairs of the two domains. The utilization of the auxiliary domain knowledge improves the generalization ability of the learned topic model. Experiments on Weizmann and KTH human action databases suggest the effectiveness of the proposed TTM for cross-domain human action recognition. PMID:21954214

  6. Transform domain steganography with blind source separation

    NASA Astrophysics Data System (ADS)

    Jouny, Ismail

    2015-05-01

    This paper applies blind source separation or independent component analysis for images that may contain mixtures of text, audio, or other images for steganography purposes. The paper focuses on separating mixtures in the transform domain such as Fourier domain or the Wavelet domain. The study addresses the effectiveness of steganography when using linear mixtures of multimedia components and the ability of standard blind sources separation techniques to discern hidden multimedia messages. Mixing in the space, frequency, and wavelet (scale) domains is compared. Effectiveness is measured using mean square error rate between original and recovered images.

  7. Cooperative interactions between paired domain and homeodomain.

    PubMed

    Jun, S; Desplan, C

    1996-09-01

    The Pax proteins are a family of transcriptional regulators involved in many developmental processes in all higher eukaryotes. They are characterized by the presence of a paired domain (PD), a bipartite DNA binding domain composed of two helix-turn-helix (HTH) motifs,the PAI and RED domains. The PD is also often associated with a homeodomain (HD) which is itself able to form homo- and hetero-dimers on DNA. Many of these proteins therefore contain three HTH motifs each able to recognize DNA. However, all PDs recognize highly related DNA sequences, and most HDs also recognize almost identical sites. We show here that different Pax proteins use multiple combinations of their HTHs to recognize several types of target sites. For instance, the Drosophila Paired protein can bind, in vitro, exclusively through its PAI domain, or through a dimer of its HD, or through cooperative interaction between PAI domain and HD. However, prd function in vivo requires the synergistic action of both the PAI domain and the HD. Pax proteins with only a PD appear to require both PAI and RED domains, while a Pax-6 isoform and a new Pax protein, Lune, may rely on the RED domain and HD. We propose a model by which Pax proteins recognize different target genes in vivo through various combinations of their DNA binding domains, thus expanding their recognition repertoire. PMID:8787739

  8. Frequency domain FIR and IIR adaptive filters

    NASA Technical Reports Server (NTRS)

    Lynn, D. W.

    1990-01-01

    A discussion of the LMS adaptive filter relating to its convergence characteristics and the problems associated with disparate eigenvalues is presented. This is used to introduce the concept of proportional convergence. An approach is used to analyze the convergence characteristics of block frequency-domain adaptive filters. This leads to a development showing how the frequency-domain FIR adaptive filter is easily modified to provide proportional convergence. These ideas are extended to a block frequency-domain IIR adaptive filter and the idea of proportional convergence is applied. Experimental results illustrating proportional convergence in both FIR and IIR frequency-domain block adaptive filters is presented.

  9. Discoidin domain receptors in disease.

    PubMed

    Borza, Corina M; Pozzi, Ambra

    2014-02-01

    Discoidin domain receptors, DDR1 and DDR2, lie at the intersection of two large receptor families, namely the extracellular matrix and tyrosine kinase receptors. As such, DDRs are uniquely positioned to function as sensors for extracellular matrix and to regulate a wide range of cell functions from migration and proliferation to cytokine secretion and extracellular matrix homeostasis/remodeling. While activation of DDRs by extracellular matrix collagens is required for normal development and tissue homeostasis, aberrant activation of these receptors following injury or in disease is detrimental. The availability of mice lacking DDRs has enabled us to identify key roles played by these receptors in disease initiation and progression. DDR1 promotes inflammation in atherosclerosis, lung fibrosis and kidney injury, while DDR2 contributes to osteoarthritis. Furthermore, both DDRs have been implicated in cancer progression. Yet the mechanisms whereby DDRs contribute to disease progression are poorly understood. In this review we highlight the mechanisms whereby DDRs regulate two important processes, namely inflammation and tissue fibrosis. In addition, we discuss the challenges of targeting DDRs in disease. Selective targeting of these receptors requires understanding of how they interact with and are activated by extracellular matrix, and whether their cellular function is dependent on or independent of receptor kinase activity. PMID:24361528

  10. Discoidin Domain Receptors in Disease

    PubMed Central

    Borza, Corina M; Pozzi, Ambra

    2014-01-01

    Discoidin domain receptors, DDR1 and DDR2, lie at the intersection of two large receptor families, namely the extracellular matrix and tyrosine kinase receptors. As such, DDRs are uniquely positioned to function as sensors for extracellular matrix and to regulate a wide range of cell functions from migration and proliferation to cytokine secretion and extracellular matrix homeostasis/remodeling. While activation of DDRs by extracellular matrix collagens is required for normal development and tissue homeostasis, aberrant activation of these receptors following injury or in disease is detrimental. The availability of mice lacking DDRs has enabled us to identify key roles played by these receptors in disease initiation and progression. DDR1 promotes inflammation in atherosclerosis, lung fibrosis and kidney injury, while DDR2 contributes to osteoarthritis. Furthermore, both DDRs have been implicated in cancer progression. Yet the mechanisms whereby DDRs contribute to diseases progression are poorly understood. In this review we highlight the mechanisms whereby DDRs regulate two important processes, namely inflammation and tissue fibrosis. In addition, we discuss the challenges of targeting DDRs in disease. Selective targeting of these receptors requires understanding of how they interact with and are activated by extracellular matrix, and whether their cellular function is dependent on or independent of receptor kinase activity. PMID:24361528

  11. Charged domain walls in ferroelectrics

    NASA Astrophysics Data System (ADS)

    Sluka, Tomas

    2014-03-01

    Solid interfaces including compositionally homogeneous ferroic domain walls (DWs) display uniquely distorted electronic structures and ionic displacements. Their intrinsic properties may therefore be fundamentally different from those of their parent matrices. Indeed, phenomena like semiconductor-metal transition, the quantum Hall effect, magnetoresistance and superconductivity were discovered at hetero-interfaces between transition metal oxides and elevated photoactivity and conductivity were reported at (multi-) ferroic DWs. Unlike hetero-interfaces, the DWs provide ``perfect'' structure by nature and can be written, displaced, and erased inside a material monolith of functioning devices. Theory predicts the existence of charged DWs which seemingly violate electrostatic compatibility due to head-to-head and tail-to-tail polarization discontinuity, but are stable because bound polarization charge is compensated by mobile charge carriers including quasi-two-dimensional electron gas. This talk will introduce current theory, engineering, control and characteristics of charged DWs, which are mobile, extremely wide and exhibit steady metallic-like conductivity up to 109 times that of the insulating bulk.

  12. Bioconvection in spatially extended domains

    NASA Astrophysics Data System (ADS)

    Karimi, A.; Paul, M. R.

    2013-05-01

    We numerically explore gyrotactic bioconvection in large spatially extended domains of finite depth using parameter values from available experiments with the unicellular alga Chlamydomonas nivalis. We numerically integrate the three-dimensional, time-dependent continuum model of Pedley [J. Fluid Mech.10.1017/S0022112088002393 195, 223 (1988)] using a high-order, parallel, spectral-element approach. We explore the long-time nonlinear patterns and dynamics found for layers with an aspect ratio of 10 over a range of Rayleigh numbers. Our results yield the pattern wavelength and pattern dynamics which we compare with available theory and experimental measurement. There is good agreement for the pattern wavelength at short times between numerics, experiment, and a linear stability analysis. At long times we find that the general sequence of patterns given by the nonlinear evolution of the governing equations correspond qualitatively to what has been described experimentally. However, at long times the patterns in numerics grow to larger wavelengths, in contrast to what is observed in experiment where the wavelength is found to decrease with time.

  13. Optical coherence domain reflectometry guidewire

    DOEpatents

    Colston, Billy W.; Everett, Matthew; Da Silva, Luiz B.; Matthews, Dennis

    2001-01-01

    A guidewire with optical sensing capabilities is based on a multiplexed optical coherence domain reflectometer (OCDR), which allows it to sense location, thickness, and structure of the arterial walls or other intra-cavity regions as it travels through the body during minimally invasive medical procedures. This information will be used both to direct the guidewire through the body by detecting vascular junctions and to evaluate the nearby tissue. The guidewire contains multiple optical fibers which couple light from the proximal to distal end. Light from the fibers at the distal end of the guidewire is directed onto interior cavity walls via small diameter optics such as gradient index lenses and mirrored corner cubes. Both forward viewing and side viewing fibers can be included. The light reflected or scattered from the cavity walls is then collected by the fibers, which are multiplexed at the proximal end to the sample arm of an optical low coherence reflectometer. The guidewire can also be used in nonmedical applications.

  14. Domain adaptation for microscopy imaging.

    PubMed

    Becker, Carlos; Christoudias, C Mario; Fua, Pascal

    2015-05-01

    Electron and light microscopy imaging can now deliver high-quality image stacks of neural structures. However, the amount of human annotation effort required to analyze them remains a major bottleneck. While machine learning algorithms can be used to help automate this process, they require training data, which is time-consuming to obtain manually, especially in image stacks. Furthermore, due to changing experimental conditions, successive stacks often exhibit differences that are severe enough to make it difficult to use a classifier trained for a specific one on another. This means that this tedious annotation process has to be repeated for each new stack. In this paper, we present a domain adaptation algorithm that addresses this issue by effectively leveraging labeled examples across different acquisitions and significantly reducing the annotation requirements. Our approach can handle complex, nonlinear image feature transformations and scales to large microscopy datasets that often involve high-dimensional feature spaces and large 3D data volumes. We evaluate our approach on four challenging electron and light microscopy applications that exhibit very different image modalities and where annotation is very costly. Across all applications we achieve a significant improvement over the state-of-the-art machine learning methods and demonstrate our ability to greatly reduce human annotation effort. PMID:25474809

  15. Intramolecular co-action of two independent photosensory modules in the fern phytochrome 3

    PubMed Central

    Kanegae, Takeshi

    2015-01-01

    Fern phytochrome3/neochrome1 (phy3/neo1) is a chimeric photoreceptor composed of a phytochrome-chromophore binding domain and an almost full-length phototropin. phy3 thus contains two different light-sensing modules; a red/far-red light receptor phytochrome and a blue light receptor phototropin. phy3 induces both red light- and blue light-dependent phototropism in phototropin-deficient Arabidopsis thaliana (phot1 phot2) seedlings. The red-light response is dependent on the phytochrome module of phy3, and the blue-light response is dependent on the phototropin module. We recently showed that both the phototropin-sensing module and the phytochrome-sensing module mediate the blue light-dependent phototropic response. Particularly under low-light conditions, these two light-sensing modules cooperate to induce the blue light-dependent phototropic response. This intramolecular co-action of two independent light-sensing modules in phy3 enhances light sensitivity, and perhaps allowed ferns to adapt to the low-light canopy conditions present in angiosperm forests. PMID:26340326

  16. Public domain optical character recognition

    NASA Astrophysics Data System (ADS)

    Garris, Michael D.; Blue, James L.; Candela, Gerald T.; Dimmick, Darrin L.; Geist, Jon C.; Grother, Patrick J.; Janet, Stanley A.; Wilson, Charles L.

    1995-03-01

    A public domain document processing system has been developed by the National Institute of Standards and Technology (NIST). The system is a standard reference form-based handprint recognition system for evaluating optical character recognition (OCR), and it is intended to provide a baseline of performance on an open application. The system's source code, training data, performance assessment tools, and type of forms processed are all publicly available. The system recognizes the handprint entered on handwriting sample forms like the ones distributed with NIST Special Database 1. From these forms, the system reads hand-printed numeric fields, upper and lowercase alphabetic fields, and unconstrained text paragraphs comprised of words from a limited-size dictionary. The modular design of the system makes it useful for component evaluation and comparison, training and testing set validation, and multiple system voting schemes. The system contains a number of significant contributions to OCR technology, including an optimized probabilistic neural network (PNN) classifier that operates a factor of 20 times faster than traditional software implementations of the algorithm. The source code for the recognition system is written in C and is organized into 11 libraries. In all, there are approximately 19,000 lines of code supporting more than 550 subroutines. Source code is provided for form registration, form removal, field isolation, field segmentation, character normalization, feature extraction, character classification, and dictionary-based postprocessing. The recognition system has been successfully compiled and tested on a host of UNIX workstations. This paper gives an overview of the recognition system's software architecture, including descriptions of the various system components along with timing and accuracy statistics.

  17. Time Domain Challenges for Exoplanets

    NASA Astrophysics Data System (ADS)

    Dawson, Rebekah Ilene

    2016-01-01

    Over the past couple decades, thousands of extra-solar planets have been discovered orbiting other stars. Most have been detected and characterized using transit and/or radial velocity time series, and these techniques have undergone huge improvements in instrumental precision. However, the improvements in precision have brought to light new statistical challenges in detecting and characterizing exoplanets in the presence of correlated noise caused by stellar activity (transits and radial velocities) and gaps in the time sampling (radial velocities). These challenges have afflicted many of the most interesting exoplanets, from Earth-like planets to planetary systems whose orbital dynamics place important constraints on how planetary systems form and evolve. In the first part of the talk, I will focus on the problem of correlated noise for characterizing transiting exoplanets using transit timing variations. I will present a comparison of several techniques using wavelets, Gaussian processes, and polynomial splines to account for correlated noise in the likelihood function when inferring planetary parameters. I will also present results on the characteristics of correlated noise that cause planets to be missed by the Kepler and homegrown pipelines despite high nominal signal-to-noise. In the second part of the talk, I will focus on the problem of aliasing caused by gaps in the radial-velocity time series on yearly, daily, and monthly timescales. I will present results on identifying aliases in the Fourier domain by taking advantage of aliasing on multiple timescales and discuss the interplay between aliasing and stellar activity for several habitable-zone "planets" that have recently been called into question as possible spurious signals caused by activity. As we push toward detecting and characterizing lower mass planets, it is essential that astrostatistical advances keep pace with advances in instrumentation.

  18. Multiple hypothesis tracking for the cyber domain

    NASA Astrophysics Data System (ADS)

    Schwoegler, Stefan; Blackman, Sam; Holsopple, Jared; Hirsch, Michael J.

    2011-09-01

    This paper discusses how methods used for conventional multiple hypothesis tracking (MHT) can be extended to domain-agnostic tracking of entities from non-kinematic constraints such as those imposed by cyber attacks in a potentially dense false alarm background. MHT is widely recognized as the premier method to avoid corrupting tracks with spurious data in the kinematic domain but it has not been extensively applied to other problem domains. The traditional approach is to tightly couple track maintenance (prediction, gating, filtering, probabilistic pruning, and target confirmation) with hypothesis management (clustering, incompatibility maintenance, hypothesis formation, and Nassociation pruning). However, by separating the domain specific track maintenance portion from the domain agnostic hypothesis management piece, we can begin to apply the wealth of knowledge gained from ground and air tracking solutions to the cyber (and other) domains. These realizations led to the creation of Raytheon's Multiple Hypothesis Extensible Tracking Architecture (MHETA). In this paper, we showcase MHETA for the cyber domain, plugging in a well established method, CUBRC's INFormation Engine for Real-time Decision making, (INFERD), for the association portion of the MHT. The result is a CyberMHT. We demonstrate the power of MHETA-INFERD using simulated data. Using metrics from both the tracking and cyber domains, we show that while no tracker is perfect, by applying MHETA-INFERD, advanced nonkinematic tracks can be captured in an automated way, perform better than non-MHT approaches, and decrease analyst response time to cyber threats.

  19. Domains of the Florida Performance Measurement System.

    ERIC Educational Resources Information Center

    Florida State Dept. of Education, Tallahassee.

    This monograph sets forth in detail the concepts included in the five domains of teaching as identified by the Florida Coalition for the Development of a Performance Evaluation System. The first domain, planning, includes the concepts: (1) content coverage; (2) utilization of instructional materials; (3) activity structure; (4) goal focusing; and…

  20. Domain Collapse in Grooved Magnetic Garnet Material

    NASA Technical Reports Server (NTRS)

    Peredo, J.; Fedyunin, Y.; Patterson, G.

    1995-01-01

    Domain collapse fields in grooved garnet material were investigated by experimental observation and numerical simulation. The results indicate that the change in domain collapse field is largely due to magnetostatic effects produced by the groove edge. A simplified model based on the effective field produced at a groove edge, and local changes in the material thickness explain the observed trends very well.!.

  1. 32 CFR 701.33 - Public domain.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 32 National Defense 5 2014-07-01 2014-07-01 false Public domain. 701.33 Section 701.33 National... DOCUMENTS AFFECTING THE PUBLIC FOIA Definitions and Terms § 701.33 Public domain. Agency records released under the provisions of FOIA and the instruction in this part to a member of the public....

  2. Domain 2: Sport Safety and Injury Prevention

    ERIC Educational Resources Information Center

    Gurchiek, Larry; Mokha, Monique Butcher

    2004-01-01

    Most coaches recognize the importance of creating a safe environment and preventing injuries of their athletes. Domain 2 is dedicated to this important aspect of coaching, and outlines specific areas within safety and injury prevention that coaches should address. Domain 2 sets the standards for facility, equipment, and environmental safety…

  3. Immunosilencing a Highly Immunogenic Protein Trimerization Domain*

    PubMed Central

    Sliepen, Kwinten; van Montfort, Thijs; Melchers, Mark; Isik, Gözde; Sanders, Rogier W.

    2015-01-01

    Many therapeutic proteins and protein subunit vaccines contain heterologous trimerization domains, such as the widely used GCN4-based isoleucine zipper (IZ) and the T4 bacteriophage fibritin foldon (Fd) trimerization domains. We found that these domains induced potent anti-IZ or anti-Fd antibody responses in animals when fused to an HIV-1 envelope glycoprotein (Env) immunogen. To dampen IZ-induced responses, we constructed an IZ domain containing four N-linked glycans (IZN4) to shield the underlying protein surface. When fused to two different vaccine antigens, HIV-1 Env and influenza hemagglutinin (HA), IZN4 strongly reduced the antibody responses against the IZ, but did not affect the antibody titers against Env or HA. Silencing of immunogenic multimerization domains with glycans might be relevant for therapeutic proteins and protein vaccines. PMID:25635058

  4. Investigation of multilayer magnetic domain lattice file

    NASA Technical Reports Server (NTRS)

    Torok, E. J.; Kamin, M.; Tolman, C. H.

    1980-01-01

    The feasibility of the self structured multilayered bubble domain memory as a mass memory medium for satellite applications is examined. Theoretical considerations of multilayer bubble supporting materials are presented, in addition to the experimental evaluation of current accessed circuitry for various memory functions. The design, fabrication, and test of four device designs is described, and a recommended memory storage area configuration is presented. Memory functions which were demonstrated include the current accessed propagation of bubble domains and stripe domains, pinning of stripe domain ends, generation of single and double bubbles, generation of arrays of coexisting strip and bubble domains in a single garnet layer, and demonstration of different values of the strip out field for single and double bubbles indicating adequate margins for data detection. All functions necessary to develop a multilayer self structured bubble memory device were demonstrated in individual experiments.

  5. Optimal Control of Flows in Moving Domains

    NASA Astrophysics Data System (ADS)

    Protas, Bartosz; Liao, Wenyuan; Glander, Donn

    2006-11-01

    This investigation concerns adjoint--based optimization of viscous incompressible flows (the Navier-Stokes problem) coupled with heat conduction involving change of phase (the Stefan problem) and occurring in domains with moving boundaries such as the free and solidification surfaces. This problem is motivated by optimization of advanced welding techniques used in automotive manufacturing. We characterize the sensitivity of a suitable cost functional defined for the system with respect to control (the heat input) using adjoint equations. Given that the shape of the domain is also a dependent variable, characterizing sensitivities necessitates the introduction of ``non-cylindrical'' calculus required to differentiate a cost functional defined on a variable domain. As a result, unlike the forward problem, the adjoint system is defined on a domain with a predetermined evolution in time and also involves ordinary differential equations defined on the domain boundary (``the adjoint transverse system''). We will discuss certain computational issues related to numerical solution of such adjoint problems.

  6. Automotion of domain walls for spintronic interconnects

    SciTech Connect

    Nikonov, Dmitri E.; Manipatruni, Sasikanth; Young, Ian A.

    2014-06-07

    We simulate “automotion,” the transport of a magnetic domain wall under the influence of demagnetization and magnetic anisotropy, in nanoscale spintronic interconnects. In contrast to spin transfer driven magnetic domain wall motion, the proposed interconnects operate without longitudinal charge current transfer, with only a transient current pulse at domain wall creation and have favorable scaling down to the 20 nm dimension. Cases of both in-plane and out-of-plane magnetization are considered. Analytical dependence of the velocity of domain walls on the angle of magnetization are compared with full micromagnetic simulations. Deceleration, attenuation and disappearance, and reflection of domain walls are demonstrated through simulation. Dependences of the magnetization angle on the current pulse parameters are studied. The energy and delay analysis suggests that automotion is an attractive option for spintronic logic interconnects.

  7. Discoidin Domains as Emerging Therapeutic Targets.

    PubMed

    Villoutreix, Bruno O; Miteva, Maria A

    2016-08-01

    Discoidin (DS) domains are found in eukaryotic and prokaryotic extracellular and transmembrane multidomain proteins. These small domains play different functional roles and can interact with phospholipids, glycans, and proteins, including collagens. DS domain-containing proteins are often involved in cellular adhesion, migration, proliferation, and matrix-remodeling events, while some play a major role in blood coagulation. Mutations in DS domains have been associated with various disease conditions. This review provides an update on the structure, function, and modulation of the DS domains, with a special emphasis on two circulating blood coagulation cofactors, factor V and factor VIII, and the transmembrane neuropilin receptors that have been targeted for inhibition by biologics and small chemical compounds. PMID:27372370

  8. Automotion of domain walls for spintronic interconnects

    NASA Astrophysics Data System (ADS)

    Nikonov, Dmitri E.; Manipatruni, Sasikanth; Young, Ian A.

    2014-06-01

    We simulate "automotion," the transport of a magnetic domain wall under the influence of demagnetization and magnetic anisotropy, in nanoscale spintronic interconnects. In contrast to spin transfer driven magnetic domain wall motion, the proposed interconnects operate without longitudinal charge current transfer, with only a transient current pulse at domain wall creation and have favorable scaling down to the 20 nm dimension. Cases of both in-plane and out-of-plane magnetization are considered. Analytical dependence of the velocity of domain walls on the angle of magnetization are compared with full micromagnetic simulations. Deceleration, attenuation and disappearance, and reflection of domain walls are demonstrated through simulation. Dependences of the magnetization angle on the current pulse parameters are studied. The energy and delay analysis suggests that automotion is an attractive option for spintronic logic interconnects.

  9. Requirements analysis, domain knowledge, and design

    NASA Technical Reports Server (NTRS)

    Potts, Colin

    1988-01-01

    Two improvements to current requirements analysis practices are suggested: domain modeling, and the systematic application of analysis heuristics. Domain modeling is the representation of relevant application knowledge prior to requirements specification. Artificial intelligence techniques may eventually be applicable for domain modeling. In the short term, however, restricted domain modeling techniques, such as that in JSD, will still be of practical benefit. Analysis heuristics are standard patterns of reasoning about the requirements. They usually generate questions of clarification or issues relating to completeness. Analysis heuristics can be represented and therefore systematically applied in an issue-based framework. This is illustrated by an issue-based analysis of JSD's domain modeling and functional specification heuristics. They are discussed in the context of the preliminary design of simple embedded systems.

  10. Using ontology for domain specific information retrieval

    NASA Astrophysics Data System (ADS)

    Shashirekha, H. L.; Murali, S.; Nagabhushan, P.

    2010-02-01

    This paper presents a system for retrieving information from a domain specific document collection made up of data rich unnatural language text documents. Instead of conventional keyword based retrieval, our system makes use of domain ontology to retrieve the information from a collection of documents. The system addresses the problem of representing unnatural language text documents and constructing a classifier model that helps in the efficient retrieval of relevant information. Query to this system may be either the key phrases in terms of concepts or a domain specific unnatural language text document. The classifier used in this system can also be used to assign multiple labels to the previously unseen text document belonging to the same domain. An empirical evaluation of the system is conducted on the domain of text documents describing the classified matrimonial advertisements to determine its performance.

  11. A Blue Light Inducible Two-Component Signal Transduction System in the Plant Pathogen Pseudomonas syringae pv. tomato☆

    PubMed Central

    Cao, Z.; Buttani, V.; Losi, A.; Gärtner, W.

    2008-01-01

    Abstract The open reading frame PSPTO2896 from the plant pathogen Pseudomonas syringae pv. tomato encodes a protein of 534 amino acids showing all salient features of a blue light-driven two-component system. The N-terminal LOV (light, oxygen, voltage) domain, potentially binding a flavin chromophore, is followed by a histidine kinase (HK) motif and a response regulator (RR). The full-length protein (PST-LOV) and, separately, the RR and the LOV+HK part (PST-LOVΔRR) were heterologously expressed and functionally characterized. The two LOV proteins showed typical LOV-like spectra and photochemical reactions, with the blue light-driven, reversible formation of a covalent flavin-cysteine bond. The fluorescence changes in the lit state of full-length PST-LOV, but not in PST-LOVΔRR, indicating a direct interaction between the LOV core and the RR module. Experiments performed with radioactive ATP uncover the light-driven kinase activity. For both PST-LOV and PST-LOVΔRR, much more radioactivity is incorporated when the protein is in the lit state. Furthermore, addition of the RR domain to the fully phosphorylated PST-LOVΔRR leads to a very fast transfer of radioactivity, indicating a highly efficient HK activity and a tight interaction between PST-LOVΔRR and RR, possibly facilitated by the LOV core itself. PMID:17905842

  12. Cholesterol stabilizes fluid phosphoinositide domains

    PubMed Central

    Jiang, Zhiping; Redfern, Roberta E.; Isler, Yasmin; Ross, Alonzo H.

    2014-01-01

    Local accumulation of phosphoinositides (PIPs) is an important factor for a broad range of cellular events including membrane trafficking and cell signaling. The negatively charged phosphoinositide headgroups can interact with cations or cationic proteins and this electrostatic interaction has been identified as the main phosphoinositide clustering mechanism. However, an increasing number of reports show that phosphoinositide-mediated signaling events are at least in some cases cholesterol dependent, suggesting other possible contributors to the segregation of phosphoinositides. Using fluorescence microscopy on giant unilamellar vesicles and monolayers at the air/water interface, we present data showing that cholesterol stabilizes fluid phosphoinositide-enriched phases. The interaction with cholesterol is observed for all investigated phosphoinositides (PI(4)P, PI(3,4)P2, PI(3,5)P2, PI(4,5)P2 and PI(3,4,5)P3) as well as phosphatidylinositol. We find that cholesterol is present in the phosphoinositide-enriched phase and that the resulting phase is fluid. Cholesterol derivatives modified at the hydroxyl group (cholestenone, cholesteryl ethyl ether) do not promote formation of phosphoinositide domains, suggesting an instrumental role of the cholesterol hydroxyl group in the observed cholesterol/phosphoinositide interaction. This leads to the hypothesis that cholesterol participates in an intermolecular hydrogen bond network formed among the phosphoinositide lipids. We had previously reported that the intra- and intermolecular hydrogen bond network between the phosphoinositide lipids leads to a reduction of the charge density at the phosphoinositide phosphomonoester groups (Kooijman et al. Biochemistry 48, (2009) 9360). We believe that cholesterol acts as a spacer between the phosphoinositide lipids, thereby reducing the electrostatic repulsion, while participating in the hydrogen bond network, leading to its further stabilization. To illustrate the effect of

  13. Nucleation of reversed domain and pinning effect on domain wall motion in nanocomposite magnets

    NASA Astrophysics Data System (ADS)

    Li, Z. B.; Shen, B. G.; Niu, E.; Sun, J. R.

    2013-08-01

    The magnetization behaviors show a strong pinning effect on domain wall motion in optimally melt-spun Pr8Fe87B5 ribbons at room temperature. According to analysis, the coercivity is determined by the nucleation field of reversed domain, and the pinning effect, which results from the weak exchange coupling at interface, makes domain nucleation processes independent and leads to non-uniform magnetization reversals. At a temperature of 60 K, owing to the weak exchange coupling between soft-hard grains, magnetization reversal undergoes processes of spring domain nucleation in soft grains and irreversible domain nucleation in hard grains, and the pinning effect remains strong among hard grains.

  14. Dzyaloshinskii-Moriya Domain Walls in Nanotubes

    NASA Astrophysics Data System (ADS)

    Tretiakov, Oleg; Goussev, Arseni; Robbins, J. M.; Slastikov, Valeriy

    2015-03-01

    We study domain walls in thin ferromagnetic nanotubes with Dzyaloshinskii-Moriya interaction (DMI). Dramatic effects arise from the interplay of space curvature and spin-orbit induced DMI on the domain wall structure in these systems. The domain walls become narrower in systems with DMI and curvature. Moreover, the domain walls created in such nanotubes can propagate without Walker breakdown for arbitrary applied currents, thus allowing for a robust and controlled domain-wall motion. The domain-wall velocity is directly proportional to the non-adiabatic spin transfer torque current term and is insensitive to the adiabatic current term. Application of an external magnetic field along the nanotube axis triggers rich dynamical response of the curved domain wall. In particular, we show that the propagation velocity is a non-linear function of both the applied field and DMI, and strongly depends on the orientation and chirality of the wall. We acknowledge support by the Grants-in-Aid for Scientific Research (No. 25800184 and No. 25247056) from the MEXT, Japan and SpinNet.

  15. Domain reduction method for atomistic simulations

    SciTech Connect

    Medyanik, Sergey N. . E-mail: medyanik@northwestern.edu; Karpov, Eduard G. . E-mail: edkarpov@gmail.com; Liu, Wing Kam . E-mail: w-liu@northwestern.edu

    2006-11-01

    In this paper, a quasi-static formulation of the method of multi-scale boundary conditions (MSBCs) is derived and applied to atomistic simulations of carbon nano-structures, namely single graphene sheets and multi-layered graphite. This domain reduction method allows for the simulation of deformable boundaries in periodic atomic lattice structures, reduces the effective size of the computational domain, and consequently decreases the cost of computations. The size of the reduced domain is determined by the value of the domain reduction parameter. This parameter is related to the distance between the boundary of the reduced domain, where MSBCs are applied, and the boundary of the full domain, where the standard displacement boundary conditions are prescribed. Two types of multi-scale boundary conditions are derived: one for simulating in-layer multi-scale boundaries in a single graphene sheet and the other for simulating inter-layer multi-scale boundaries in multi-layered graphite. The method is tested on benchmark nano-indentation problems and the results are consistent with the full domain solutions.

  16. Benchmark Generation using Domain Specific Modeling

    SciTech Connect

    Bui, Ngoc B.; Zhu, Liming; Gorton, Ian; Liu, Yan

    2007-08-01

    Performance benchmarks are domain specific applications that are specialized to a certain set of technologies and platforms. The development of a benchmark application requires mapping the performance specific domain concepts to an implementation and producing complex technology and platform specific code. Domain Specific Modeling (DSM) promises to bridge the gap between application domains and implementations by allowing designers to specify solutions in domain-specific abstractions and semantics through Domain Specific Languages (DSL). This allows generation of a final implementation automatically from high level models. The modeling and task automation benefits obtained from this approach usually justify the upfront cost involved. This paper employs a DSM based approach to invent a new DSL, DSLBench, for benchmark generation. DSLBench and its associated code generation facilities allow the design and generation of a completely deployable benchmark application for performance testing from a high level model. DSLBench is implemented using Microsoft Domain Specific Language toolkit. It is integrated with the Visual Studio 2005 Team Suite as a plug-in to provide extra modeling capabilities for performance testing. We illustrate the approach using a case study based on .Net and C#.

  17. Structural domain walls in polar hexagonal manganites

    NASA Astrophysics Data System (ADS)

    Kumagai, Yu

    2014-03-01

    The domain structure in the multiferroic hexagonal manganites is currently intensely investigated, motivated by the observation of intriguing sixfold topological defects at their meeting points [Choi, T. et al,. Nature Mater. 9, 253 (2010).] and nanoscale electrical conductivity at the domain walls [Wu, W. et al., Phys. Rev. Lett. 108, 077203 (2012).; Meier, D. et al., Nature Mater. 11, 284 (2012).], as well as reports of coupling between ferroelectricity, magnetism and structural antiphase domains [Geng, Y. et al., Nano Lett. 12, 6055 (2012).]. The detailed structure of the domain walls, as well as the origin of such couplings, however, was previously not fully understood. In the present study, we have used first-principles density functional theory to calculate the structure and properties of the low-energy structural domain walls in the hexagonal manganites [Kumagai, Y. and Spaldin, N. A., Nature Commun. 4, 1540 (2013).]. We find that the lowest energy domain walls are atomically sharp, with {210}orientation, explaining the orientation of recently observed stripe domains and suggesting their topological protection [Chae, S. C. et al., Phys. Rev. Lett. 108, 167603 (2012).]. We also explain why ferroelectric domain walls are always simultaneously antiphase walls, propose a mechanism for ferroelectric switching through domain-wall motion, and suggest an atomistic structure for the cores of the sixfold topological defects. This work was supported by ETH Zurich, the European Research Council FP7 Advanced Grants program me (grant number 291151), the JSPS Postdoctoral Fellowships for Research Abroad, and the MEXT Elements Strategy Initiative to Form Core Research Center TIES.

  18. The Evolution and Functional Role of Flavin-based Prokaryotic Photoreceptors.

    PubMed

    Losi, Aba; Mandalari, Carmen; Gärtner, Wolfgang

    2015-01-01

    Flavin-based photoreceptor proteins of the LOV (light, oxygen and voltage) superfamily are ubiquitous and appear to be essential blue-light sensing systems not only in plants, algae and fungi, but also in prokaryotes, where they are represented in more than 10% of known species. Despite their broad occurrence, only in few cases LOV proteins have been correlated with important phenomena such as bacterial infectivity, selective growth patterns or/and stress responses; nevertheless these few known roles are helping us understand the multiple ways by which prokaryotes can exploit these soluble blue-light photoreceptors. Given the large number of sequences now deposited in databases, it becomes meaningful to define a signature for bona fide LOV domains, a procedure that facilitates identification of proteins with new properties and phylogenetic analysis. The latter clearly evidences that a class of LOV proteins from alpha-proteobacteria is the closest prokaryotic relative of eukaryotic LOV domains, whereas cyanobacterial sequences cluster with the archaeal and the other bacterial LOV domains. Distance trees built for LOV domains suggest complex evolutionary patterns, possibly involving multiple horizontal gene transfer events. Based on available data, the in vivo relevance and evolution of prokaryotic LOV is discussed. PMID:26138219

  19. Domain adaptation from multiple sources: a domain-dependent regularization approach.

    PubMed

    Duan, Lixin; Xu, Dong; Tsang, Ivor Wai-Hung

    2012-03-01

    In this paper, we propose a new framework called domain adaptation machine (DAM) for the multiple source domain adaption problem. Under this framework, we learn a robust decision function (referred to as target classifier) for label prediction of instances from the target domain by leveraging a set of base classifiers which are prelearned by using labeled instances either from the source domains or from the source domains and the target domain. With the base classifiers, we propose a new domain-dependent regularizer based on smoothness assumption, which enforces that the target classifier shares similar decision values with the relevant base classifiers on the unlabeled instances from the target domain. This newly proposed regularizer can be readily incorporated into many kernel methods (e.g., support vector machines (SVM), support vector regression, and least-squares SVM (LS-SVM)). For domain adaptation, we also develop two new domain adaptation methods referred to as FastDAM and UniverDAM. In FastDAM, we introduce our proposed domain-dependent regularizer into LS-SVM as well as employ a sparsity regularizer to learn a sparse target classifier with the support vectors only from the target domain, which thus makes the label prediction on any test instance very fast. In UniverDAM, we additionally make use of the instances from the source domains as Universum to further enhance the generalization ability of the target classifier. We evaluate our two methods on the challenging TRECIVD 2005 dataset for the large-scale video concept detection task as well as on the 20 newsgroups and email spam datasets for document retrieval. Comprehensive experiments demonstrate that FastDAM and UniverDAM outperform the existing multiple source domain adaptation methods for the two applications. PMID:24808555

  20. Asymmetric counter propagation of domain walls

    NASA Astrophysics Data System (ADS)

    Andrade-Silva, I.; Clerc, M. G.; Odent, V.

    2016-07-01

    Far from equilibrium systems show different states and domain walls between them. These walls, depending on the type of connected equilibria, exhibit a rich spatiotemporal dynamics. Here, we investigate the asymmetrical counter propagation of domain walls in an in-plane-switching cell filled with a nematic liquid crystal. Experimentally, we characterize the shape and speed of the domain walls. Based on the molecular orientation, we infer that the counter propagative walls have different elastic deformations. These deformations are responsible of the asymmetric counter propagating fronts. Theoretically, based on symmetry arguments, we propose a simple bistable model under the influence of a nonlinear gradient, which qualitatively describes the observed dynamics.

  1. Quasiparticles near domain walls in hexagonal superconductors

    NASA Astrophysics Data System (ADS)

    Mukherjee, S. P.; Samokhin, K. V.

    2016-02-01

    We calculate the energy spectrum of quasiparticles trapped by a domain wall separating different time-reversal symmetry-breaking ground states in a hexagonal superconductor, such as UPt3. The bound-state energy is found to be strongly dependent on the gap symmetry, the domain-wall orientation, the quasiparticle's direction of semiclassical propagation, and the phase difference between the domains. We calculate the corresponding density of states and show how one can use its prominent features, in particular, the zero-energy singularity, to distinguish between different pairing symmetries.

  2. Domain-decomposed preconditionings for transport operators

    NASA Technical Reports Server (NTRS)

    Chan, Tony F.; Gropp, William D.; Keyes, David E.

    1991-01-01

    The performance was tested of five different interface preconditionings for domain decomposed convection diffusion problems, including a novel one known as the spectral probe, while varying mesh parameters, Reynolds number, ratio of subdomain diffusion coefficients, and domain aspect ratio. The preconditioners are representative of the range of practically computable possibilities that have appeared in the domain decomposition literature for the treatment of nonoverlapping subdomains. It is shown that through a large number of numerical examples that no single preconditioner can be considered uniformly superior or uniformly inferior to the rest, but that knowledge of particulars, including the shape and strength of the convection, is important in selecting among them in a given problem.

  3. Quasiparticles near domain walls in hexagonal superconductors

    NASA Astrophysics Data System (ADS)

    Mukherjee, Soumya; Samokhin, Kirill

    We calculate the energy spectrum of quasiparticles trapped by a domain wall separating different time reversal symmetry-breaking ground states in a hexagonal superconductor, such as UPt3. The bound state energy is found to be strongly dependent on the gap symmetry, the domain wall orientation, the quasiparticle's direction of semiclassical propagation, and the phase difference between the domains. We calculate the corresponding density of states and show how one can use its prominent features, in particular, the zero-energy singularity, to distinguish between different pairing symmetries. Discovery Grant from the Natural Sciences and Engineering Research Council of Canada.

  4. Domain Naming Practices and World Wide Web Search Tactics.

    ERIC Educational Resources Information Center

    Koehler, Wallace Jr.

    1998-01-01

    Discusses Internet domain naming practices and indicates which Web search engines can effectively search on domain names. Explains top-level domain (TLD) (ex. http://www.access.gpo.gov - ".gov" = top level; ".gpo" = second level; ".access" = third level; and "www" = fourth level domain). Outlines seven new TLD names and discusses using domains in…

  5. Separating Cognitive and Content Domains in Mathematical Competence

    ERIC Educational Resources Information Center

    Harks, Birgit; Klieme, Eckhard; Hartig, Johannes; Leiss, Dominik

    2014-01-01

    The present study investigates the empirical separability of mathematical (a) content domains, (b) cognitive domains, and (c) content-specific cognitive domains. There were 122 items representing two content domains (linear equations vs. theorem of Pythagoras) combined with two cognitive domains (modeling competence vs. technical competence)…

  6. Supporting multiple domains in a single reuse repository

    NASA Technical Reports Server (NTRS)

    Eichmann, David

    1992-01-01

    Domain analysis typically results in the construction of a domain-specific repository. Such a repository imposes artificial boundaries on the sharing of similar assets between related domains. A lattice-based approach to repository modeling can preserve a reuser's domain specific view of the repository, while avoiding replication of commonly used assets and supporting a more general perspective on domain interrelationships.

  7. Time domain reflectometry for SLC BPM system

    NASA Astrophysics Data System (ADS)

    Thompson, D. R.

    1985-03-01

    A maintenance manual for troubleshooting installed SLC Position Monitor stripline assemblies and the associated cabling, using time Domain Reflectometry is presented. Once a technician becomes familiar with this manual's procedures, the Table of Contents can serve as a checklist.

  8. Domain wall manipulation with a magnetic tip.

    PubMed

    Stapelfeldt, T; Wieser, R; Vedmedenko, E Y; Wiesendanger, R

    2011-07-01

    A theoretical concept of local manipulation of magnetic domain walls is introduced. In the proposed procedure, a domain wall is driven by a spin-polarized current induced by a magnetic tip, as used in a scanning tunneling microscope, placed above a magnetic nanostripe and then moved along its long axis with a current flowing through the vacuum barrier. The angular momentum from the spin-polarized current exerts a torque on the magnetic moments underneath the tip and leads to a displacement of the domain wall. Particularly, the manipulation of a ferromagnetic 180° transverse domain wall has been studied by means of Landau-Lifshitz-Gilbert dynamics and Monte Carlo simulations. Different relative orientations of the tip and the sample magnetization have been considered. PMID:21797636

  9. Substructure coupling in the frequency domain

    NASA Technical Reports Server (NTRS)

    1985-01-01

    Frequency domain analysis was found to be a suitable method for determining the transient response of systems subjected to a wide variety of loads. However, since a large number of calculations are performed within the discrete frequency loop, the method loses it computational efficiency if the loads must be represented by a large number of discrete frequencies. It was also discovered that substructure coupling in the frequency domain work particularly well for analyzing structural system with a small number of interface and loaded degrees of freedom. It was discovered that substructure coupling in the frequency domain can lead to an efficient method of obtaining natural frequencies of undamped structures. It was also found that the damped natural frequencies of a system may be determined using frequency domain techniques.

  10. Resistance domain in type II superconductors

    SciTech Connect

    Gurevich, A.V.; Mints, R.G.

    1980-01-05

    We show that traveling domains with a finite resistance can exist in type II superconductors in the presence of a transport current. An experiment in which this effect generates an alternating electric field and current is proposed.

  11. Notch Transmembrane Domain: Secondary Structure and Topology

    PubMed Central

    2016-01-01

    The Notch signaling pathway is critical in development, neuronal maintenance, and hematopoiesis. An obligate step in the activation of this pathway is cleavage of its transmembrane (TM) domain by γ-secretase. While the soluble domains have been extensively studied, little has been done to characterize its TM and flanking juxtamembrane (JM) segments. Here, we present the results of nuclear magnetic resonance (NMR) studies of the human Notch1 TM/JM domain. The TM domain is largely α-helical. While the flanking JM segments do not adopt regular secondary structure, they interact with the membrane surface, suggesting membrane interactions may play a role in modulating its cleavage by γ-secretase and subsequent NOTCH signaling function. PMID:26023825

  12. Electric fingerprint of voltage sensor domains.

    PubMed

    Souza, Caio S; Amaral, Cristiano; Treptow, Werner

    2014-12-01

    A dynamic transmembrane voltage field has been suggested as an intrinsic element in voltage sensor (VS) domains. Here, the dynamic field contribution to the VS energetics was analyzed via electrostatic calculations applied to a number of atomistic structures made available recently. We find that the field is largely static along with the molecular motions of the domain, and more importantly, it is minimally modified across VS variants. This finding implies that sensor domains transfer approximately the same amount of gating charges when moving the electrically charged S4 helix between fixed microscopic configurations. Remarkably, the result means that the observed operational diversity of the domain, including the extension, rate, and voltage dependence of the S4 motion, as dictated by the free energy landscape theory, must be rationalized in terms of dominant variations of its chemical free energy. PMID:25422443

  13. Electric fingerprint of voltage sensor domains

    PubMed Central

    Souza, Caio S.; Amaral, Cristiano; Treptow, Werner

    2014-01-01

    A dynamic transmembrane voltage field has been suggested as an intrinsic element in voltage sensor (VS) domains. Here, the dynamic field contribution to the VS energetics was analyzed via electrostatic calculations applied to a number of atomistic structures made available recently. We find that the field is largely static along with the molecular motions of the domain, and more importantly, it is minimally modified across VS variants. This finding implies that sensor domains transfer approximately the same amount of gating charges when moving the electrically charged S4 helix between fixed microscopic configurations. Remarkably, the result means that the observed operational diversity of the domain, including the extension, rate, and voltage dependence of the S4 motion, as dictated by the free energy landscape theory, must be rationalized in terms of dominant variations of its chemical free energy. PMID:25422443

  14. Gravitational waves from collapsing domain walls

    SciTech Connect

    Hiramatsu, Takashi; Kawasaki, Masahiro; Saikawa, Ken'ichi E-mail: kawasaki@icrr.u-tokyo.ac.jp

    2010-05-01

    We study the production of gravitational waves from cosmic domain walls created during phase transition in the early universe. We investigate the process of formation and evolution of domain walls by running three dimensional lattice simulations. If we introduce an approximate discrete symmetry, walls become metastable and finally disappear. This process might occur by a pressure difference between two vacua if a quantum tunneling is neglected. We calculate the spectrum of gravitational waves produced by collapsing metastable domain walls. Extrapolating the numerical results, we find that the signal of gravitational waves produced by domain walls whose energy scale is around 10{sup 10}-10{sup 12}GeV will be observable in the next generation gravitational wave interferometers.

  15. Broken-Line Functions with Unbroken Domains.

    ERIC Educational Resources Information Center

    Satianov, Pavel; Fried, Michael; Amit, Miriam

    1999-01-01

    Presents a method for introducing students to broken-line functions with unbroken domains. Concludes that a unit on broken-line functions should enhance students' understanding of the function concept. (ASK)

  16. Tuning Protein Autoinhibition by Domain Destabilization

    PubMed Central

    Cho, Jae-Hyun; Muralidharan, Vasant; Vila-Perello, Miquel; Raleigh, Daniel P.; Muir, Tom W.; Palmer, Arthur G.

    2012-01-01

    Activation of many multi-domain signaling proteins requires rearrangement of autoinhibitory interdomain interactions that occlude activator binding sites. In one model for activation, the major inactive conformation exists in equilibrium with activated-like conformations that can be stabilized by ligand binding or post-translational modifications. The molecular basis for this model is established for the archetypal signaling adapter protein Crk-II by measuring the thermodynamics and kinetics of the equilibrium between autoinhibited and activated-like states using fluorescence and NMR spectroscopies, together with segmental isotopic labeling via expressed protein ligation. The results demonstrate that intramolecular domain-domain interactions both stabilize the autoinhibited state and induce the activated-like conformation. A combination of favorable interdomain interactions and unfavorable intradomain structural changes fine-tunes the population of the activated-like conformation and allows facile response to activators. This mechanism suggests a general strategy for optimization of autoinhibitory interactions of multi-domain proteins. PMID:21532593

  17. Improving the consistency of domain annotation within the Conserved Domain Database

    PubMed Central

    Derbyshire, Myra K.; Gonzales, Noreen R.; Lu, Shennan; He, Jane; Marchler, Gabriele H.; Wang, Zhouxi; Marchler-Bauer, Aron

    2015-01-01

    When annotating protein sequences with the footprints of evolutionarily conserved domains, conservative score or E-value thresholds need to be applied for RPS-BLAST hits, to avoid many false positives. We notice that manual inspection and classification of hits gathered at a higher threshold can add a significant amount of valuable domain annotation. We report an automated algorithm that ‘rescues’ valuable borderline-scoring domain hits that are well-supported by domain architecture (DA, the sequential order of conserved domains in a protein query), including tandem repeats of domain hits reported at a more conservative threshold. This algorithm is now available as a selectable option on the public conserved domain search (CD-Search) pages. We also report on the possibility to ‘suppress’ domain hits close to the threshold based on a lack of well-supported DA and to implement this conservatively as an option in live conserved domain searches and for pre-computed results. Improving domain annotation consistency will in turn reduce the fraction of NR sequences with incomplete DAs. URL: http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi PMID:25767294

  18. Between-domain relations of students' academic emotions and their judgments of school domain similarity

    PubMed Central

    Goetz, Thomas; Haag, Ludwig; Lipnevich, Anastasiya A.; Keller, Melanie M.; Frenzel, Anne C.; Collier, Antonie P. M.

    2014-01-01

    With the aim to deepen our understanding of the between-domain relations of academic emotions, a series of three studies was conducted. We theorized that between-domain relations of trait (i.e., habitual) emotions reflected students' judgments of domain similarities, whereas between-domain relations of state (i.e., momentary) emotions did not. This supposition was based on the accessibility model of emotional self-report, according to which individuals' beliefs tend to strongly impact trait, but not state emotions. The aim of Study 1 (interviews; N = 40; 8th and 11th graders) was to gather salient characteristics of academic domains from students' perspective. In Study 2 (N = 1709; 8th and 11th graders) the 13 characteristics identified in Study 1 were assessed along with academic emotions in four different domains (mathematics, physics, German, and English) using a questionnaire-based trait assessment. With respect to the same domains, state emotions were assessed in Study 3 (N = 121; 8th and 11th graders) by employing an experience sampling approach. In line with our initial assumptions, between-domain relations of trait but not state academic emotions reflected between-domain relations of domain characteristics. Implications for research and practice are discussed. PMID:25374547

  19. Dual-domain point diffraction interferometer.

    PubMed

    Naulleau, P P; Goldberg, K A

    1999-06-01

    The phase-shifting point diffraction interferometer has recently been developed and implemented at Lawrence Berkeley National Laboratory to meet the significant metrology challenge of characterizing extreme ultraviolet projection lithography systems. Here we present a refined version of this interferometer that overcomes the original design's susceptibility to noise attributed to scattered light. The theory of the new hybrid spatial- and temporal-domain (dual-domain) point diffraction interferometer is described in detail and experimental results are presented. PMID:18319953

  20. Planning with Continuous Resources in Stochastic Domains

    NASA Technical Reports Server (NTRS)

    Mausam, Mausau; Benazera, Emmanuel; Brafman, Roneu; Hansen, Eric

    2005-01-01

    We consider the problem of optimal planning in stochastic domains with metric resource constraints. Our goal is to generate a policy whose expected sum of rewards is maximized for a given initial state. We consider a general formulation motivated by our application domain--planetary exploration--in which the choice of an action at each step may depend on the current resource levels. We adapt the forward search algorithm AO* to handle our continuous state space efficiently.

  1. A time domain technique for mechanism extraction

    NASA Technical Reports Server (NTRS)

    Dominek, Allen K.; Peters, Leon, Jr.; Burnside, Walter D.

    1987-01-01

    The properties of scattered fields from a structure can be better evaluated from the characteristics of the individual scatterers. Decomposition techniques can be classified either as a matrix or an integral formulation. With either formulation, aspect pattern of frequency information of a scattering center can be obtained. Emphasis is placed on an integral (time domain) isolation extraction technique to obtain the frequency characteristics of scattering mechanisms. This technique has its origins in the time domain interpretation of scattered fields.

  2. Moving Towards Domain Wall Devices in Ferroics

    NASA Astrophysics Data System (ADS)

    Gregg, Marty

    Domain walls in ferroelectric, ferroelastic and multiferroic oxides are distinct functional materials in their own right. They can be conducting, or even superconducting, when surrounding domains are insulating; they can demonstrate magnetism when the surrounding bulk is non-magnetic and they can contain ordered electrical dipoles when the matrix containing them is non-polar. Since domain walls can also be created, destroyed, and controllably moved from place to place, there is an amazing opportunity for us to design new forms of devices in which functionality is actively and dynamically deployed (now you see it; now you don't). This is the essence of the emerging field known as ``domain wall nanoelectronics''. In time, this arena of research could change the way we think of nanoscale functional devices, moving increasingly towards agile circuitry and neuromorphic device architectures. While the control of domain wall injection, movement and annihilation has been developed rather well in the nanomagnetics community (in race-track and domain wall logic research), similar research has not been widely performed in nanoscale ferroelectrics, ferroelastics and multiferroics. This talk will discuss progress that has been made to date and the way in which nanomagnetics research can be used as a source of inspiration. Site-specific domain wall injection and motion control in both proper and improper ferroelectrics using inhomogeneous electric and elastic fields, as well as dielectric patterning in uniaxial ferroelectrics, will be specifically considered. As will be shown, sufficient control has been developed to allow the creation of a diode for domain wall motion in ferroelectrics, for example. The author acknowledges support from the Engineering and Physical Sciences Research Council (EPSRC).

  3. Multi-domain training enhances attentional control.

    PubMed

    Binder, Julia C; Martin, Mike; Zöllig, Jacqueline; Röcke, Christina; Mérillat, Susan; Eschen, Anne; Jäncke, Lutz; Shing, Yee Lee

    2016-06-01

    Multi-domain training potentially increases the likelihood of overlap in processing components with transfer tasks and everyday life, and hence is a promising training approach for older adults. To empirically test this, 84 healthy older adults aged 64 to 75 years were randomly assigned to one of three single-domain training conditions (inhibition, visuomotor function, spatial navigation) or to the simultaneous training of all three cognitive functions (multi-domain training condition). All participants trained on an iPad at home for 50 training sessions. Before and after the training, and at a 6-month follow-up measurement, cognitive functioning and training transfer were assessed with a neuropsychological test battery including tests targeting the trained functions (near transfer) and transfer to executive functions (far transfer: attentional control, working memory, speed). Participants in all four training groups showed a linear increase in training performance over the 50 training sessions. Using a latent difference score model, the multi-domain training group, compared with the single-domain training groups, showed more improvement on the far transfer attentional control composite. Individuals with initially lower baseline performance showed higher training-related improvements, indicating that training compensated for lower initial cognitive performance. At the 6-month follow-up, performance on the cognitive test battery remained stable. This is one of the first studies to investigate systematically multi-domain training including comparable single-domain training conditions. Our findings suggest that multi-domain training enhances attentional control involved in handling several different tasks at the same time, an aspect in everyday life that is particularly challenging for older people. (PsycINFO Database Record PMID:27294719

  4. Constant Domain-regulated Antibody Catalysis*

    PubMed Central

    Sapparapu, Gopal; Planque, Stephanie; Mitsuda, Yukie; McLean, Gary; Nishiyama, Yasuhiro; Paul, Sudhir

    2012-01-01

    Some antibodies contain variable (V) domain catalytic sites. We report the superior amide and peptide bond-hydrolyzing activity of the same heavy and light chain V domains expressed in the IgM constant domain scaffold compared with the IgG scaffold. The superior catalytic activity of recombinant IgM was evident using two substrates, a small model peptide that is hydrolyzed without involvement of high affinity epitope binding, and HIV gp120, which is recognized specifically by noncovalent means prior to the hydrolytic reaction. The catalytic activity was inhibited by an electrophilic phosphonate diester, consistent with a nucleophilic catalytic mechanism. All 13 monoclonal IgMs tested displayed robust hydrolytic activities varying over a 91-fold range, consistent with expression of the catalytic functions at distinct levels by different V domains. The catalytic activity of polyclonal IgM was superior to polyclonal IgG from the same sera, indicating that on average IgMs express the catalytic function at levels greater than IgGs. The findings indicate a favorable effect of the remote IgM constant domain scaffold on the integrity of the V-domain catalytic site and provide a structural basis for conceiving antibody catalysis as a first line immune function expressed at high levels prior to development of mature IgG class antibodies. PMID:22948159

  5. Domain wall geometry controls conduction in ferroelectrics.

    PubMed

    Vasudevan, R K; Morozovska, A N; Eliseev, E A; Britson, J; Yang, J-C; Chu, Y-H; Maksymovych, P; Chen, L Q; Nagarajan, V; Kalinin, S V

    2012-11-14

    A new paradigm of domain wall nanoelectronics has emerged recently, in which the domain wall in a ferroic is itself an active device element. The ability to spatially modulate the ferroic order parameter within a single domain wall allows the physical properties to be tailored at will and hence opens vastly unexplored device possibilities. Here, we demonstrate via ambient and ultrahigh-vacuum (UHV) scanning probe microscopy (SPM) measurements in bismuth ferrite that the conductivity of the domain walls can be modulated by up to 500% in the spatial dimension as a function of domain wall curvature. Landau-Ginzburg-Devonshire calculations reveal the conduction is a result of carriers or vacancies migrating to neutralize the charge at the formed interface. Phase-field modeling indicates that anisotropic potential distributions can occur even for initially uncharged walls, from polarization dynamics mediated by elastic effects. These results are the first proof of concept for modulation of charge as a function of domain wall geometry by a proximal probe, thereby expanding potential applications for oxide ferroics in future nanoscale electronics. PMID:22994244

  6. Structured hints : extracting and abstracting domain expertise.

    SciTech Connect

    Hereld, M.; Stevens, R.; Sterling, T.; Gao, G. R.; Mathematics and Computer Science; California Inst. of Tech.; Louisiana State Univ.; Univ. of Delaware

    2009-03-16

    We propose a new framework for providing information to help optimize domain-specific application codes. Its design addresses problems that derive from the widening gap between the domain problem statement by domain experts and the architectural details of new and future high-end computing systems. The design is particularly well suited to program execution models that incorporate dynamic adaptive methodologies for live tuning of program performance and resource utilization. This new framework, which we call 'structured hints', couples a vocabulary of annotations to a suite of performance metrics. The immediate target is development of a process by which a domain expert describes characteristics of objects and methods in the application code that would not be readily apparent to the compiler; the domain expert provides further information about what quantities might provide the best indications of desirable effect; and the interactive preprocessor identifies potential opportunities for the domain expert to evaluate. Our development of these ideas is progressing in stages from case study, through manual implementation, to automatic or semi-automatic implementation. In this paper we discuss results from our case study, an examination of a large simulation of a neural network modeled after the neocortex.

  7. POU domain factors in neural development.

    PubMed

    Schonemann, M D; Ryan, A K; Erkman, L; McEvilly, R J; Bermingham, J; Rosenfeld, M G

    1998-01-01

    Transcription factors serve critical roles in the progressive development of general body plan, organ commitment, and finally, specific cell types. Comparison of the biological roles of a series of individual members within a family permits some generalizations to be made regarding the developmental events that are likely to be regulated by a particular class of transcription factors. Here, we evidence that the developmental functions of the family of transcription factors characterized by the POU DNA binding motif exerts roles in mammalian development. The POU domain family of transcription factors was defined following the observation that the products of three mammalian genes, Pit-1, Oct-1, and Oct-2, and the protein encoded by the C. elegans gene unc-86, shared a region of homology, known as the POU domain. The POU domain is a bipartite DNA binding domain, consisting of two highly conserved regions, tethered by a variable linker. The approximately 75 amino acid N-terminal region was called the POU-specific domain and the C-terminal 60 amino acid region, the POU-homeodomain. High-affinity site-specific DNA binding by POU domain transcription factors requires both the POU-specific and the POU-homeodomain. Resolution of the crystal structures of Oct-1 and Pit-1 POU domains bound to DNA as a monomer and homodimer, respectively, confirmed several of the in vitro findings regarding interactions of this bipartite DNA binding domain with DNA and has provided important information regarding the flexibility and versatility of POU domain proteins. Overall the crystal structure of a monomer of the Oct-1 POU domain bound to the octamer element was similar to that predicted by the NMR solution structures of the POU-specific domain and the POU-homeodomain in isolation, with the POU-specific domain consists of four alpha helices, with the second and third helices forming a structure similar to the helix-turn-helix motif of the lambda and 434 repressors; several of the DNA base

  8. Human-computer interface incorporating personal and application domains

    DOEpatents

    Anderson, Thomas G.

    2004-04-20

    The present invention provides a human-computer interface. The interface includes provision of an application domain, for example corresponding to a three-dimensional application. The user is allowed to navigate and interact with the application domain. The interface also includes a personal domain, offering the user controls and interaction distinct from the application domain. The separation into two domains allows the most suitable interface methods in each: for example, three-dimensional navigation in the application domain, and two- or three-dimensional controls in the personal domain. Transitions between the application domain and the personal domain are under control of the user, and the transition method is substantially independent of the navigation in the application domain. For example, the user can fly through a three-dimensional application domain, and always move to the personal domain by moving a cursor near one extreme of the display.

  9. Human-computer interface incorporating personal and application domains

    DOEpatents

    Anderson, Thomas G.

    2011-03-29

    The present invention provides a human-computer interface. The interface includes provision of an application domain, for example corresponding to a three-dimensional application. The user is allowed to navigate and interact with the application domain. The interface also includes a personal domain, offering the user controls and interaction distinct from the application domain. The separation into two domains allows the most suitable interface methods in each: for example, three-dimensional navigation in the application domain, and two- or three-dimensional controls in the personal domain. Transitions between the application domain and the personal domain are under control of the user, and the transition method is substantially independent of the navigation in the application domain. For example, the user can fly through a three-dimensional application domain, and always move to the personal domain by moving a cursor near one extreme of the display.

  10. A simple method for converting frequency domain aerodynamics to the time domain

    NASA Technical Reports Server (NTRS)

    Dowell, E. H.

    1980-01-01

    A simple, direct procedure was developed for converting frequency domain aerodynamics into indicial aerodynamics. The data required for aerodynamic forces in the frequency domain may be obtained from any available (linear) theory. The method retains flexibility for the analyst and is based upon the particular character of the frequency domain results. An evaluation of the method was made for incompressible, subsonic, and transonic two dimensional flows.

  11. Low energy electron imaging of domains and domain walls in magnesium-doped lithium niobate.

    PubMed

    Nataf, G F; Grysan, P; Guennou, M; Kreisel, J; Martinotti, D; Rountree, C L; Mathieu, C; Barrett, N

    2016-01-01

    The understanding of domain structures, specifically domain walls, currently attracts a significant attention in the field of (multi)-ferroic materials. In this article, we analyze contrast formation in full field electron microscopy applied to domains and domain walls in the uniaxial ferroelectric lithium niobate, which presents a large 3.8 eV band gap and for which conductive domain walls have been reported. We show that the transition from Mirror Electron Microscopy (MEM - electrons reflected) to Low Energy Electron Microscopy (LEEM - electrons backscattered) gives rise to a robust contrast between domains with upwards (Pup) and downwards (Pdown) polarization, and provides a measure of the difference in surface potential between the domains. We demonstrate that out-of-focus conditions of imaging produce contrast inversion, due to image distortion induced by charged surfaces, and also carry information on the polarization direction in the domains. Finally, we show that the intensity profile at domain walls provides experimental evidence for a local stray, lateral electric field. PMID:27608605

  12. Low energy electron imaging of domains and domain walls in magnesium-doped lithium niobate

    PubMed Central

    Nataf, G. F.; Grysan, P.; Guennou, M.; Kreisel, J.; Martinotti, D.; Rountree, C. L.; Mathieu, C.; Barrett, N.

    2016-01-01

    The understanding of domain structures, specifically domain walls, currently attracts a significant attention in the field of (multi)-ferroic materials. In this article, we analyze contrast formation in full field electron microscopy applied to domains and domain walls in the uniaxial ferroelectric lithium niobate, which presents a large 3.8 eV band gap and for which conductive domain walls have been reported. We show that the transition from Mirror Electron Microscopy (MEM – electrons reflected) to Low Energy Electron Microscopy (LEEM – electrons backscattered) gives rise to a robust contrast between domains with upwards (Pup) and downwards (Pdown) polarization, and provides a measure of the difference in surface potential between the domains. We demonstrate that out-of-focus conditions of imaging produce contrast inversion, due to image distortion induced by charged surfaces, and also carry information on the polarization direction in the domains. Finally, we show that the intensity profile at domain walls provides experimental evidence for a local stray, lateral electric field. PMID:27608605

  13. A new and unexpected domain-domain interaction in the AraC protein.

    PubMed

    Cole, Stephanie Dirla; Schleif, Robert

    2012-05-01

    An interaction between the dimerization domains and DNA binding domains of the dimeric AraC protein has previously been shown to facilitate repression of the Escherichia coli araBAD operon by AraC in the absence of arabinose. A new interaction between the domains of AraC in the presence of arabinose is reported here, the regulatory consequences of which are unknown. Evidence for the interaction is the following: the dissociation rate of arabinose-bound AraC from half-site DNA is considerably faster than that of free DNA binding domain, and the affinity of the dimerization domains for arabinose is increased when half-site DNA is bound. In addition, an increase in the fluorescence intensity of tryptophan residues located in the arabinose-bound dimerization domain is observed upon binding of half-site DNA to the DNA binding domains. Direct physical evidence of the new domain-domain interaction is demonstrated by chemical crosslinking and NMR experiments. PMID:22383259

  14. Dual-domain point diffraction interferometer

    DOEpatents

    Naulleau, Patrick P.; Goldberg, Kenneth Alan

    2000-01-01

    A hybrid spatial/temporal-domain point diffraction interferometer (referred to as the dual-domain PS/PDI) that is capable of suppressing the scattered-reference-light noise that hinders the conventional PS/PDI is provided. The dual-domain PS/PDI combines the separate noise-suppression capabilities of the widely-used phase-shifting and Fourier-transform fringe pattern analysis methods. The dual-domain PS/PDI relies on both a more restrictive implementation of the image plane PS/PDI mask and a new analysis method to be applied to the interferograms generated and recorded by the modified PS/PDI. The more restrictive PS/PDI mask guarantees the elimination of spatial-frequency crosstalk between the signal and the scattered-light noise arising from scattered-reference-light interfering with the test beam. The new dual-domain analysis method is then used to eliminate scattered-light noise arising from both the scattered-reference-light interfering with the test beam and the scattered-reference-light interfering with the "true" pinhole-diffracted reference light. The dual-domain analysis method has also been demonstrated to provide performance enhancement when using the non-optimized standard PS/PDI design. The dual-domain PS/PDI is essentially a three-tiered filtering system composed of lowpass spatial-filtering the test-beam electric field using the more restrictive PS/PDI mask, bandpass spatial-filtering the individual interferogram irradiance frames making up the phase-shifting series, and bandpass temporal-filtering the phase-shifting series as a whole.

  15. Algorithms for propagating uncertainty across heterogeneous domains

    SciTech Connect

    Cho, Heyrim; Yang, Xiu; Venturi, D.; Karniadakis, George E.

    2015-12-30

    We address an important research area in stochastic multi-scale modeling, namely the propagation of uncertainty across heterogeneous domains characterized by partially correlated processes with vastly different correlation lengths. This class of problems arise very often when computing stochastic PDEs and particle models with stochastic/stochastic domain interaction but also with stochastic/deterministic coupling. The domains may be fully embedded, adjacent or partially overlapping. The fundamental open question we address is the construction of proper transmission boundary conditions that preserve global statistical properties of the solution across different subdomains. Often, the codes that model different parts of the domains are black-box and hence a domain decomposition technique is required. No rigorous theory or even effective empirical algorithms have yet been developed for this purpose, although interfaces defined in terms of functionals of random fields (e.g., multi-point cumulants) can overcome the computationally prohibitive problem of preserving sample-path continuity across domains. The key idea of the different methods we propose relies on combining local reduced-order representations of random fields with multi-level domain decomposition. Specifically, we propose two new algorithms: The first one enforces the continuity of the conditional mean and variance of the solution across adjacent subdomains by using Schwarz iterations. The second algorithm is based on PDE-constrained multi-objective optimization, and it allows us to set more general interface conditions. The effectiveness of these new algorithms is demonstrated in numerical examples involving elliptic problems with random diffusion coefficients, stochastically advected scalar fields, and nonlinear advection-reaction problems with random reaction rates.

  16. Polar domain walls trigger magnetoelectric coupling

    PubMed Central

    Fontcuberta, Josep; Skumryev, Vassil; Laukhin, Vladimir; Granados, Xavier; Salje, Ekhard K. H.

    2015-01-01

    Interface physics in oxides heterostructures is pivotal in material’s science. Domain walls (DWs) in ferroic systems are examples of naturally occurring interfaces, where order parameter of neighboring domains is modified and emerging properties may develop. Here we show that electric tuning of ferroelastic domain walls in SrTiO3 leads to dramatic changes of the magnetic domain structure of a neighboring magnetic layer (La1/2Sr1/2MnO3) epitaxially clamped on a SrTiO3 substrate. We show that the properties of the magnetic layer are intimately connected to the existence of polar regions at twin boundaries of SrTiO3, developing at , that can be electrically modulated. These findings illustrate that by exploiting the responsiveness of DWs nanoregions to external stimuli, even in absence of any domain contribution, prominent and adjustable macroscopic reactions of neighboring layers can be obtained. We conclude that polar DWs, known to exist in other materials, can be used to trigger tunable responses and may lead to new ways for the manipulation of interfacial emerging properties. PMID:26387597

  17. The architecture of the protein domain universe.

    PubMed

    Dokholyan, Nikolay V

    2005-03-14

    Understanding the design of the universe of protein structures may provide insights into protein evolution. We study the architecture of the protein domain universe, which has been found to poses peculiar scale-free properties. We examine the origin of these scale-free properties of the graph of protein domain structures (PDUG) and determine that that the PDUG is not modular, i.e. it does not consist of modules with uniform properties. Instead, we find the PDUG to be self-similar at all scales. We further characterize the PDUG architecture by studying the properties of the hub nodes that are responsible for the scale-free connectivity of the PDUG. We introduce a measure of the betweenness centrality of protein domains in the PDUG and find a power-law distribution of the betweenness centrality values. The scale-free distribution of hubs in the protein universe suggests that a set of specific statistical mechanics models, such as the self-organized criticality model, can potentially identify the principal driving forces of protein evolution. We also find a gatekeeper protein domain, removal of which partitions the largest cluster into two large sub-clusters. We suggest that the loss of such gatekeeper protein domains in the course of evolution is responsible for the creation of new fold families. PMID:15777630

  18. Direct measurement of antiferromagnetic domain fluctuations.

    PubMed

    Shpyrko, O G; Isaacs, E D; Logan, J M; Feng, Yejun; Aeppli, G; Jaramillo, R; Kim, H C; Rosenbaum, T F; Zschack, P; Sprung, M; Narayanan, S; Sandy, A R

    2007-05-01

    Measurements of magnetic noise emanating from ferromagnets owing to domain motion were first carried out nearly 100 years ago, and have underpinned much science and technology. Antiferromagnets, which carry no net external magnetic dipole moment, yet have a periodic arrangement of the electron spins extending over macroscopic distances, should also display magnetic noise. However, this must be sampled at spatial wavelengths of the order of several interatomic spacings, rather than the macroscopic scales characteristic of ferromagnets. Here we present a direct measurement of the fluctuations in the nanometre-scale superstructure of spin- and charge-density waves associated with antiferromagnetism in elemental chromium. The technique used is X-ray photon correlation spectroscopy, where coherent X-ray diffraction produces a speckle pattern that serves as a 'fingerprint' of a particular magnetic domain configuration. The temporal evolution of the patterns corresponds to domain walls advancing and retreating over micrometre distances. This work demonstrates a useful measurement tool for antiferromagnetic domain wall engineering, but also reveals a fundamental finding about spin dynamics in the simplest antiferromagnet: although the domain wall motion is thermally activated at temperatures above 100 K, it is not so at lower temperatures, and indeed has a rate that saturates at a finite value-consistent with quantum fluctuations-on cooling below 40 K. PMID:17476263

  19. Generalized vector calculus on convex domain

    NASA Astrophysics Data System (ADS)

    Agrawal, Om P.; Xu, Yufeng

    2015-06-01

    In this paper, we apply recently proposed generalized integral and differential operators to develop generalized vector calculus and generalized variational calculus for problems defined over a convex domain. In particular, we present some generalization of Green's and Gauss divergence theorems involving some new operators, and apply these theorems to generalized variational calculus. For fractional power kernels, the formulation leads to fractional vector calculus and fractional variational calculus for problems defined over a convex domain. In special cases, when certain parameters take integer values, we obtain formulations for integer order problems. Two examples are presented to demonstrate applications of the generalized variational calculus which utilize the generalized vector calculus developed in the paper. The first example leads to a generalized partial differential equation and the second example leads to a generalized eigenvalue problem, both in two dimensional convex domains. We solve the generalized partial differential equation by using polynomial approximation. A special case of the second example is a generalized isoperimetric problem. We find an approximate solution to this problem. Many physical problems containing integer order integrals and derivatives are defined over arbitrary domains. We speculate that future problems containing fractional and generalized integrals and derivatives in fractional mechanics will be defined over arbitrary domains, and therefore, a general variational calculus incorporating a general vector calculus will be needed for these problems. This research is our first attempt in that direction.

  20. Domain switching of fatigued ferroelectric thin films

    SciTech Connect

    Tak Lim, Yun; Yeog Son, Jong E-mail: hoponpop@ulsan.ac.kr; Shin, Young-Han E-mail: hoponpop@ulsan.ac.kr

    2014-05-12

    We investigate the domain wall speed of a ferroelectric PbZr{sub 0.48}Ti{sub 0.52}O{sub 3} (PZT) thin film using an atomic force microscope incorporated with a mercury-probe system to control the degree of electrical fatigue. The depolarization field in the PZT thin film decreases with increasing the degree of electrical fatigue. We find that the wide-range activation field previously reported in ferroelectric domains result from the change of the depolarization field caused by the electrical fatigue. Domain wall speed exhibits universal behavior to the effective electric field (defined by an applied electric field minus the depolarization field), regardless of the degree of the electrical fatigue.

  1. Multilevel domain decomposition for electronic structure calculations

    SciTech Connect

    Barrault, M. . E-mail: maxime.barrault@edf.fr; Cances, E. . E-mail: cances@cermics.enpc.fr; Hager, W.W. . E-mail: hager@math.ufl.edu; Le Bris, C. . E-mail: lebris@cermics.enpc.fr

    2007-03-01

    We introduce a new multilevel domain decomposition method (MDD) for electronic structure calculations within semi-empirical and density functional theory (DFT) frameworks. This method iterates between local fine solvers and global coarse solvers, in the spirit of domain decomposition methods. Using this approach, calculations have been successfully performed on several linear polymer chains containing up to 40,000 atoms and 200,000 atomic orbitals. Both the computational cost and the memory requirement scale linearly with the number of atoms. Additional speed-up can easily be obtained by parallelization. We show that this domain decomposition method outperforms the density matrix minimization (DMM) method for poor initial guesses. Our method provides an efficient preconditioner for DMM and other linear scaling methods, variational in nature, such as the orbital minimization (OM) procedure.

  2. Entropic inequalities in classical and quantum domains

    NASA Astrophysics Data System (ADS)

    Man'ko, Margarita A.

    2010-09-01

    Different kinds of entropy associated with probability distribution functions characterizing the system state in classical and quantum domains are reviewed. Shannon entropy and Rényi entropy are discussed. The notion of tomographic entropy determined by the probability distribution in the phase space of the classical system and by the density operator of the quantum system is considered. Inequalities for the tomographic entropies in classical and quantum domains are studied, and a difference in the form of these inequalities in corresponding domains is suggested as a test to clarify the classicality and quantumness of the system state in quantum optics experiments. A new bound for tomographic entropy (ln πe)Φ(θ) depending on the local oscillator phase difference in homodyne photon detection experiments is discussed.

  3. Domain walls as probes of gravity

    SciTech Connect

    Dvali, Gia; Gabadadze, Gregory; Pujolas, Oriol; Rahman, Rakibur

    2007-06-15

    We show that domain walls are probes that enable one to distinguish large-distance modified gravity from general relativity (GR) at short distances. For example, low-tension domain walls are stealth in modified gravity, while they do produce global gravitational effects in GR. We demonstrate this by finding exact solutions for various domain walls in the DGP model. A wall with tension lower than the fundamental Planck scale does not inflate and has no gravitational effects on a 4D observer, since its 4D tension is completely screened by gravity itself. We argue that this feature remains valid in a generic class of models of infrared modified gravity. As a byproduct, we obtain exact solutions for supermassive codimension-2 branes.

  4. On automating domain connectivity for overset grids

    NASA Technical Reports Server (NTRS)

    Chiu, Ing-Tsau; Meakin, Robert L.

    1995-01-01

    An alternative method for domain connectivity among systems of overset grids is presented. Reference uniform Cartesian systems of points are used to achieve highly efficient domain connectivity, and form the basis for a future fully automated system. The Cartesian systems are used to approximate body surfaces and to map the computational space of component grids. By exploiting the characteristics of Cartesian systems, Chimera type hole-cutting and identification of donor elements for intergrid boundary points can be carried out very efficiently. The method is tested for a range of geometrically complex multiple-body overset grid systems. A dynamic hole expansion/contraction algorithm is also implemented to obtain optimum domain connectivity; however, it is tested only for geometry of generic shapes.

  5. Domain Size Distribution in Segregating Binary Superfluids

    NASA Astrophysics Data System (ADS)

    Takeuchi, Hiromitsu

    2016-05-01

    Domain size distribution in phase separating binary Bose-Einstein condensates is studied theoretically by numerically solving the Gross-Pitaevskii equations at zero temperature. We show that the size distribution in the domain patterns arising from the dynamic instability obeys a power law in a scaling regime according to the dynamic scaling analysis based on the percolation theory. The scaling behavior is kept during the relaxation dynamics until the characteristic domain size becomes comparable to the linear size of the system, consistent with the dynamic scaling hypothesis of the phase-ordering kinetics. Our numerical experiments indicate the existence of a different scaling regime in the size distribution function, which can be caused by the so-called coreless vortices.

  6. On thick domain walls in general relativity

    NASA Technical Reports Server (NTRS)

    Goetz, Guenter; Noetzold, Dirk

    1989-01-01

    Planar scalar field configurations in general relativity differ considerably from those in flat space. It is shown that static domain walls of finite thickness in curved space-time do not possess a reflection symmetry. At infinity, the space-time tends to the Taub vacuum on one side of the wall and to the Minkowski vacuum (Rindler space-time) on the other. Massive test particles are always accelerated towards the Minkowski side, i.e., domain walls are attractive on the Taub side, but repulsive on the Minkowski side (Taub-vacuum cleaner). It is also proved that the pressure in all directions is always negative. Finally, a brief comment is made concerning the possibility of infinite, i.e., bigger than horizon size, domain walls in our universe. All of the results are independent of the form of the potential V(phi) greater than or equal to 0 of the scalar field phi.

  7. Time domain reflectometry in time variant plasmas

    NASA Technical Reports Server (NTRS)

    Scherner, Michael J.

    1992-01-01

    The effects of time-dependent electron density fluctuations on a synthesized time domain reflectometry response of a one-dimensional cold plasma sheath are considered. Numerical solutions of the Helmholtz wave equation, which describes the electric field of a normally incident plane wave in a specified static electron density profile, are used. A study of the effects of Doppler shifts resulting from moving density fluctuations in the electron density profile of the sheath is included. Varying electron density levels corrupt time domain and distance measurements. Reducing or modulating the electron density levels of a given electron density profile affects the time domain response of a plasma and results in motion of the turning point, and the effective motion has a significant effect on measuring electron density locations.

  8. Domain walls and the creation of strings

    NASA Astrophysics Data System (ADS)

    Bergshoeff, Eric; Gran, Ulf; Linares, Román; Nielsen, Mikkel; Roest, Diederik

    2003-08-01

    The phenomenon of creation of strings, occurring when particles pass through a domain wall and related to the Hanany Witten effect via dualities, is discussed in ten and nine dimensions. We consider both the particle actions in massive backgrounds and the 1/4-supersymmetric particle string domain-wall supergravity solutions and discuss their physical interpretation. In 10D we discuss the D0 F1 D8 system in massive IIA theory while in 9D the SL(2, Bbb R)-generalization is constructed. It consists of (p, q)-particles, (r, s)-strings and the double domain-wall solution of the three different 9D gauged supergravities where a subgroup of SL(2, Bbb R) is gauged.

  9. Targeting SH2 domains in breast cancer

    PubMed Central

    Morlacchi, Pietro; Robertson, Fredika M; Klostergaard, Jim; McMurray, John S

    2014-01-01

    Breast cancer is among the most commonly diagnosed cancer types in women worldwide and is the second leading cause of cancer-related disease in the USA. SH2 domains recruit signaling proteins to phosphotyrosine residues on aberrantly activated growth factor and cytokine receptors and contribute to cancer cell cycling, metastasis, angiogenesis and so on. Herein we review phosphopeptide mimetic and small-molecule approaches targeting the SH2 domains of Grb2, Grb7 and STAT3 that inhibit their targets and reduce proliferation in in vitro breast cancer models. Only STAT3 inhibitors have been evaluated in in vivo models and have led to tumor reduction. Taken together, these studies suggest that targeting SH2 domains is an important approach to the treatment of breast cancer. PMID:25495984

  10. Comparing and Contrasting Consensus versus Empirical Domains

    PubMed Central

    Jason, Leonard A.; Kot, Bobby; Sunnquist, Madison; Brown, Abigail; Reed, Jordan; Furst, Jacob; Newton, Julia L.; Strand, Elin Bolle; Vernon, Suzanne D.

    2015-01-01

    Background Since the publication of the CFS case definition [1], there have been a number of other criteria proposed including the Canadian Consensus Criteria [2] and the Myalgic Encephalomyelitis: International Consensus Criteria. [3] Purpose The current study compared these domains that were developed through consensus methods to one obtained through more empirical approaches using factor analysis. Methods Using data mining, we compared and contrasted fundamental features of consensus-based criteria versus empirical latent factors. In general, these approaches found the domain of Fatigue/Post-exertional malaise as best differentiating patients from controls. Results Findings indicated that the Fukuda et al. criteria had the worst sensitivity and specificity. Conclusions These outcomes might help both theorists and researchers better determine which fundamental domains to be used for the case definition. PMID:26977374

  11. Conduction at domain walls in oxide multiferroics

    SciTech Connect

    Seidel, Jan; Martin, Lane W; He, Q; Zhan, Q; Rother, A; Hawkridge, M. E.; Maksymovych, Petro; Yu, Pu; Gajek, Martin; Balke, Nina; Kalinin, Sergei V; Gemming, S; Catalan, G; Scott, J F; Spalding, Nicola A; Orenstein, J; Ramesh, R.

    2009-01-01

    Domain walls may play an important role in future electronic devices, given their small size as well as the fact that their location can be controlled. Here, we report the observation of room-temperature electronic conductivity at ferroelectric domain walls in the insulating multiferroic BiFeO{sub 3}. The origin and nature of the observed conductivity are probed using a combination of conductive atomic force microscopy, high-resolution transmission electron microscopy and first-principles density functional computations. Our analyses indicate that the conductivity correlates with structurally driven changes in both the electrostatic potential and the local electronic structure, which shows a decrease in the bandgap at the domain wall. Additionally, we demonstrate the potential for device applications of such conducting nanoscale features.

  12. A Domain Description Language for Data Processing

    NASA Technical Reports Server (NTRS)

    Golden, Keith

    2003-01-01

    We discuss an application of planning to data processing, a planning problem which poses unique challenges for domain description languages. We discuss these challenges and why the current PDDL standard does not meet them. We discuss DPADL (Data Processing Action Description Language), a language for describing planning domains that involve data processing. DPADL is a declarative, object-oriented language that supports constraints and embedded Java code, object creation and copying, explicit inputs and outputs for actions, and metadata descriptions of existing and desired data. DPADL is supported by the IMAGEbot system, which we are using to provide automation for an ecological forecasting application. We compare DPADL to PDDL and discuss changes that could be made to PDDL to make it more suitable for representing planning domains that involve data processing actions.

  13. Electric-field-driven dynamics of magnetic domain walls in magnetic nanowires patterned on ferroelectric domains

    NASA Astrophysics Data System (ADS)

    Van de Wiele, Ben; Leliaert, Jonathan; Franke, Kévin J. A.; van Dijken, Sebastiaan

    2016-03-01

    Strong coupling of magnetic domain walls onto straight ferroelastic boundaries of a ferroelectric layer enables full and reversible electric-field control of magnetic domain wall motion. In this paper, the dynamics of this new driving mechanism is analyzed using micromagnetic simulations. We show that transverse domain walls with a near-180° spin structure are stabilized in magnetic nanowires and that electric fields can move these walls with high velocities. Above a critical velocity, which depends on material parameters, nanowire geometry and the direction of domain wall motion, the magnetic domain walls depin abruptly from the ferroelastic boundaries. Depinning evolves either smoothly or via the emission and annihilation of a vortex or antivortex core (Walker breakdown). In both cases, the magnetic domain wall slows down after depinning in an oscillatory fashion and eventually comes to a halt. The simulations provide design rules for hybrid ferromagnetic-ferroelectric domain-wall-based devices and indicate that material disorder and structural imperfections only influence Walker-breakdown-like depinning at high domain wall velocities.

  14. Matter antimatter domains: A possible solution to the CP domain wall problem in the early universe

    NASA Technical Reports Server (NTRS)

    Mohanty, A. K.; Stecker, F. W.

    1984-01-01

    An SU(5) grand unified theory model is used to show how the degeneracy between vacua with different spontaneously broken charge parity can be dynamically lifted by a condensate of heavy fermion pairs. This drives a phase transition to a unique vacuum state with definite charge parity. The transition eliminates the domain walls in a matter antimatter symmetric domain cosmology.

  15. Structural basis for the regulation of enzymatic activity of Regnase-1 by domain-domain interactions

    PubMed Central

    Yokogawa, Mariko; Tsushima, Takashi; Noda, Nobuo N.; Kumeta, Hiroyuki; Enokizono, Yoshiaki; Yamashita, Kazuo; Standley, Daron M.; Takeuchi, Osamu; Akira, Shizuo; Inagaki, Fuyuhiko

    2016-01-01

    Regnase-1 is an RNase that directly cleaves mRNAs of inflammatory genes such as IL-6 and IL-12p40, and negatively regulates cellular inflammatory responses. Here, we report the structures of four domains of Regnase-1 from Mus musculus—the N-terminal domain (NTD), PilT N-terminus like (PIN) domain, zinc finger (ZF) domain and C-terminal domain (CTD). The PIN domain harbors the RNase catalytic center; however, it is insufficient for enzymatic activity. We found that the NTD associates with the PIN domain and significantly enhances its RNase activity. The PIN domain forms a head-to-tail oligomer and the dimer interface overlaps with the NTD binding site. Interestingly, mutations blocking PIN oligomerization had no RNase activity, indicating that both oligomerization and NTD binding are crucial for RNase activity in vitro. These results suggest that Regnase-1 RNase activity is tightly controlled by both intramolecular (NTD-PIN) and intermolecular (PIN-PIN) interactions. PMID:26927947

  16. Continuous and discontinuous domains: an algorithm for the automatic generation of reliable protein domain definitions.

    PubMed Central

    Siddiqui, A. S.; Barton, G. J.

    1995-01-01

    An algorithm is presented for the fast and accurate definition of protein structural domains from coordinate data without prior knowledge of the number or type of domains. The algorithm explicitly locates domains that comprise one or two continuous segments of protein chain. Domains that include more than two segments are also located. The algorithm was applied to a nonredundant database of 230 protein structures and the results compared to domain definitions obtained from the literature, or by inspection of the coordinates on molecular graphics. For 70% of the proteins, the derived domains agree with the reference definitions, 18% show minor differences and only 12% (28 proteins) show very different definitions. Three screens were applied to identify the derived domains least likely to agree with the subjective definition set. These screens revealed a set of 173 proteins, 97% of which agree well with the subjective definitions. The algorithm represents a practical domain identification tool that can be run routinely on the entire structural database. Adjustment of parameters also allows smaller compact units to be identified in proteins. PMID:7663343

  17. Intellectual Growth in Children as a Function of Domain Specific and Domain General Working Memory Subgroups

    ERIC Educational Resources Information Center

    Swanson, H. Lee

    2011-01-01

    This study examined whether children's growth on measures of fluid (Raven Colored Progressive Matrices) and crystallized (reading and math achievement) intelligence was attributable to domain-specific or domain-general functions of working memory (WM). A sample of 290 elementary school children was tested on measures of intelligence across three…

  18. Application of modern tensor calculus to engineered domain structures. 2. Tensor distinction of domain states.

    PubMed

    Kopský, Vojtech

    2006-03-01

    The theory of domain states is reviewed as a prerequisite for consideration of tensorial distinction of domain states. It is then shown that the parameters of the first domain in a ferroic phase transition from a set of isomorphic groups of the same oriented Laue class can be systematically and suitably represented in terms of typical variables. On replacing these variables by actual tensor components according to the previous paper, we can reveal the tensorial parameters associated with each particular symmetry descent. Parameters are distinguished by the ireps to which they belong and this can be used to determine which of them are the principal parameters that distinguish all domain states, in contrast to secondary parameters which are common to several domain states. In general, the parameters are expressed as the covariant components of the tensors. A general procedure is described which is designed to transform the results to Cartesian components. It consists of two parts: the first, called the labelling of covariants, and its inverse, called the conversion equations. Transformation of parameters from the first domain state to other states is now reduced to irreducible subspaces whose maximal dimension is three in contrast with higher dimensions of tensor spaces. With this method, we can explicitly calculate tensor parameters for all domain states. To find the distinction of pairs of domain states, it is suitable to use the concept of the twinning group which is briefly described. PMID:16489243

  19. Conducting Ferroelectric Walls, Domain Topology, and Domain Switching Kinetics in a Hybrid Improper Ferroelectric

    NASA Astrophysics Data System (ADS)

    Cheong, Sang-Wook; Rutgers Center For Emergent Materials Team

    Charged polar interfaces such as charged ferroelectric domain walls or heterostructured interfaces of ZnO/(Zn,Mg)O and LaAlO 3 /SrTiO 3 , across which the normal component of electric polarization changes suddenly, can host large two-dimensional conduction. Charged ferroelectric domain walls can be highly conducting but energetically unfavored; however, they were found to be mysteriously abundant in hybrid improper ferroelectric (Ca,Sr) 3 Ti 2 O 7 single crystals. From the exploration of antiphase domain boundaries, which are hidden in piezoresponse force microscopy, using dark-field electron microscopy, we have explored the macroscopic topology of polarization domains and antiphase domains. We found that the macroscopic domain topology is directly responsible for the presence of charged domain walls, and is closely related with the polarization domain switching mechanism in (Ca,Sr) 3 Ti 2 O 7 . Rutgers Center for Emergent Materials and Department of Physics and Astronomy, Rutgers University, Piscataway, New Jersey 08854, USA.

  20. SH3 Domains Differentially Stimulate Distinct Dynamin I Assembly Modes and G Domain Activity

    PubMed Central

    Krishnan, Sai; Collett, Michael; Robinson, Phillip J.

    2015-01-01

    Dynamin I is a highly regulated GTPase enzyme enriched in nerve terminals which mediates vesicle fission during synaptic vesicle endocytosis. One regulatory mechanism involves its interactions with proteins containing Src homology 3 (SH3) domains. At least 30 SH3 domain-containing proteins bind dynamin at its proline-rich domain (PRD). Those that stimulate dynamin activity act by promoting its oligomerisation. We undertook a systematic parallel screening of 13 glutathione-S-transferase (GST)-tagged endocytosis-related SH3 domains on dynamin binding, GTPase activity and oligomerisation. No correlation was found between dynamin binding and their potency to stimulate GTPase activity. There was limited correlation between the extent of their ability to stimulate dynamin activity and the level of oligomerisation, indicating an as yet uncharacterised allosteric coupling of the PRD and G domain. We examined the two variants, dynamin Iab and Ibb, which differ in the alternately splice middle domain α2 helix. They responded differently to the panel of SH3s, with the extent of stimulation between the splice variants varying greatly between the SH3s. This study reveals that SH3 binding can act as a heterotropic allosteric regulator of the G domain via the middle domain α2 helix, suggesting an involvement of this helix in communicating the PRD-mediated allostery. This indicates that SH3 binding both stabilises multiple conformations of the tetrameric building block of dynamin, and promotes assembly of dynamin-SH3 complexes with distinct rates of GTP hydrolysis. PMID:26659814

  1. Structural basis for the regulation of enzymatic activity of Regnase-1 by domain-domain interactions.

    PubMed

    Yokogawa, Mariko; Tsushima, Takashi; Noda, Nobuo N; Kumeta, Hiroyuki; Enokizono, Yoshiaki; Yamashita, Kazuo; Standley, Daron M; Takeuchi, Osamu; Akira, Shizuo; Inagaki, Fuyuhiko

    2016-01-01

    Regnase-1 is an RNase that directly cleaves mRNAs of inflammatory genes such as IL-6 and IL-12p40, and negatively regulates cellular inflammatory responses. Here, we report the structures of four domains of Regnase-1 from Mus musculus-the N-terminal domain (NTD), PilT N-terminus like (PIN) domain, zinc finger (ZF) domain and C-terminal domain (CTD). The PIN domain harbors the RNase catalytic center; however, it is insufficient for enzymatic activity. We found that the NTD associates with the PIN domain and significantly enhances its RNase activity. The PIN domain forms a head-to-tail oligomer and the dimer interface overlaps with the NTD binding site. Interestingly, mutations blocking PIN oligomerization had no RNase activity, indicating that both oligomerization and NTD binding are crucial for RNase activity in vitro. These results suggest that Regnase-1 RNase activity is tightly controlled by both intramolecular (NTD-PIN) and intermolecular (PIN-PIN) interactions. PMID:26927947

  2. Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations

    PubMed Central

    Lund, Eivind; Oldenburg, Anja R.; Collas, Philippe

    2014-01-01

    Nuclear lamins contact the genome at the nuclear periphery through large domains and are involved in chromatin organization. Among broad peak calling algorithms available to date, none are suited for mapping lamin–genome interactions genome wide. We disclose a novel algorithm, enriched domain detector (EDD), for analysis of broad enrichment domains from chromatin immunoprecipitation (ChIP)-seq data. EDD enables discovery of genomic domains interacting with broadly distributed proteins, such as A- and B-type lamins affinity isolated by ChIP. The advantages of EDD over existing broad peak callers are sensitivity to domain width rather than enrichment strength at a particular site, and robustness against local variations. PMID:24782521

  3. A non-chromatographic protein purification strategy using Src 3 homology domains as generalized capture domains.

    PubMed

    Kim, Heejae; Chen, Wilfred

    2016-09-20

    Protein purification using inverse phase transition of elastin-like polypeptide (ELP) domains is a useful alternative to chromatography. Genetic fusions of ELP domains to various proteins have the ability to reversibly transition between soluble monomers and micron-sized aggregates and this has been used to selectively purify many ELP fusions. Affinity domains can enhance this technology by using specific protein binding domains to enable ELP mediated affinity capture (EMAC) of proteins of interest (POI) that have been fused to corresponding affinity ligands. In this paper, we highlight the use of Src homology 3 (SH3) domains and corresponding peptide ligands in EMAC that have differential binding affinities towards SH3 for efficient capture and elution of proteins. Furthermore, differences between capture and elution of a monomeric and a multimeric protein were also studied. PMID:27457699

  4. Elongation factor TFIIS contains three structural domains: solution structure of domain II.

    PubMed Central

    Morin, P E; Awrey, D E; Edwards, A M; Arrowsmith, C H

    1996-01-01

    Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. Limited proteolytic digestion showed that yeast TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III) are required for transcription activity. The structure of domain III has been solved previously by using NMR spectroscopy. Here, we report the NMR-derived structure of domain II: a three-helix bundle built around a hydrophobic core composed largely of three tyrosines protruding from one face of the C-terminal helix. The arrangement of known inactivating mutations of TFIIS suggests that two surfaces of domain II are critical for transcription activity. Images Fig. 1 Fig. 2 Fig. 3 PMID:8855225

  5. On automating domain connectivity for overset grids

    NASA Technical Reports Server (NTRS)

    Chiu, Ing-Tsau

    1994-01-01

    An alternative method for domain connectivity among systems of overset grids is presented. Reference uniform Cartesian systems of points are used to achieve highly efficient domain connectivity, and form the basis for a future fully automated system. The Cartesian systems are used to approximated body surfaces and to map the computational space of component grids. By exploiting the characteristics of Cartesian Systems, Chimera type hole-cutting and identification of donor elements for intergrid boundary points can be carried out very efficiently. The method is tested for a range of geometrically complex multiple-body overset grid systems.

  6. Time-domain Raman analytical forward solvers.

    PubMed

    Martelli, Fabrizio; Binzoni, Tiziano; Sekar, Sanathana Konugolu Venkata; Farina, Andrea; Cavalieri, Stefano; Pifferi, Antonio

    2016-09-01

    A set of time-domain analytical forward solvers for Raman signals detected from homogeneous diffusive media is presented. The time-domain solvers have been developed for two geometries: the parallelepiped and the finite cylinder. The potential presence of a background fluorescence emission, contaminating the Raman signal, has also been taken into account. All the solvers have been obtained as solutions of the time dependent diffusion equation. The validation of the solvers has been performed by means of comparisons with the results of "gold standard" Monte Carlo simulations. These forward solvers provide an accurate tool to explore the information content encoded in the time-resolved Raman measurements. PMID:27607645

  7. Biodiversity of voltage sensor domain proteins.

    PubMed

    Okamura, Yasushi

    2007-06-01

    The six-transmembrane type voltage-gated ion channels play an essential role in neuronal excitability, muscle contraction, and secretion. The voltage sensor domain (VSD) is the key element of voltage-gated ion channels for sensing transmembrane potential, and has been studied at the levels of both biophysics and protein structure. Two recently identified proteins containing VSD without a pore domain showed unexpected biological roles: regulation of phosphatase activity and proton permeation. These proteins not only provide novel platforms to understand mechanisms of voltage sensing and ion permeation but also highlight previously unappreciated roles of membrane potential in non-neuronal cells. PMID:17347852

  8. Convergence Analysis of a Domain Decomposition Paradigm

    SciTech Connect

    Bank, R E; Vassilevski, P S

    2006-06-12

    We describe a domain decomposition algorithm for use in several variants of the parallel adaptive meshing paradigm of Bank and Holst. This algorithm has low communication, makes extensive use of existing sequential solvers, and exploits in several important ways data generated as part of the adaptive meshing paradigm. We show that for an idealized version of the algorithm, the rate of convergence is independent of both the global problem size N and the number of subdomains p used in the domain decomposition partition. Numerical examples illustrate the effectiveness of the procedure.

  9. Casimir forces in the time domain: Theory

    SciTech Connect

    Rodriguez, Alejandro W.; McCauley, Alexander P.; Joannopoulos, John D.; Johnson, Steven G.

    2009-07-15

    We present a method to compute Casimir forces in arbitrary geometries and for arbitrary materials based on the finite-difference time-domain (FDTD) scheme. The method involves the time evolution of electric and magnetic fields in response to a set of current sources, in a modified medium with frequency-independent conductivity. The advantage of this approach is that it allows one to exploit existing FDTD software, without modification, to compute Casimir forces. In this paper, we focus on the derivation, implementation choices, and essential properties of the time-domain algorithm, both considered analytically and illustrated in the simplest parallel-plate geometry.

  10. Standing gravitational waves from domain walls

    SciTech Connect

    Gogberashvili, Merab; Myrzakul, Shynaray; Singleton, Douglas

    2009-07-15

    We construct a plane symmetric, standing gravitational wave for a domain wall plus a massless scalar field. The scalar field can be associated with a fluid which has the properties of 'stiff' matter, i.e., matter in which the speed of sound equals the speed of light. Although domain walls are observationally ruled out in the present era, the solution has interesting features which might shed light on the character of exact nonlinear wave solutions to Einstein's equations. Additionally this solution may act as a template for higher dimensional 'brane-world' model standing waves.

  11. Detector nonlinearity in frequency-domain fluorometry.

    PubMed

    Wirth, M J; Burbage, J D; Zulli, S L

    1993-02-20

    Frequency-domain fluorometry relies on the measurement of the phase and amplitudes of the Fourier components of the time-dependent fluorescence signal. Experimental results that show that a conventional photomultiplier is subject to intensity-dependent phase shifts are presented. The measurements indicate that this is a problem well below the maximum linear current of the photomultiplier response. These results have important implications in frequency-domain fluorescence anisotropy experiments, in which the parallel and the perpendicular components of the emission intensity are inherently different from one another: a phase shift can be introduced by the photomultiplier. PMID:20802776

  12. [Development of domain specific search engines].

    PubMed

    Takai, T; Tokunaga, M; Maeda, K; Kaminuma, T

    2000-01-01

    As cyber space exploding in a pace that nobody has ever imagined, it becomes very important to search cyber space efficiently and effectively. One solution to this problem is search engines. Already a lot of commercial search engines have been put on the market. However these search engines respond with such cumbersome results that domain specific experts can not tolerate. Using a dedicate hardware and a commercial software called OpenText, we have tried to develop several domain specific search engines. These engines are for our institute's Web contents, drugs, chemical safety, endocrine disruptors, and emergent response for chemical hazard. These engines have been on our Web site for testing. PMID:11534132

  13. Predicting detection performance with model observers: Fourier domain or spatial domain?

    NASA Astrophysics Data System (ADS)

    Chen, Baiyu; Yu, Lifeng; Leng, Shuai; Kofler, James; Favazza, Christopher; Vrieze, Thomas; McCollough, Cynthia

    2016-03-01

    The use of Fourier domain model observer is challenged by iterative reconstruction (IR), because IR algorithms are nonlinear and IR images have noise texture different from that of FBP. A modified Fourier domain model observer, which incorporates nonlinear noise and resolution properties, has been proposed for IR and needs to be validated with human detection performance. On the other hand, the spatial domain model observer is theoretically applicable to IR, but more computationally intensive than the Fourier domain method. The purpose of this study is to compare the modified Fourier domain model observer to the spatial domain model observer with both FBP and IR images, using human detection performance as the gold standard. A phantom with inserts of various low contrast levels and sizes was repeatedly scanned 100 times on a third-generation, dual-source CT scanner at 5 dose levels and reconstructed using FBP and IR algorithms. The human detection performance of the inserts was measured via a 2-alternative-forced-choice (2AFC) test. In addition, two model observer performances were calculated, including a Fourier domain non-prewhitening model observer and a spatial domain channelized Hotelling observer. The performance of these two mode observers was compared in terms of how well they correlated with human observer performance. Our results demonstrated that the spatial domain model observer correlated well with human observers across various dose levels, object contrast levels, and object sizes. The Fourier domain observer correlated well with human observers using FBP images, but overestimated the detection performance using IR images.

  14. Predicting detection performance with model observers: Fourier domain or spatial domain?

    PubMed Central

    Chen, Baiyu; Yu, Lifeng; Leng, Shuai; Kofler, James; Favazza, Christopher; Vrieze, Thomas; McCollough, Cynthia

    2016-01-01

    The use of Fourier domain model observer is challenged by iterative reconstruction (IR), because IR algorithms are nonlinear and IR images have noise texture different from that of FBP. A modified Fourier domain model observer, which incorporates nonlinear noise and resolution properties, has been proposed for IR and needs to be validated with human detection performance. On the other hand, the spatial domain model observer is theoretically applicable to IR, but more computationally intensive than the Fourier domain method. The purpose of this study is to compare the modified Fourier domain model observer to the spatial domain model observer with both FBP and IR images, using human detection performance as the gold standard. A phantom with inserts of various low contrast levels and sizes was repeatedly scanned 100 times on a third-generation, dual-source CT scanner at 5 dose levels and reconstructed using FBP and IR algorithms. The human detection performance of the inserts was measured via a 2-alternative-forced-choice (2AFC) test. In addition, two model observer performances were calculated, including a Fourier domain non-prewhitening model observer and a spatial domain channelized Hotelling observer. The performance of these two mode observers was compared in terms of how well they correlated with human observer performance. Our results demonstrated that the spatial domain model observer correlated well with human observers across various dose levels, object contrast levels, and object sizes. The Fourier domain observer correlated well with human observers using FBP images, but overestimated the detection performance using IR images. PMID:27239086

  15. Rsp5 WW domains interact directly with the carboxyl-terminal domain of RNA polymerase II.

    PubMed

    Chang, A; Cheang, S; Espanel, X; Sudol, M

    2000-07-01

    RSP5 is an essential gene in Saccharomyces cerevisiae and was recently shown to form a physical and functional complex with RNA polymerase II (RNA pol II). The amino-terminal half of Rsp5 consists of four domains: a C2 domain, which binds membrane phospholipids; and three WW domains, which are protein interaction modules that bind proline-rich ligands. The carboxyl-terminal half of Rsp5 contains a HECT (homologous to E6-AP carboxyl terminus) domain that catalytically ligates ubiquitin to proteins and functionally classifies Rsp5 as an E3 ubiquitin-protein ligase. The C2 and WW domains are presumed to act as membrane localization and substrate recognition modules, respectively. We report that the second (and possibly third) Rsp5 WW domain mediates binding to the carboxyl-terminal domain (CTD) of the RNA pol II large subunit. The CTD comprises a heptamer (YSPTSPS) repeated 26 times and a PXY core that is critical for interaction with a specific group of WW domains. An analysis of synthetic peptides revealed a minimal CTD sequence that is sufficient to bind to the second Rsp5 WW domain (Rsp5 WW2) in vitro and in yeast two-hybrid assays. Furthermore, we found that specific "imperfect" CTD repeats can form a complex with Rsp5 WW2. In addition, we have shown that phosphorylation of this minimal CTD sequence on serine, threonine and tyrosine residues acts as a negative regulator of the Rsp5 WW2-CTD interaction. In view of the recent data pertaining to phosphorylation-driven interactions between the RNA pol II CTD and the WW domain of Ess1/Pin1, we suggest that CTD dephosphorylation may be a prerequisite for targeted RNA pol II degradation. PMID:10781604

  16. A PH domain in ACAP1 possesses key features of the BAR domain in promoting membrane curvature.

    PubMed

    Pang, Xiaoyun; Fan, Jun; Zhang, Yan; Zhang, Kai; Gao, Bingquan; Ma, Jun; Li, Jian; Deng, Yuchen; Zhou, Qiangjun; Egelman, Edward H; Hsu, Victor W; Sun, Fei

    2014-10-13

    The BAR (Bin-Amphiphysin-Rvs) domain undergoes dimerization to produce a curved protein structure, which superimposes onto membrane through electrostatic interactions to sense and impart membrane curvature. In some cases, a BAR domain also possesses an amphipathic helix that inserts into the membrane to induce curvature. ACAP1 (Arfgap with Coil coil, Ankyrin repeat, and PH domain protein 1) contains a BAR domain. Here, we show that this BAR domain can neither bind membrane nor impart curvature, but instead requires a neighboring PH (Pleckstrin Homology) domain to achieve these functions. Specific residues within the PH domain are responsible for both membrane binding and curvature generation. The BAR domain adjacent to the PH domain instead interacts with the BAR domains of neighboring ACAP1 proteins to enable clustering at the membrane. Thus, we have uncovered the molecular basis for an unexpected and unconventional collaboration between PH and BAR domains in membrane bending. PMID:25284369

  17. Critical role of domain crystallinity, domain purity and domain interface sharpness for reduced bimolecular recombination in polymer solar cells

    DOE PAGESBeta

    Venkatesan, Swaminathan; Chen, Jihua; Ngo, Evan C.; Dubey, Ashish; Khatiwada, Devendra; Zhang, Cheng; Qiao, Qiquan

    2014-12-31

    In this study, inverted bulk heterojunction solar cells were fabricated using poly(3-hexylthiophene) (P3HT) blended with two different fullerene derivatives namely phenyl-C61-butyric acid methyl ester (PC60BM) and indene-C60 bis-adduct (IC60BA). The effects of annealing temperatures on the morphology, optical and structural properties were studied and correlated to differences in photovoltaic device performance. It was observed that annealing temperature significantly improved the performance of P3HT:IC60BA solar cells while P3HT:PC60BM cells showed relatively less improvement. The performance improvement is attributed to the extent of fullerene mixing with polymer domains. Energy filtered transmission electron microscopy (EFTEM) and x-ray diffraction (XRD) results showed that ICBAmore » mixes with disordered P3HT much more readily than PC60BM which leads to lower short circuit current density and fill factor for P3HT:IC60BA cells annealed below 120°C. Annealing above 120°C improves the crystallinity of P3HT in case of P3HT:IC60BA whereas in P3HT:PC60BM films, annealing above 80°C leads to negligible change in crystallinity. Crystallization of P3HT also leads to higher domain purity as seen EFTEM. Further it is seen that cells processed with additive nitrobenzene (NB) showed enhanced short circuit current density and power conversion efficiency regardless of the fullerene derivative used. Addition of NB led to nanoscale phase separation between purer polymer and fullerene domains. Kelvin probe force microscopy (KPFM) images showed that enhanced domain purity in additive casted films led to a sharper interface between polymer and fullerene. Lastly, enhanced domain purity and interfacial sharpness led to lower bimolecular recombination and higher mobility and charge carrier lifetime in NB modified devices.« less

  18. The Loyal Opposition Comments on Plan Domain Description Languages

    NASA Technical Reports Server (NTRS)

    Frank, Jeremy; Golden, Keith; Jonsson, Ari

    2003-01-01

    In this paper we take a critical look at PDDL 2.1 as designers and users of plan domain description languages. We describe planning domains that have features which are hard to model using PDDL 2.1. We then offer some suggestions on domain description language design, and describe how these suggestions make modeling our chosen domains easier.

  19. Reporting Valid and Reliable Overall Scores and Domain Scores

    ERIC Educational Resources Information Center

    Yao, Lihua

    2010-01-01

    In educational assessment, overall scores obtained by simply averaging a number of domain scores are sometimes reported. However, simply averaging the domain scores ignores the fact that different domains have different score points, that scores from those domains are related, and that at different score points the relationship between overall…

  20. Conceptualizing Indicator Domains for Evaluating Action Research

    ERIC Educational Resources Information Center

    Piggot-Irvine, Eileen; Rowe, Wendy; Ferkins, Lesley

    2015-01-01

    The focus of this paper is to share thinking about meta-level evaluation of action research (AR), and to introduce indicator domains for assessing and measuring inputs, outputs and outcomes. Meta-level and multi-site evaluation has been rare in AR beyond project implementation and participant satisfaction. The paper is the first of several…

  1. Value Added Reselling and Public Domain Data.

    ERIC Educational Resources Information Center

    Davenport, Lizzie; Cronin, Blaise

    1987-01-01

    Discusses the reasons behind the trend of distribution of public domain statistics by private, commercial agencies in the United States and Great Britain, identifies marketable materials and marketing strategies, and explores possible disadvantages in terms of the public good and the possibility that governments will no longer collect statistical…

  2. Factor Score Reliabilities and Domain Validities.

    ERIC Educational Resources Information Center

    Gorsuch, Richard L.

    1980-01-01

    Kaiser and Michael reported a formula for factor scores giving an internal consistency reliability and its square root, the domain validity. Using this formula is inappropriate if variables are included which have trival weights rather than salient weights for the factor for which the score is being computed. (Author/RL)

  3. Domain General Constraints on Statistical Learning

    ERIC Educational Resources Information Center

    Thiessen, Erik D.

    2011-01-01

    All theories of language development suggest that learning is constrained. However, theories differ on whether these constraints arise from language-specific processes or have domain-general origins such as the characteristics of human perception and information processing. The current experiments explored constraints on statistical learning of…

  4. Promoting the Affective Domain within Online Education

    ERIC Educational Resources Information Center

    Roche, Stephen H.

    2013-01-01

    In the past decade Higher Education Institutions have experienced tremendous growth in enrollments. To meet this demand, many higher education institutions have embraced online education and its requisite technologies. Online education has matured, and studies focusing on the cognitive domain indicate that distance education is as effective as the…

  5. The Different Roles of Aggrecan Interaction Domains

    PubMed Central

    2012-01-01

    The aggregating proteoglycans of the lectican family are important components of extracellular matrices. Aggrecan is the most well studied of these and is central to cartilage biomechanical properties and skeletal development. Key to its biological function is the fixed charge of the many glycosaminoglycan chains, that provide the basis for the viscoelastic properties necessary for load distribution over the articular surface. This review is focused on the globular domains of aggrecan and their role in anchoring the proteoglycans to other extracellular matrix components. The N-terminal G1 domain is vital in that it binds the proteoglycan to hyaluronan in ternary complex with link protein, retaining the proteoglycan in the tissue. The importance of the C-terminal G3 domain interactions has recently been emphasized by two different human hereditary disorders: autosomal recessive aggrecan-type spondyloepimetaphyseal dysplasia and autosomal dominant familial osteochondritis dissecans. In these two conditions, different missense mutations in the aggrecan C-type lectin repeat have been described. The resulting amino acid replacements affect the ligand interactions of the G3 domain, albeit with widely different phenotypic outcomes. PMID:23019016

  6. Kinesin tail domains are intrinsically disordered.

    PubMed

    Seeger, Mark A; Zhang, Yongbo; Rice, Sarah E

    2012-10-01

    Kinesin motor proteins transport a wide variety of molecular cargoes in a spatially and temporally regulated manner. Kinesin motor domains, which hydrolyze ATP to produce a directed mechanical force along a microtubule, are well conserved throughout the entire superfamily. Outside of the motor domains, kinesin sequences diverge along with their transport functions. The nonmotor regions, particularly the tails, respond to a wide variety of structural and molecular cues that enable kinesins to carry specific cargoes in response to particular cellular signals. Here, we demonstrate that intrinsic disorder is a common structural feature of kinesins. A bioinformatics survey of the full-length sequences of all 43 human kinesins predicts that significant regions of intrinsically disordered residues are present in all kinesins. These regions are concentrated in the nonmotor domains, particularly in the tails and near sites for ligand binding or post-translational modifications. In order to experimentally verify these predictions, we expressed and purified the tail domains of kinesins representing three different families (Kif5B, Kif10, and KifC3). Circular dichroism and NMR spectroscopy experiments demonstrate that the isolated tails are disordered in vitro, yet they retain their functional microtubule-binding activity. On the basis of these results, we propose that intrinsic disorder is a common structural feature that confers functional specificity to kinesins. PMID:22674872

  7. Kinesin Tail Domains Are Intrinsically Disordered

    PubMed Central

    Seeger, Mark A.; Zhang, Yongbo; Rice, Sarah E.

    2012-01-01

    Kinesin motor proteins transport a wide variety of molecular cargoes in a spatially and temporally regulated manner. Kinesin motor domains, which hydrolyze ATP to produce a directed mechanical force along a microtubule, are well conserved throughout the entire superfamily. Outside of the motor domains, kinesin sequences diverge along with their transport functions. The non-motor regions, particularly the tails, respond to a wide variety of structural and molecular cues that enable kinesins to carry specific cargoes in response to particular cellular signals. Here, we demonstrate that intrinsic disorder is a common structural feature of kinesins. A bioinformatics survey of the full-length sequences of all 43 human kinesins predicts that significant regions of intrinsically disordered residues are present in all kinesins. These regions are concentrated in the non-motor domains, particularly in the tails and near sites for ligand binding or post-translational modifications. In order to experimentally verify these predictions, we expressed and purified the tail domains of kinesins representing three different families (Kif5B, Kif10, and KifC3). Circular dichroism (CD) and NMR spectroscopy experiments demonstrate that the isolated tails are disordered in vitro, yet they retain their functional microtubule-binding activity. Based on these results, we propose that intrinsic disorder is a common structural feature that confers functional specificity to kinesins. PMID:22674872

  8. Microdissection of Shoot Meristem Functional Domains

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The shoot apical meristem (SAM) maintains a pool of indeterminate cells within the SAM proper, while lateral organs are initiated from the SAM periphery. Laser microdissection–microarray technology was used to compare transcriptional profiles within these SAM domains to identify novel maize genes th...

  9. Efficient integration method for fictitious domain approaches

    NASA Astrophysics Data System (ADS)

    Duczek, Sascha; Gabbert, Ulrich

    2015-10-01

    In the current article, we present an efficient and accurate numerical method for the integration of the system matrices in fictitious domain approaches such as the finite cell method (FCM). In the framework of the FCM, the physical domain is embedded in a geometrically larger domain of simple shape which is discretized using a regular Cartesian grid of cells. Therefore, a spacetree-based adaptive quadrature technique is normally deployed to resolve the geometry of the structure. Depending on the complexity of the structure under investigation this method accounts for most of the computational effort. To reduce the computational costs for computing the system matrices an efficient quadrature scheme based on the divergence theorem (Gauß-Ostrogradsky theorem) is proposed. Using this theorem the dimension of the integral is reduced by one, i.e. instead of solving the integral for the whole domain only its contour needs to be considered. In the current paper, we present the general principles of the integration method and its implementation. The results to several two-dimensional benchmark problems highlight its properties. The efficiency of the proposed method is compared to conventional spacetree-based integration techniques.

  10. Adaptive Random Testing with Combinatorial Input Domain

    PubMed Central

    Lu, Yansheng

    2014-01-01

    Random testing (RT) is a fundamental testing technique to assess software reliability, by simply selecting test cases in a random manner from the whole input domain. As an enhancement of RT, adaptive random testing (ART) has better failure-detection capability and has been widely applied in different scenarios, such as numerical programs, some object-oriented programs, and mobile applications. However, not much work has been done on the effectiveness of ART for the programs with combinatorial input domain (i.e., the set of categorical data). To extend the ideas to the testing for combinatorial input domain, we have adopted different similarity measures that are widely used for categorical data in data mining and have proposed two similarity measures based on interaction coverage. Then, we propose a new version named ART-CID as an extension of ART in combinatorial input domain, which selects an element from categorical data as the next test case such that it has the lowest similarity against already generated test cases. Experimental results show that ART-CID generally performs better than RT, with respect to different evaluation metrics. PMID:24772036

  11. The formation and evolution of domain walls

    NASA Technical Reports Server (NTRS)

    Press, William H.; Ryden, Barbara S.; Spergel, David N.

    1991-01-01

    Domain walls are sheet-like defects produced when the low energy vacuum has isolated degenerate minima. The researchers' computer code follows the evolution of a scalar field, whose dynamics are determined by its Lagrangian density. The topology of the scalar field determines the evolution of the domain walls. This approach treats both wall dynamics and reconnection. The researchers investigated not only potentials that produce single domain walls, but also potentials that produce a network of walls and strings. These networks arise in axion models where the U(1) Peccei-Quinn symmetry is broken into Z sub N discrete symmetries. If N equals 1, the walls are bounded by strings and the network quickly disappears. For N greater than 1, the network of walls and strings behaved qualitatively just as the wall network shown in the figures given here. This both confirms the researchers' pessimistic view that domain walls cannot play an important role in the formation of large scale structure and implies that axion models with multiple minimum can be cosmologically disastrous.

  12. Behavior Domains in Theory and in Practice

    ERIC Educational Resources Information Center

    McDonald, Roderick P.

    2003-01-01

    The concept of a behavior domain is a reasonable and essential foundation for psychometric work based on true score theory, the linear model of common factor analysis, and the nonlinear models of item response theory. Investigators applying these models to test data generally treat the true scores or factors or traits as abstractive psychological…

  13. Time-Domain Simulation of RF Couplers

    SciTech Connect

    Smithe, David; Carlsson, Johan; Austin, Travis

    2009-11-26

    We have developed a finite-difference time-domain (FDTD) fluid-like approach to integrated plasma-and-coupler simulation [1], and show how it can be used to model LH and ICRF couplers in the MST and larger tokamaks.[2] This approach permits very accurate 3-D representation of coupler geometry, and easily includes non-axi-symmetry in vessel wall, magnetic equilibrium, and plasma density. The plasma is integrated with the FDTD Maxwell solver in an implicit solve that steps over electron time-scales, and permits tenuous plasma in the coupler itself, without any need to distinguish or interface between different regions of vacuum and/or plasma. The FDTD algorithm is also generalized to incorporate a time-domain sheath potential [3] on metal structures within the simulation, to look for situations where the sheath potential might generate local sputtering opportunities. Benchmarking of the time-domain sheath algorithm has been reported in the references. Finally, the time-domain software [4] permits the use of particles, either as field diagnostic (test particles) or to self-consistently compute plasma current from the applied RF power.

  14. The Fourth Domain of Educational Objectives: Induction.

    ERIC Educational Resources Information Center

    Holleman, Wes

    1985-01-01

    Tests the claim to comprehensiveness of Bloom's taxonomy of educational objectives by analyzing educational objectives of some freshmen orientation programs and those connected with human developmental tasks. It is concluded that the taxonomy should be enlarged with a fourth domain: actual induction into tasks for which students are being…

  15. Nucleic acids encoding a cellulose binding domain

    DOEpatents

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc A.; Doi, Roy H.

    1996-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  16. Nucleic acids encoding a cellulose binding domain

    DOEpatents

    Shoseyov, O.; Shpiegl, I.; Goldstein, M.A.; Doi, R.H.

    1996-03-05

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 15 figs.

  17. Public Domain Microcomputer Software for Forestry.

    ERIC Educational Resources Information Center

    Martin, Les

    A project was conducted to develop a computer forestry/forest products bibliography applicable to high school and community college vocational/technical programs. The project director contacted curriculum clearinghouses, computer companies, and high school and community college instructors in order to obtain listings of public domain programs for…

  18. Memetic Algorithms, Domain Knowledge, and Financial Investing

    ERIC Educational Resources Information Center

    Du, Jie

    2012-01-01

    While the question of how to use human knowledge to guide evolutionary search is long-recognized, much remains to be done to answer this question adequately. This dissertation aims to further answer this question by exploring the role of domain knowledge in evolutionary computation as applied to real-world, complex problems, such as financial…

  19. Domain structure of Fe-based microwires

    NASA Astrophysics Data System (ADS)

    Baranov, S. A.; Laroze, D.; Vargas, P.; Vazquez, M.

    2006-02-01

    Some magnetic characteristics of the Fe-based cast amorphous glass-coated microwires with positive magnetostriction constant are investigated. The residual stress distributions in this type of microwires determine the domain structures and the switching field behavior; in particular, we present a phenomenological law of its temperature dependence, which has a very good agreement with the experimental data.

  20. An English language interface for constrained domains

    NASA Technical Reports Server (NTRS)

    Page, Brenda J.

    1989-01-01

    The Multi-Satellite Operations Control Center (MSOCC) Jargon Interpreter (MJI) demonstrates an English language interface for a constrained domain. A constrained domain is defined as one with a small and well delineated set of actions and objects. The set of actions chosen for the MJI is from the domain of MSOCC Applications Executive (MAE) Systems Test and Operations Language (STOL) directives and contains directives for signing a cathode ray tube (CRT) on or off, calling up or clearing a display page, starting or stopping a procedure, and controlling history recording. The set of objects chosen consists of CRTs, display pages, STOL procedures, and history files. Translation from English sentences to STOL directives is done in two phases. In the first phase, an augmented transition net (ATN) parser and dictionary are used for determining grammatically correct parsings of input sentences. In the second phase, grammatically typed sentences are submitted to a forward-chaining rule-based system for interpretation and translation into equivalent MAE STOL directives. Tests of the MJI show that it is able to translate individual clearly stated sentences into the subset of directives selected for the prototype. This approach to an English language interface may be used for similarly constrained situations by modifying the MJI's dictionary and rules to reflect the change of domain.

  1. The dynamics of domain walls and strings

    NASA Technical Reports Server (NTRS)

    Gregory, Ruth; Haws, David; Garfinkle, David

    1989-01-01

    The leading order finite-width corrections to the equation of motion describing the motion of a domain wall are derived. The regime in which this equation of motion is invalid is discussed. Spherically and cylindrically symmetric solutions to this equation of motion are found. A misconception that has arisen in recent years regarding the rigidity (or otherwise) of cosmic strings is also clarified.

  2. Attractive membrane domains control lateral diffusion.

    PubMed

    Forstner, Martin B; Martin, Douglas S; Rückerl, Florian; Käs, Josef A; Selle, Carsten

    2008-05-01

    Lipid membranes play a fundamental role in vital cellular functions such as signal transduction. Many of these processes rely on lateral diffusion within the membrane, generally a complex fluid containing ordered microdomains. However, little attention has been paid to the alterations in transport dynamics of a diffusing species caused by long-range interactions with membrane domains. In this paper, we address the effect of such interactions on diffusive transport by studying lateral diffusion in a phase-separated Langmuir phospholipid monolayer via single-particle tracking. We find that attractive dipole-dipole interactions between condensed phase domains and diffusing probe beads lead to transient confinement at the phase boundaries, causing a transition from two- to one-dimensional diffusion. Using Brownian dynamics simulations, the long-term diffusion constant for such a system is found to have a sensitive, Boltzmann-like, dependence on the interaction strength. In addition, this interaction strength is shown to be a strong function of the ratio of domain to particle size. As similar interactions are expected in biological membranes, the modulation of diffusive transport dynamics by varying interaction strength and/or domain size may offer cells selective spatial and temporal control over signaling processes. PMID:18643101

  3. Domain growth kinetics in stratifying foam films

    NASA Astrophysics Data System (ADS)

    Zhang, Yiran; Sharma, Vivek

    2015-11-01

    Baking bread, brewing cappuccino, pouring beer, washing dishes, shaving, shampooing, whipping eggs and blowing bubbles all involve creation of aqueous foam films. Typical foam films consist of two surfactant-laden surfaces that are ~ 5 nm - 10 micron apart. Sandwiched between these interfacial layers is a fluid that drains primarily under the influence of viscous and interfacial forces, including disjoining pressure. Interestingly, a layered ordering of micelles inside the foam films (thickness <100 nm) leads to a stepwise thinning phenomena called stratification, which results in a thickness-dependent variation in reflected light intensity, visualized as progressively darker shades of gray. Thinner, darker domains spontaneously grow within foam films. We show that the domain expansion dynamics exhibit two distinct growth regimes with characteristic scaling laws. Though several studies have focused on the expansion dynamics of isolated domains that exhibit a diffusion-like scaling, the change in expansion kinetics observed after domains contact with the Plateau border has not been reported and analyzed before.

  4. Scalable Domain Decomposed Monte Carlo Particle Transport

    NASA Astrophysics Data System (ADS)

    O'Brien, Matthew Joseph

    In this dissertation, we present the parallel algorithms necessary to run domain decomposed Monte Carlo particle transport on large numbers of processors (millions of processors). Previous algorithms were not scalable, and the parallel overhead became more computationally costly than the numerical simulation. The main algorithms we consider are: • Domain decomposition of constructive solid geometry: enables extremely large calculations in which the background geometry is too large to fit in the memory of a single computational node. • Load Balancing: keeps the workload per processor as even as possible so the calculation runs efficiently. • Global Particle Find: if particles are on the wrong processor, globally resolve their locations to the correct processor based on particle coordinate and background domain. • Visualizing constructive solid geometry, sourcing particles, deciding that particle streaming communication is completed and spatial redecomposition. These algorithms are some of the most important parallel algorithms required for domain decomposed Monte Carlo particle transport. We demonstrate that our previous algorithms were not scalable, prove that our new algorithms are scalable, and run some of the algorithms up to 2 million MPI processes on the Sequoia supercomputer.

  5. Simplified technique demonstrates magnetic domain switching

    NASA Technical Reports Server (NTRS)

    1967-01-01

    Light from a conventional photographic light source is polarized and projected through thin samples of gadolinium iron garnet and then observed with a conventional polarizing microscope. A distinctive change in color from red to yellow is observed as the magnetic domains are switched.

  6. Layer tracking, asymptotics, and domain decomposition

    NASA Technical Reports Server (NTRS)

    Brown, D. L.; Chin, R. C. Y.; Hedstrom, G. W.; Manteuffel, T. A.

    1991-01-01

    A preliminary report is presented on the work on the tracking of internal layers in a singularly-perturbed convection-diffusion equation. It is shown why such tracking may be desirable, and it is also shown how to do it using domain decomposition based on asymptotic analysis.

  7. Center domains and their phenomenological consequences.

    PubMed

    Asakawa, Masayuki; Bass, Steffen A; Müller, Berndt

    2013-05-17

    We argue that the domain structure of deconfined QCD matter, which can be inferred from the properties of the Polyakov loop, can simultaneously explain the two most prominent experimentally verified features of the quark-gluon plasma, namely its large opacity as well as its near ideal fluid properties. PMID:25167399

  8. Scalable Domain Decomposed Monte Carlo Particle Transport

    SciTech Connect

    O'Brien, Matthew Joseph

    2013-12-05

    In this dissertation, we present the parallel algorithms necessary to run domain decomposed Monte Carlo particle transport on large numbers of processors (millions of processors). Previous algorithms were not scalable, and the parallel overhead became more computationally costly than the numerical simulation.

  9. Teachers' Domain Evaluation Report. CCT Reports

    ERIC Educational Resources Information Center

    Pasnik, Shelley; Keisch, Deborah

    2004-01-01

    This report is the result of a five-month study; it is comprised of two components: (1) an overview of the current knowledge base regarding how rich media resources, like Teachers' Domain, can support teaching and learning in K-12 schools; and (2) case studies of teachers, technology coordinators and administrators' perceptions and potential use…

  10. Developing Domain Ontologies for Course Content

    ERIC Educational Resources Information Center

    Boyce, Sinead; Pahl, Claus

    2007-01-01

    Ontologies have the potential to play an important role in instructional design and the development of course content. They can be used to represent knowledge about content, supporting instructors in creating content or learners in accessing content in a knowledge-guided way. While ontologies exist for many subject domains, their quality and…

  11. Kernel Manifold Alignment for Domain Adaptation.

    PubMed

    Tuia, Devis; Camps-Valls, Gustau

    2016-01-01

    The wealth of sensory data coming from different modalities has opened numerous opportunities for data analysis. The data are of increasing volume, complexity and dimensionality, thus calling for new methodological innovations towards multimodal data processing. However, multimodal architectures must rely on models able to adapt to changes in the data distribution. Differences in the density functions can be due to changes in acquisition conditions (pose, illumination), sensors characteristics (number of channels, resolution) or different views (e.g. street level vs. aerial views of a same building). We call these different acquisition modes domains, and refer to the adaptation problem as domain adaptation. In this paper, instead of adapting the trained models themselves, we alternatively focus on finding mappings of the data sources into a common, semantically meaningful, representation domain. This field of manifold alignment extends traditional techniques in statistics such as canonical correlation analysis (CCA) to deal with nonlinear adaptation and possibly non-corresponding data pairs between the domains. We introduce a kernel method for manifold alignment (KEMA) that can match an arbitrary number of data sources without needing corresponding pairs, just few labeled examples in all domains. KEMA has interesting properties: 1) it generalizes other manifold alignment methods, 2) it can align manifolds of very different complexities, performing a discriminative alignment preserving each manifold inner structure, 3) it can define a domain-specific metric to cope with multimodal specificities, 4) it can align data spaces of different dimensionality, 5) it is robust to strong nonlinear feature deformations, and 6) it is closed-form invertible, which allows transfer across-domains and data synthesis. To authors' knowledge this is the first method addressing all these important issues at once. We also present a reduced-rank version of KEMA for computational

  12. Kernel Manifold Alignment for Domain Adaptation

    PubMed Central

    Tuia, Devis; Camps-Valls, Gustau

    2016-01-01

    The wealth of sensory data coming from different modalities has opened numerous opportunities for data analysis. The data are of increasing volume, complexity and dimensionality, thus calling for new methodological innovations towards multimodal data processing. However, multimodal architectures must rely on models able to adapt to changes in the data distribution. Differences in the density functions can be due to changes in acquisition conditions (pose, illumination), sensors characteristics (number of channels, resolution) or different views (e.g. street level vs. aerial views of a same building). We call these different acquisition modes domains, and refer to the adaptation problem as domain adaptation. In this paper, instead of adapting the trained models themselves, we alternatively focus on finding mappings of the data sources into a common, semantically meaningful, representation domain. This field of manifold alignment extends traditional techniques in statistics such as canonical correlation analysis (CCA) to deal with nonlinear adaptation and possibly non-corresponding data pairs between the domains. We introduce a kernel method for manifold alignment (KEMA) that can match an arbitrary number of data sources without needing corresponding pairs, just few labeled examples in all domains. KEMA has interesting properties: 1) it generalizes other manifold alignment methods, 2) it can align manifolds of very different complexities, performing a discriminative alignment preserving each manifold inner structure, 3) it can define a domain-specific metric to cope with multimodal specificities, 4) it can align data spaces of different dimensionality, 5) it is robust to strong nonlinear feature deformations, and 6) it is closed-form invertible, which allows transfer across-domains and data synthesis. To authors’ knowledge this is the first method addressing all these important issues at once. We also present a reduced-rank version of KEMA for computational

  13. Simplicity and Specificity in Language: Domain-General Biases Have Domain-Specific Effects

    PubMed Central

    Culbertson, Jennifer; Kirby, Simon

    2016-01-01

    The extent to which the linguistic system—its architecture, the representations it operates on, the constraints it is subject to—is specific to language has broad implications for cognitive science and its relation to evolutionary biology. Importantly, a given property of the linguistic system can be “specific” to the domain of language in several ways. For example, if the property evolved by natural selection under the pressure of the linguistic function it serves then the property is domain-specific in the sense that its design is tailored for language. Equally though, if that property evolved to serve a different function or if that property is domain-general, it may nevertheless interact with the linguistic system in a way that is unique. This gives a second sense in which a property can be thought of as specific to language. An evolutionary approach to the language faculty might at first blush appear to favor domain-specificity in the first sense, with individual properties of the language faculty being specifically linguistic adaptations. However, we argue that interactions between learning, culture, and biological evolution mean any domain-specific adaptations that evolve will take the form of weak biases rather than hard constraints. Turning to the latter sense of domain-specificity, we highlight a very general bias, simplicity, which operates widely in cognition and yet interacts with linguistic representations in domain-specific ways. PMID:26793132

  14. PTEN-PDZ domain interactions: binding of PTEN to PDZ domains of PTPN13.

    PubMed

    Sotelo, Natalia S; Schepens, Jan T G; Valiente, Miguel; Hendriks, Wiljan J A J; Pulido, Rafael

    2015-05-01

    Protein modular interactions mediated by PDZ domains are essential for the establishment of functional protein networks controlling diverse cellular functions. The tumor suppressor PTEN possesses a C-terminal PDZ-binding motif (PDZ-BM) that is recognized by a specific set of PDZ domains from scaffolding and regulatory proteins. Here, we review the current knowledge on PTEN-PDZ domain interactions and tumor suppressor networks, describe methodology suitable to analyze these interactions, and report the binding of PTEN and the PDZ domain-containing protein tyrosine phosphatase PTPN13. Yeast two-hybrid and GST pull-down analyses showed that PTEN binds to PDZ2/PTPN13 domain in a manner that depends on the specific PTPN13 PDZ domain arrangement involving the interdomain region between PDZ1 and PDZ2. Furthermore, a specific binding profile of PTEN to PDZ2/PTPN13 domain was observed by mutational analysis of the PTEN PDZ-BM. Our results disclose a PDZ-mediated physical interaction of PTEN and PTPN13 with potential relevance in tumor suppression and cell homeostasis. PMID:25448478

  15. Bacterial Pleckstrin Homology Domains: A Prokaryotic Origin for the PH Domain

    PubMed Central

    Xu, Qingping; Bateman, Alex; Finn, Robert D.; Abdubek, Polat; Astakhova, Tamara; Axelrod, Herbert L.; Bakolitsa, Constantina; Carlton, Dennis; Chen, Connie; Chiu, Hsiu-Ju; Chiu, Michelle; Clayton, Thomas; Das, Debanu; Deller, Marc C.; Duan, Lian; Ellrott, Kyle; Ernst, Dustin; Farr, Carol L.; Feuerhelm, Julie; Grant, Joanna C.; Grzechnik, Anna; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K.; Klock, Heath E.; Knuth, Mark W.; Kozbial, Piotr; Krishna, S. Sri; Kumar, Abhinav; Marciano, David; McMullan, Daniel; Miller, Mitchell D.; Morse, Andrew T.; Nigoghossian, Edward; Nopakun, Amanda; Okach, Linda; Puckett, Christina; Reyes, Ron; Rife, Christopher L.; Sefcovic, Natasha; Tien, Henry J.; Trame, Christine B.; van den Bedem, Henry; Weekes, Dana; Wooten, Tiffany; Hodgson, Keith O.; Wooley, John; Elsliger, Marc-André; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A.

    2010-01-01

    Pleckstrin homology (PH) domains have been identified only in eukaryotic proteins to date. We have determined crystal structures for three members of an uncharacterized protein family (Pfam PF08000), which provide compelling evidence for the existence of PH-like domains in bacteria (PHb). The first two structures contain a single PHb domain that forms a dome-shaped, oligomeric ring with C5 symmetry. The third structure has an additional helical hairpin attached at the C-terminus and forms a similar but much larger ring with C12 symmetry. Thus, both molecular assemblies exhibit rare, higher-order, cyclic symmetry but preserve a similar arrangement of their PHb domains, which gives rise to a conserved hydrophilic surface at the intersection of the β-strands of adjacent protomers that likely mediates protein–protein interactions. As a result of these structures, additional families of PHb domains were identified, suggesting that PH domains are much more widespread than originally anticipated. Thus, rather than being a eukaryotic innovation, the PH domain superfamily appears to have existed before prokaryotes and eukaryotes diverged. PMID:19913036

  16. Crystallographic studies on protein misfolding: Domain swapping and amyloid formation in the SH3 domain.

    PubMed

    Cámara-Artigas, Ana

    2016-07-15

    Oligomerization by 3D domain swapping is found in a variety of proteins of diverse size, fold and function. In the early 1960s this phenomenon was postulated for the oligomers of ribonuclease A, but it was not until the 1990s that X-ray diffraction provided the first experimental evidence of this special manner of oligomerization. Nowadays, structural information has allowed the identification of these swapped oligomers in over one hundred proteins. Although the functional relevance of this phenomenon is not clear, this alternative folding of protomers into intertwined oligomers has been related to amyloid formation. Studies on proteins that develop 3D domain swapping might provide some clues on the early stages of amyloid formation. The SH3 domain is a small modular domain that has been used as a model to study the basis of protein folding. Among SH3 domains, the c-Src-SH3 domain emerges as a helpful model to study 3D domain swapping and amyloid formation. PMID:26924596

  17. Simplicity and Specificity in Language: Domain-General Biases Have Domain-Specific Effects.

    PubMed

    Culbertson, Jennifer; Kirby, Simon

    2015-01-01

    The extent to which the linguistic system-its architecture, the representations it operates on, the constraints it is subject to-is specific to language has broad implications for cognitive science and its relation to evolutionary biology. Importantly, a given property of the linguistic system can be "specific" to the domain of language in several ways. For example, if the property evolved by natural selection under the pressure of the linguistic function it serves then the property is domain-specific in the sense that its design is tailored for language. Equally though, if that property evolved to serve a different function or if that property is domain-general, it may nevertheless interact with the linguistic system in a way that is unique. This gives a second sense in which a property can be thought of as specific to language. An evolutionary approach to the language faculty might at first blush appear to favor domain-specificity in the first sense, with individual properties of the language faculty being specifically linguistic adaptations. However, we argue that interactions between learning, culture, and biological evolution mean any domain-specific adaptations that evolve will take the form of weak biases rather than hard constraints. Turning to the latter sense of domain-specificity, we highlight a very general bias, simplicity, which operates widely in cognition and yet interacts with linguistic representations in domain-specific ways. PMID:26793132

  18. Crystal structure of domain-swapped STE20 OSR1 kinase domain

    SciTech Connect

    Lee, Seung-Jae; Cobb, Melanie H.; Goldsmith, Elizabeth J.

    2009-09-15

    OSR1 (oxidative stress-responsive-1) and SPAK (Ste20/Sps1-related proline/alanine-rich kinase) belong to the GCK-VI subfamily of Ste20 group kinases. OSR1 and SPAK are key regulators of NKCCs (Na{sup +}/K{sup +}/2Cl{sup -} cotransporters) and activated by WNK family members (with-no-lysine kinase), mutations of which are known to cause Gordon syndrome, an autosomal dominant form of inherited hypertension. The crystal structure of OSR1 kinase domain has been solved at 2.25 {angstrom}. OSR1 forms a domain-swapped dimer in an inactive conformation, in which P+1 loop and {alpha}EF helix are swapped between dimer-related monomers. Structural alignment with nonswapped Ste20 TAO2 kinase indicates that the integrity of chemical interactions in the kinase domain is well preserved in the domain-swapped interfaces. The OSR1 kinase domain has now been added to a growing list of domain-swapped protein kinases recently reported, suggesting that the domain-swapping event provides an additional layer of complexity in regulating protein kinase activity.

  19. The acidic domains of the Toc159 chloroplast preprotein receptor family are intrinsically disordered protein domains

    PubMed Central

    2009-01-01

    Background The Toc159 family of proteins serve as receptors for chloroplast-destined preproteins. They directly bind to transit peptides, and exhibit preprotein substrate selectivity conferred by an unknown mechanism. The Toc159 receptors each include three domains: C-terminal membrane, central GTPase, and N-terminal acidic (A-) domains. Although the function(s) of the A-domain remains largely unknown, the amino acid sequences are most variable within these domains, suggesting they may contribute to the functional specificity of the receptors. Results The physicochemical properties of the A-domains are characteristic of intrinsically disordered proteins (IDPs). Using CD spectroscopy we show that the A-domains of two Arabidopsis Toc159 family members (atToc132 and atToc159) are disordered at physiological pH and temperature and undergo conformational changes at temperature and pH extremes that are characteristic of IDPs. Conclusions Identification of the A-domains as IDPs will be important for determining their precise function(s), and suggests a role in protein-protein interactions, which may explain how these proteins serve as receptors for such a wide variety of preprotein substrates. PMID:20042108

  20. Comparison of frequency-domain and time-domain rotorcraft vibration control methods

    NASA Technical Reports Server (NTRS)

    Gupta, N. K.

    1984-01-01

    Active control of rotor-induced vibration in rotorcraft has received significant attention recently. Two classes of techniques have been proposed. The more developed approach works with harmonic analysis of measured time histories and is called the frequency-domain approach. The more recent approach computes the control input directly using the measured time history data and is called the time-domain approach. The report summarizes the results of a theoretical investigation to compare the two approaches. Five specific areas were addressed: (1) techniques to derive models needed for control design (system identification methods), (2) robustness with respect to errors, (3) transient response, (4) susceptibility to noise, and (5) implementation difficulties. The system identification methods are more difficult for the time-domain models. The time-domain approach is more robust (e.g., has higher gain and phase margins) than the frequency-domain approach. It might thus be possible to avoid doing real-time system identification in the time-domain approach by storing models at a number of flight conditions. The most significant error source is the variation in open-loop vibrations caused by pilot inputs, maneuvers or gusts. The implementation requirements are similar except that the time-domain approach can be much simpler to implement if real-time system identification were not necessary.

  1. Leveraging domain information to restructure biological prediction

    PubMed Central

    2011-01-01

    Background It is commonly believed that including domain knowledge in a prediction model is desirable. However, representing and incorporating domain information in the learning process is, in general, a challenging problem. In this research, we consider domain information encoded by discrete or categorical attributes. A discrete or categorical attribute provides a natural partition of the problem domain, and hence divides the original problem into several non-overlapping sub-problems. In this sense, the domain information is useful if the partition simplifies the learning task. The goal of this research is to develop an algorithm to identify discrete or categorical attributes that maximally simplify the learning task. Results We consider restructuring a supervised learning problem via a partition of the problem space using a discrete or categorical attribute. A naive approach exhaustively searches all the possible restructured problems. It is computationally prohibitive when the number of discrete or categorical attributes is large. We propose a metric to rank attributes according to their potential to reduce the uncertainty of a classification task. It is quantified as a conditional entropy achieved using a set of optimal classifiers, each of which is built for a sub-problem defined by the attribute under consideration. To avoid high computational cost, we approximate the solution by the expected minimum conditional entropy with respect to random projections. This approach is tested on three artificial data sets, three cheminformatics data sets, and two leukemia gene expression data sets. Empirical results demonstrate that our method is capable of selecting a proper discrete or categorical attribute to simplify the problem, i.e., the performance of the classifier built for the restructured problem always beats that of the original problem. Conclusions The proposed conditional entropy based metric is effective in identifying good partitions of a classification

  2. ECOD: An Evolutionary Classification of Protein Domains

    PubMed Central

    Kinch, Lisa N.; Pei, Jimin; Shi, Shuoyong; Kim, Bong-Hyun; Grishin, Nick V.

    2014-01-01

    Understanding the evolution of a protein, including both close and distant relationships, often reveals insight into its structure and function. Fast and easy access to such up-to-date information facilitates research. We have developed a hierarchical evolutionary classification of all proteins with experimentally determined spatial structures, and presented it as an interactive and updatable online database. ECOD (Evolutionary Classification of protein Domains) is distinct from other structural classifications in that it groups domains primarily by evolutionary relationships (homology), rather than topology (or “fold”). This distinction highlights cases of homology between domains of differing topology to aid in understanding of protein structure evolution. ECOD uniquely emphasizes distantly related homologs that are difficult to detect, and thus catalogs the largest number of evolutionary links among structural domain classifications. Placing distant homologs together underscores the ancestral similarities of these proteins and draws attention to the most important regions of sequence and structure, as well as conserved functional sites. ECOD also recognizes closer sequence-based relationships between protein domains. Currently, approximately 100,000 protein structures are classified in ECOD into 9,000 sequence families clustered into close to 2,000 evolutionary groups. The classification is assisted by an automated pipeline that quickly and consistently classifies weekly releases of PDB structures and allows for continual updates. This synchronization with PDB uniquely distinguishes ECOD among all protein classifications. Finally, we present several case studies of homologous proteins not recorded in other classifications, illustrating the potential of how ECOD can be used to further biological and evolutionary studies. PMID:25474468

  3. REvolver: modeling sequence evolution under domain constraints.

    PubMed

    Koestler, Tina; von Haeseler, Arndt; Ebersberger, Ingo

    2012-09-01

    Simulating the change of protein sequences over time in a biologically realistic way is fundamental for a broad range of studies with a focus on evolution. It is, thus, problematic that typically simulators evolve individual sites of a sequence identically and independently. More realistic simulations are possible; however, they are often prohibited by limited knowledge concerning site-specific evolutionary constraints or functional dependencies between amino acids. As a consequence, a protein's functional and structural characteristics are rapidly lost in the course of simulated evolution. Here, we present REvolver (www.cibiv.at/software/revolver), a program that simulates protein sequence alteration such that evolutionarily stable sequence characteristics, like functional domains, are maintained. For this purpose, REvolver recruits profile hidden Markov models (pHMMs) for parameterizing site-specific models of sequence evolution in an automated fashion. pHMMs derived from alignments of homologous proteins or protein domains capture information regarding which sequence sites remained conserved over time and where in a sequence insertions or deletions are more likely to occur. Thus, they describe constraints on the evolutionary process acting on these sequences. To demonstrate the performance of REvolver as well as its applicability in large-scale simulation studies, we evolved the entire human proteome up to 1.5 expected substitutions per site. Simultaneously, we analyzed the preservation of Pfam and SMART domains in the simulated sequences over time. REvolver preserved 92% of the Pfam domains originally present in the human sequences. This value drops to 15% when traditional models of amino acid sequence evolution are used. Thus, REvolver represents a significant advance toward a realistic simulation of protein sequence evolution on a proteome-wide scale. Further, REvolver facilitates the simulation of a protein family with a user-defined domain architecture at

  4. Architecture and function of metallopeptidase catalytic domains

    PubMed Central

    Cerdà-Costa, Núria; Gomis-Rüth, Francesc Xavier

    2014-01-01

    The cleavage of peptide bonds by metallopeptidases (MPs) is essential for life. These ubiquitous enzymes participate in all major physiological processes, and so their deregulation leads to diseases ranging from cancer and metastasis, inflammation, and microbial infection to neurological insults and cardiovascular disorders. MPs cleave their substrates without a covalent intermediate in a single-step reaction involving a solvent molecule, a general base/acid, and a mono-or dinuclear catalytic metal site. Most monometallic MPs comprise a short metal-binding motif (HEXXH), which includes two metal-binding histidines and a general base/acid glutamate, and they are grouped into the zincin tribe of MPs. The latter divides mainly into the gluzincin and metzincin clans. Metzincins consist of globular ∼130–270-residue catalytic domains, which are usually preceded by N-terminal pro-segments, typically required for folding and latency maintenance. The catalytic domains are often followed by C-terminal domains for substrate recognition and other protein–protein interactions, anchoring to membranes, oligomerization, and compartmentalization. Metzincin catalytic domains consist of a structurally conserved N-terminal subdomain spanning a five-stranded β-sheet, a backing helix, and an active-site helix. The latter contains most of the metal-binding motif, which is here characteristically extended to HEXXHXXGXX(H,D). Downstream C-terminal subdomains are generally shorter, differ more among metzincins, and mainly share a conserved loop—the Met-turn—and a C-terminal helix. The accumulated structural data from more than 300 deposited structures of the 12 currently characterized metzincin families reviewed here provide detailed knowledge of the molecular features of their catalytic domains, help in our understanding of their working mechanisms, and form the basis for the design of novel drugs. PMID:24596965

  5. A mixed finite element domain decomposition method for nearly elastic wave equations in the frequency domain

    SciTech Connect

    Feng, Xiaobing

    1996-12-31

    A non-overlapping domain decomposition iterative method is proposed and analyzed for mixed finite element methods for a sequence of noncoercive elliptic systems with radiation boundary conditions. These differential systems describe the motion of a nearly elastic solid in the frequency domain. The convergence of the iterative procedure is demonstrated and the rate of convergence is derived for the case when the domain is decomposed into subdomains in which each subdomain consists of an individual element associated with the mixed finite elements. The hybridization of mixed finite element methods plays a important role in the construction of the discrete procedure.

  6. The BTB domains of the potassium channel tetramerization domain proteins prevalently assume pentameric states.

    PubMed

    Smaldone, Giovanni; Pirone, Luciano; Pedone, Emilia; Marlovits, Thomas; Vitagliano, Luigi; Ciccarelli, Luciano

    2016-06-01

    Potassium channel tetramerization domain-containing (KCTD) proteins are involved in fundamental physio-pathological processes. Here, we report an analysis of the oligomeric state of the Bric-à-brack, Tram-track, Broad complex (BTB) domains of seven distinct KCTDs belonging to five major clades of the family evolution tree. Despite their functional and sequence variability, present electron microscopy data highlight the occurrence of well-defined pentameric states for all domains. Our data also show that these states coexist with alternative forms which include open pentamers. Thermal denaturation analyses conducted using KCTD1 as a model suggest that, in these proteins, different domains cooperate to their overall stability. Finally, negative-stain electron micrographs of KCTD6(BTB) in complex with Cullin3 show the presence of assemblies with a five-pointed pinwheel shape. PMID:27152988

  7. High order expanding domain methods for the solution of Poisson's equation in infinite domains

    NASA Astrophysics Data System (ADS)

    Anderson, Christopher R.

    2016-06-01

    In this paper we present a discrete Fourier transform based procedure to evaluate the infinite domain solution of Poisson's equation at points in a rectangular computational region. The numerical procedure is a modification of an "expanding domain" type method where one obtains approximations of increasing accuracy by expanding the computational domain. The modification presented here is one that leads to approximations that converge with high order rates of convergence with respect to domain size. Spectrally accurate approximations are used to approximate differential operators and so the method possesses very high rates of convergence with respect to mesh size as well. Computational results on both two and three dimensional test problems are presented that demonstrate the accuracy and computational efficiency of the procedure.

  8. Critical role of domain crystallinity, domain purity and domain interface sharpness for reduced bimolecular recombination in polymer solar cells

    SciTech Connect

    Venkatesan, Swaminathan; Chen, Jihua; Ngo, Evan C.; Dubey, Ashish; Khatiwada, Devendra; Zhang, Cheng; Qiao, Qiquan

    2014-12-31

    In this study, inverted bulk heterojunction solar cells were fabricated using poly(3-hexylthiophene) (P3HT) blended with two different fullerene derivatives namely phenyl-C61-butyric acid methyl ester (PC60BM) and indene-C60 bis-adduct (IC60BA). The effects of annealing temperatures on the morphology, optical and structural properties were studied and correlated to differences in photovoltaic device performance. It was observed that annealing temperature significantly improved the performance of P3HT:IC60BA solar cells while P3HT:PC60BM cells showed relatively less improvement. The performance improvement is attributed to the extent of fullerene mixing with polymer domains. Energy filtered transmission electron microscopy (EFTEM) and x-ray diffraction (XRD) results showed that ICBA mixes with disordered P3HT much more readily than PC60BM which leads to lower short circuit current density and fill factor for P3HT:IC60BA cells annealed below 120°C. Annealing above 120°C improves the crystallinity of P3HT in case of P3HT:IC60BA whereas in P3HT:PC60BM films, annealing above 80°C leads to negligible change in crystallinity. Crystallization of P3HT also leads to higher domain purity as seen EFTEM. Further it is seen that cells processed with additive nitrobenzene (NB) showed enhanced short circuit current density and power conversion efficiency regardless of the fullerene derivative used. Addition of NB led to nanoscale phase separation between purer polymer and fullerene domains. Kelvin probe force microscopy (KPFM) images showed that enhanced domain purity in additive casted films led to a sharper interface between polymer and fullerene. Lastly, enhanced domain purity and interfacial sharpness led to lower bimolecular recombination and higher mobility and charge carrier lifetime in NB modified devices.

  9. Ribosomal small subunit domains radiate from a central core.

    PubMed

    Gulen, Burak; Petrov, Anton S; Okafor, C Denise; Vander Wood, Drew; O'Neill, Eric B; Hud, Nicholas V; Williams, Loren Dean

    2016-01-01

    The domain architecture of a large RNA can help explain and/or predict folding, function, biogenesis and evolution. We offer a formal and general definition of an RNA domain and use that definition to experimentally characterize the rRNA of the ribosomal small subunit. Here the rRNA comprising a domain is compact, with a self-contained system of molecular interactions. A given rRNA helix or stem-loop must be allocated uniquely to a single domain. Local changes such as mutations can give domain-wide effects. Helices within a domain have interdependent orientations, stabilities and interactions. With these criteria we identify a core domain (domain A) of small subunit rRNA. Domain A acts as a hub, linking the four peripheral domains and imposing orientational and positional restraints on the other domains. Experimental characterization of isolated domain A, and mutations and truncations of it, by methods including selective 2'OH acylation analyzed by primer extension and circular dichroism spectroscopy are consistent with our architectural model. The results support the utility of the concept of an RNA domain. Domain A, which exhibits structural similarity to tRNA, appears to be an essential core of the small ribosomal subunit. PMID:26876483

  10. Ribosomal small subunit domains radiate from a central core

    NASA Astrophysics Data System (ADS)

    Gulen, Burak; Petrov, Anton S.; Okafor, C. Denise; Vander Wood, Drew; O'Neill, Eric B.; Hud, Nicholas V.; Williams, Loren Dean

    2016-02-01

    The domain architecture of a large RNA can help explain and/or predict folding, function, biogenesis and evolution. We offer a formal and general definition of an RNA domain and use that definition to experimentally characterize the rRNA of the ribosomal small subunit. Here the rRNA comprising a domain is compact, with a self-contained system of molecular interactions. A given rRNA helix or stem-loop must be allocated uniquely to a single domain. Local changes such as mutations can give domain-wide effects. Helices within a domain have interdependent orientations, stabilities and interactions. With these criteria we identify a core domain (domain A) of small subunit rRNA. Domain A acts as a hub, linking the four peripheral domains and imposing orientational and positional restraints on the other domains. Experimental characterization of isolated domain A, and mutations and truncations of it, by methods including selective 2‧OH acylation analyzed by primer extension and circular dichroism spectroscopy are consistent with our architectural model. The results support the utility of the concept of an RNA domain. Domain A, which exhibits structural similarity to tRNA, appears to be an essential core of the small ribosomal subunit.

  11. Ribosomal small subunit domains radiate from a central core

    PubMed Central

    Gulen, Burak; Petrov, Anton S.; Okafor, C. Denise; Vander Wood, Drew; O’Neill, Eric B.; Hud, Nicholas V.; Williams, Loren Dean

    2016-01-01

    The domain architecture of a large RNA can help explain and/or predict folding, function, biogenesis and evolution. We offer a formal and general definition of an RNA domain and use that definition to experimentally characterize the rRNA of the ribosomal small subunit. Here the rRNA comprising a domain is compact, with a self-contained system of molecular interactions. A given rRNA helix or stem-loop must be allocated uniquely to a single domain. Local changes such as mutations can give domain-wide effects. Helices within a domain have interdependent orientations, stabilities and interactions. With these criteria we identify a core domain (domain A) of small subunit rRNA. Domain A acts as a hub, linking the four peripheral domains and imposing orientational and positional restraints on the other domains. Experimental characterization of isolated domain A, and mutations and truncations of it, by methods including selective 2′OH acylation analyzed by primer extension and circular dichroism spectroscopy are consistent with our architectural model. The results support the utility of the concept of an RNA domain. Domain A, which exhibits structural similarity to tRNA, appears to be an essential core of the small ribosomal subunit. PMID:26876483

  12. Skyrmion domain wall collision and domain wall-gated skyrmion logic

    NASA Astrophysics Data System (ADS)

    Xing, Xiangjun; Pong, Philip W. T.; Zhou, Yan

    2016-08-01

    Skyrmions and domain walls are significant spin textures of great technological relevance to magnetic memory and logic applications, where they can be used as carriers of information. The unique topology of skyrmions makes them display emergent dynamical properties as compared with domain walls. Some studies have demonstrated that the two topologically inequivalent magnetic objects could be interconverted by using cleverly designed geometric structures. Here, we numerically address the skyrmion domain wall collision in a magnetic racetrack by introducing relative motion between the two objects based on a specially designed junction. An electric current serves as the driving force that moves a skyrmion toward a trapped domain wall pair. We see different types of collision dynamics depending on the driving parameters. Most importantly, the modulation of skyrmion transport using domain walls is realized in this system, allowing a set of domain wall-gated logical NOT, NAND, and NOR gates to be constructed. This work provides a skyrmion-based spin-logic architecture that is fully compatible with racetrack memories.

  13. Scalable video coding in frequency domain

    NASA Astrophysics Data System (ADS)

    Civanlar, Mehmet R.; Puri, Atul

    1992-11-01

    Scalable video coding is important in a number of applications where video needs to be decoded and displayed at a variety of resolution scales. It is more efficient than simulcasting, in which all desired resolution scales are coded totally independent of one another within the constraint of a fixed available bandwidth. In this paper, we focus on scalability using the frequency domain approach. We employ the framework proposed for the ongoing second phase of Motion Picture Experts Group (MPEG-2) standard to study the performance of one such scheme and investigate improvements aimed at increasing its efficiency. Practical issues related to multiplexing of encoded data of various resolution scales to facilitate decoding are considered. Simulations are performed to investigate the potential of a chosen frequency domain scheme. Various prospects and limitations are also discussed.

  14. Myonuclear domains in muscle adaptation and disease

    NASA Technical Reports Server (NTRS)

    Allen, D. L.; Roy, R. R.; Edgerton, V. R.

    1999-01-01

    Adult skeletal muscle fibers are among the few cell types that are truly multinucleated. Recently, evidence has accumulated supporting a role for the modulation of myonuclear number during muscle remodeling in response to injury, adaptation, and disease. These studies have demonstrated that muscle hypertrophy is associated with, and is dependent on, the addition of newly formed myonuclei via the fusion of myogenic cells to the adult myofiber, whereas muscle atrophy and disease appear to be associated with the loss of myonuclei, possibly through apoptotic-like mechanisms. Moreover, these studies also have demonstrated that myonuclear domain size, i. e., the amount of cytoplasm per myonucleus, is unchanged following the acute phase of hypertrophy but is reduced following atrophy. Together these data demonstrate that modulation of myonuclear number or myonuclear domain size (or both) is a mechanism contributing to the remodeling of adult skeletal muscle in response to alterations in the level of normal neuromuscular activity. Copyright 1999 John Wiley & Sons, Inc.

  15. Space Domain Awareness for Manned GEO Servicing

    NASA Astrophysics Data System (ADS)

    Blake, T.

    2010-09-01

    The Defense Advanced Research Projects Agency (DARPA) is embarking on a joint program to service spacecraft in Geosynchronous (GEO) Orbit. This ambitious program, known as R5 (Rendezvous, Refuel, Refurbish, Repair, and Reposition), will develop the technologies required to extend the life of billions of dollars of invested in building, launching and operating GEO spacecraft. Inherent in the R5 program, is the need for high quality awareness of the space domain at GEO. Servicing non-operational spacecraft in GEO will require enhanced debris detect/track and space weather monitoring for crew safety, as well as high resolution characterization of the spacecraft to understand the status of the spacecraft to manifest the repair mission. This paper will briefly describe the GEO space domain sensor and data processing requirements to support the R5 program and outline DARPA’s program plans to develop these capabilities. Distribution Statement A (Approved for Public Release, Distribution Unlimited). DISTAR case 15410.

  16. Membrane Domain Formation on Nanostructured Scaffolds

    NASA Astrophysics Data System (ADS)

    Collier, Charles; Liu, Fangjie; Srijanto, Bernadeta

    The spatial organization of lipids and proteins in biological membranes seems to have a functional role in the life of a cell. Separation of the lipids into distinct domains of greater order and anchoring to the cytoskeleton are two main mechanisms for organizing the membrane in cells. We propose a novel model membrane consisting of a lipid bilayer suspended over a nanostructured scaffold consisting of arrays of fabricated nanopillars. Unlike traditional model membranes, our model will have well-defined lateral structure and distributed substrate attachments that will emulate the connections of cellular membranes to the underlying cytoskeleton. Membranes will be characterized using neutron reflectometry, atomic force microscopy and fluorescence to verify a suspended, planar geometry with restricted diffusion at suspension points, and free diffusion in between. This architecture will allow the controlled study of lipid domain reorganization, viral infection and signal transduction that depend on the lateral structure of the membrane.

  17. Inhomogeneous rotation in ferroelastic domain patterns

    NASA Astrophysics Data System (ADS)

    Jacobs, A. E.; Curnoe, S. H.; Desai, R. C.

    2004-03-01

    We study static, two-dimensional domain patterns obtained by numerical minimization of the strain energy for proper triangular→centered-rectangular (T-CR) and square→rectangular ferroelastics. Applications are made to hexagonal→orthorhombic and related materials (lead orthovanadate, Mg_3Cd, Ta_4N, etc) and YBa_2Cu_3O_7-δ. Examinatin of the local rotation, the local energy density and the non-order-parameter strains reveals wedge and other disclinations responsible for the complexity of the patterns. The rotation might be observed in birefringence imaging. We report also unusual structures obtained near Tc in T-CR systems, including trapped high-T phase and pencil-like domains.

  18. Domain Growth Kinetics in Stratifying Foam Films

    NASA Astrophysics Data System (ADS)

    Zhang, Yiran; Sharma, Vivek

    2015-03-01

    Baking bread, brewing cappuccino, pouring beer, washing dishes, shaving, shampooing, whipping eggs and blowing bubbles all involve creation of aqueous foam films. Typical foam films consist of two surfactant-laden surfaces that are μ 5 nm - 10 micron apart. Sandwiched between these interfacial layers is a fluid that drains primarily under the influence of viscous and interfacial forces, including disjoining pressure. Interestingly, for certain low molecular weight surfactants, a layered ordering of micelles inside the foam films (thickness <100 nm) leads to a stepwise thinning phenomena called stratification. We experimentally elucidate the influence of these different driving forces, and confinement on drainage kinetics of horizontal stratifying foam films. Thinner, darker domains spontaneously grow within foam films. Quantitative characterization of domain growth visualized in a using Scheludko-type thin film cell and a theoretical model based on lubrication analysis, provide critical insights into hydrodynamics of thin foam films, and the strength and nature of surface forces, including supramolecular oscillatory structural forces.

  19. Entropy gives rise to topologically associating domains

    PubMed Central

    Vasquez, Paula A.; Hult, Caitlin; Adalsteinsson, David; Lawrimore, Josh; Forest, Mark G.; Bloom, Kerry

    2016-01-01

    We investigate chromosome organization within the nucleus using polymer models whose formulation is closely guided by experiments in live yeast cells. We employ bead-spring chromosome models together with loop formation within the chains and the presence of nuclear bodies to quantify the extent to which these mechanisms shape the topological landscape in the interphase nucleus. By investigating the genome as a dynamical system, we show that domains of high chromosomal interactions can arise solely from the polymeric nature of the chromosome arms due to entropic interactions and nuclear confinement. In this view, the role of bio-chemical related processes is to modulate and extend the duration of the interacting domains. PMID:27257057

  20. Entropy gives rise to topologically associating domains.

    PubMed

    Vasquez, Paula A; Hult, Caitlin; Adalsteinsson, David; Lawrimore, Josh; Forest, Mark G; Bloom, Kerry

    2016-07-01

    We investigate chromosome organization within the nucleus using polymer models whose formulation is closely guided by experiments in live yeast cells. We employ bead-spring chromosome models together with loop formation within the chains and the presence of nuclear bodies to quantify the extent to which these mechanisms shape the topological landscape in the interphase nucleus. By investigating the genome as a dynamical system, we show that domains of high chromosomal interactions can arise solely from the polymeric nature of the chromosome arms due to entropic interactions and nuclear confinement. In this view, the role of bio-chemical related processes is to modulate and extend the duration of the interacting domains. PMID:27257057

  1. LHC RF System Time-Domain Simulation

    SciTech Connect

    Mastorides, T.; Rivetta, C.; /SLAC

    2010-09-14

    Non-linear time-domain simulations have been developed for the Positron-Electron Project (PEP-II) and the Large Hadron Collider (LHC). These simulations capture the dynamic behavior of the RF station-beam interaction and are structured to reproduce the technical characteristics of the system (noise contributions, non-linear elements, and more). As such, they provide useful results and insight for the development and design of future LLRF feedback systems. They are also a valuable tool for the study of diverse longitudinal beam dynamics effects such as coupled-bunch impedance driven instabilities and single bunch longitudinal emittance growth. Results from these studies and related measurements from PEP-II and LHC have been presented in multiple places. This report presents an example of the time-domain simulation implementation for the LHC.

  2. Defect junctions and domain wall dynamics

    SciTech Connect

    Avelino, P.P.; Oliveira, J.C.R.E.; Martins, C.J.A.P.; Menezes, J.; Menezes, R.

    2006-06-15

    We study a number of domain wall forming models where various types of defect junctions can exist. These illustrate some of the mechanisms that will determine the evolution of defect networks with junctions. Understanding these mechanisms is vital for a proper assessment of a number of cosmological scenarios: we will focus on the issue of whether or not cosmological frustrated domain wall networks can exist at all, but our results are also relevant for the dynamics of cosmic (super)strings, where junctions are expected to be ubiquitous. We also define and discuss the properties that would make up the ideal model in terms of hypothetical frustrated wall networks, and provide an explicit construction for such a model. We carry out a number of numerical simulations of the evolution of these networks, analyze and contrast their results, and discuss their implications for our no-frustration conjecture.

  3. Structural and Histone Binding Ability Characterizations of Human PWWP Domains

    SciTech Connect

    Wu, Hong; Zeng, Hong; Lam, Robert; Tempel, Wolfram; Amaya, Maria F.; Xu, Chao; Dombrovski, Ludmila; Qiu, Wei; Wang, Yanming; Min, Jinrong

    2013-09-25

    The PWWP domain was first identified as a structural motif of 100-130 amino acids in the WHSC1 protein and predicted to be a protein-protein interaction domain. It belongs to the Tudor domain 'Royal Family', which consists of Tudor, chromodomain, MBT and PWWP domains. While Tudor, chromodomain and MBT domains have long been known to bind methylated histones, PWWP was shown to exhibit histone binding ability only until recently. The PWWP domain has been shown to be a DNA binding domain, but sequence analysis and previous structural studies show that the PWWP domain exhibits significant similarity to other 'Royal Family' members, implying that the PWWP domain has the potential to bind histones. In order to further explore the function of the PWWP domain, we used the protein family approach to determine the crystal structures of the PWWP domains from seven different human proteins. Our fluorescence polarization binding studies show that PWWP domains have weak histone binding ability, which is also confirmed by our NMR titration experiments. Furthermore, we determined the crystal structures of the BRPF1 PWWP domain in complex with H3K36me3, and HDGF2 PWWP domain in complex with H3K79me3 and H4K20me3. PWWP proteins constitute a new family of methyl lysine histone binders. The PWWP domain consists of three motifs: a canonical {beta}-barrel core, an insertion motif between the second and third {beta}-strands and a C-terminal {alpha}-helix bundle. Both the canonical {beta}-barrel core and the insertion motif are directly involved in histone binding. The PWWP domain has been previously shown to be a DNA binding domain. Therefore, the PWWP domain exhibits dual functions: binding both DNA and methyllysine histones.

  4. An intelligent tutor for the space domain

    NASA Technical Reports Server (NTRS)

    Swigger, Kathleen; Loveland, Harry

    1987-01-01

    An intelligent tutoring system for the space domain is described. This system was developed on a Xerox 1108 using LOOPS and provides an environment for discovering principles of ground tracks as a direct function of the orbital elements. Some of the more practical design and implementation issues associated with the development of intelligent tutoring systems are examined. Some solutions to the problems and some suggestions for future research are offered.

  5. Time Domain Modelling of a Reciprocating Engine

    NASA Astrophysics Data System (ADS)

    Li, H.; Stone, B. J.

    1999-01-01

    This paper describes the application of a time domain systems approach to the modelling of a reciprocating engine. The engine model includes the varying inertia effects resulting from the motion of the piston and con-rod. The cylinder pressure measured under operating conditions is used to force the model and the resulting motion compared with the measured response. The results obtained indicate that the model is very good.

  6. Domain adaptation for Alzheimer's disease diagnostics.

    PubMed

    Wachinger, Christian; Reuter, Martin

    2016-10-01

    With the increasing prevalence of Alzheimer's disease, research focuses on the early computer-aided diagnosis of dementia with the goal to understand the disease process, determine risk and preserving factors, and explore preventive therapies. By now, large amounts of data from multi-site studies have been made available for developing, training, and evaluating automated classifiers. Yet, their translation to the clinic remains challenging, in part due to their limited generalizability across different datasets. In this work, we describe a compact classification approach that mitigates overfitting by regularizing the multinomial regression with the mixed ℓ1/ℓ2 norm. We combine volume, thickness, and anatomical shape features from MRI scans to characterize neuroanatomy for the three-class classification of Alzheimer's disease, mild cognitive impairment and healthy controls. We demonstrate high classification accuracy via independent evaluation within the scope of the CADDementia challenge. We, furthermore, demonstrate that variations between source and target datasets can substantially influence classification accuracy. The main contribution of this work addresses this problem by proposing an approach for supervised domain adaptation based on instance weighting. Integration of this method into our classifier allows us to assess different strategies for domain adaptation. Our results demonstrate (i) that training on only the target training set yields better results than the naïve combination (union) of source and target training sets, and (ii) that domain adaptation with instance weighting yields the best classification results, especially if only a small training component of the target dataset is available. These insights imply that successful deployment of systems for computer-aided diagnostics to the clinic depends not only on accurate classifiers that avoid overfitting, but also on a dedicated domain adaptation strategy. PMID:27262241

  7. Image domain propeller fast spin echo☆

    PubMed Central

    Skare, Stefan; Holdsworth, Samantha J.; Lilja, Anders; Bammer, Roland

    2013-01-01

    A new pulse sequence for high-resolution T2-weighted (T2-w) imaging is proposed –image domain propeller fast spin echo (iProp-FSE). Similar to the T2-w PROPELLER sequence, iProp-FSE acquires data in a segmented fashion, as blades that are acquired in multiple TRs. However, the iProp-FSE blades are formed in the image domain instead of in the k-space domain. Each iProp-FSE blade resembles a single-shot fast spin echo (SSFSE) sequence with a very narrow phase-encoding field of view (FOV), after which N rotated blade replicas yield the final full circular FOV. Our method of combining the image domain blade data to a full FOV image is detailed, and optimal choices of phase-encoding FOVs and receiver bandwidths were evaluated on phantom and volunteers. The results suggest that a phase FOV of 15–20%, a receiver bandwidth of ±32–63 kHz and a subsequent readout time of about 300 ms provide a good tradeoff between signal-to-noise ratio (SNR) efficiency and T2 blurring. Comparisons between iProp-FSE, Cartesian FSE and PROPELLER were made on single-slice axial brain data, showing similar T2-w tissue contrast and SNR with great anatomical conspicuity at similar scan times –without colored noise or streaks from motion. A new slice interleaving order is also proposed to improve the multislice capabilities of iProp-FSE. PMID:23200683

  8. Metrology for terahertz time-domain spectrometers

    NASA Astrophysics Data System (ADS)

    Molloy, John F.; Naftaly, Mira

    2015-12-01

    In recent years the terahertz time-domain spectrometer (THz TDS) [1] has emerged as a key measurement device for spectroscopic investigations in the frequency range of 0.1-5 THz. To date, almost every type of material has been studied using THz TDS, including semiconductors, ceramics, polymers, metal films, liquid crystals, glasses, pharmaceuticals, DNA molecules, proteins, gases, composites, foams, oils, and many others. Measurements with a TDS are made in the time domain; conversion from the time domain data to a frequency spectrum is achieved by applying the Fourier Transform, calculated numerically using the Fast Fourier Transform (FFT) algorithm. As in many other types of spectrometer, THz TDS requires that the sample data be referenced to similarly acquired data with no sample present. Unlike frequency-domain spectrometers which detect light intensity and measure absorption spectra, a TDS records both amplitude and phase information, and therefore yields both the absorption coefficient and the refractive index of the sample material. The analysis of the data from THz TDS relies on the assumptions that: a) the frequency scale is accurate; b) the measurement of THz field amplitude is linear; and c) that the presence of the sample does not affect the performance characteristics of the instrument. The frequency scale of a THz TDS is derived from the displacement of the delay line; via FFT, positioning errors may give rise to frequency errors that are difficult to quantify. The measurement of the field amplitude in a THz TDS is required to be linear with a dynamic range of the order of 10 000. And attention must be given to the sample positioning and handling in order to avoid sample-related errors.

  9. Domain decomposition methods for mortar finite elements

    SciTech Connect

    Widlund, O.

    1996-12-31

    In the last few years, domain decomposition methods, previously developed and tested for standard finite element methods and elliptic problems, have been extended and modified to work for mortar and other nonconforming finite element methods. A survey will be given of work carried out jointly with Yves Achdou, Mario Casarin, Maksymilian Dryja and Yvon Maday. Results on the p- and h-p-version finite elements will also be discussed.

  10. Domain decomposition multigrid for unstructured grids

    SciTech Connect

    Shapira, Yair

    1997-01-01

    A two-level preconditioning method for the solution of elliptic boundary value problems using finite element schemes on possibly unstructured meshes is introduced. It is based on a domain decomposition and a Galerkin scheme for the coarse level vertex unknowns. For both the implementation and the analysis, it is not required that the curves of discontinuity in the coefficients of the PDE match the interfaces between subdomains. Generalizations to nonmatching or overlapping grids are made.

  11. Dynamic Domains in Data Production Planning

    NASA Technical Reports Server (NTRS)

    Golden, Keith; Pang, Wanlin

    2005-01-01

    This paper discusses a planner-based approach to automating data production tasks, such as producing fire forecasts from satellite imagery and weather station data. Since the set of available data products is large, dynamic and mostly unknown, planning techniques developed for closed worlds are unsuitable. We discuss a number of techniques we have developed to cope with data production domains, including a novel constraint propagation algorithm based on planning graphs and a constraint-based approach to interleaved planning, sensing and execution.

  12. MBT domain proteins in development and disease

    PubMed Central

    Bonasio, Roberto; Lecona, Emilio; Reinberg, Danny

    2013-01-01

    The Malignant Brain Tumor (MBT) domain is a “chromatin reader”, a protein module that binds to post-translational modifications on histone tails that are thought to affect a variety of chromatin processes, including transcription. More specifically, MBT domains recognize mono- and di-methylated lysines at a number of different positions on histone H3 and H4 tails. Three Drosophila proteins, SCM, L(3)MBT and SFMBT contain multiple adjacent MBT repeats and have critical roles in development, maintenance of cell identity, and tumor suppression. Although they function in different pathways, these proteins all localize to chromatin in vivo and repress transcription by a currently unknown molecular mechanism that requires the MBT domains. The human genome contains several homologues of these MBT proteins, some of which have been linked to important gene regulatory pathways, such as E2F/Rb- and Polycomb-mediated repression, and to the insurgence of certain neurological tumors. Here, we review the genetics, biochemistry, and cell biology of MBT proteins and their role in development and disease. PMID:19778625

  13. Time-Domain Filtering of Metasurfaces

    NASA Astrophysics Data System (ADS)

    Wakatsuchi, Hiroki

    2015-11-01

    In general electromagnetic response of each material to a continuous wave does not vary in time domain if the frequency component remains the same. Recently, it turned out that integrating several circuit elements including schottky diodes with periodically metallised surfaces, or the so-called metasurfaces, leads to selectively absorbing specific types of waveforms or pulse widths even at the same frequency. These waveform-selective metasurfaces effectively showed different absorbing performances for different widths of pulsed sine waves by gradually varying their electromagnetic responses in time domain. Here we study time-filtering effects of such circuit-based metasurfaces illuminated by continuous sine waves. Moreover, we introduce extra circuit elements to these structures to enhance the time-domain control capability. These time-varying properties are expected to give us another degree of freedom to control electromagnetic waves and thus contribute to developing new kinds of electromagnetic applications and technologies, e.g. time-windowing wireless communications and waveform conversion.

  14. Time-Domain Filtering of Metasurfaces.

    PubMed

    Wakatsuchi, Hiroki

    2015-01-01

    In general electromagnetic response of each material to a continuous wave does not vary in time domain if the frequency component remains the same. Recently, it turned out that integrating several circuit elements including schottky diodes with periodically metallised surfaces, or the so-called metasurfaces, leads to selectively absorbing specific types of waveforms or pulse widths even at the same frequency. These waveform-selective metasurfaces effectively showed different absorbing performances for different widths of pulsed sine waves by gradually varying their electromagnetic responses in time domain. Here we study time-filtering effects of such circuit-based metasurfaces illuminated by continuous sine waves. Moreover, we introduce extra circuit elements to these structures to enhance the time-domain control capability. These time-varying properties are expected to give us another degree of freedom to control electromagnetic waves and thus contribute to developing new kinds of electromagnetic applications and technologies, e.g. time-windowing wireless communications and waveform conversion. PMID:26564027

  15. Allosteric Communication in the Dynein Motor Domain

    PubMed Central

    Bhabha, Gira; Cheng, Hui-Chun; Zhang, Nan; Moeller, Arne; Liao, Maofu; Speir, Jeffrey A.; Cheng, Yifan; Vale, Ronald D.

    2014-01-01

    SUMMARY Dyneins power microtubule motility using ring-shaped, AAA-containing motor domains. Here, we report X-ray and electron microscopy (EM) structures of yeast dynein bound to different ATP analogs, which collectively provide insight into the roles of dynein’s two major ATPase sites, AAA1 and AAA3, in the conformational change mechanism. ATP binding to AAA1 triggers a cascade of conformational changes that propagate to all six AAA domains and cause a large movement of the “linker,” dynein’s mechanical element. In contrast to the role of AAA1 in driving motility, nucleotide transitions in AAA3 gate the transmission of conformational changes between AAA1 and the linker, suggesting that AAA3 acts as a regulatory switch. Further structural and mutational studies also uncover a role for the linker in regulating the catalytic cycle of AAA1. Together, these results reveal how dynein’s two major ATP-binding sites initiate and modulate conformational changes in the motor domain during motility. PMID:25417161

  16. Time-domain robotic vision application

    NASA Technical Reports Server (NTRS)

    Tolliver, C. L.

    1987-01-01

    The quest for the highest resolution microwaves imaging and the principle of time-domain imaging is the primary motivation for recent developments in time-domain techniques. With the present technology fast time varying signals can now be measured and recorded both in magnitude and in phase. It has also enhanced the ability to extract relevant details concerning the scattering object. In the past, the inference of object geometry or shape from scattered signals has received substantial attention in radar technology. Various inverse scattering theories were proposed to develop analytical solutions to this problem. Furthermore, the random inversion, frequenty swept holography, and the synthetic radar imaging, all of which have two things in common: the physical optic far-field approximation and the utilization of the channels as an extra physical dimension, were also advanced significantly. Despite the inherent vectorial nature of electromagnetic waves, these scalar treatments have brought forth some promising results in practice with notable examples in subsurface and structure sounding. The use of time-domain imaging for space robotic vision applications was proposed. A multisensor approach to vision was shown to have several advantages over the video-only approach.

  17. PDZ domain from Dishevelled -- a specificity study.

    PubMed

    Śmietana, Katarzyna; Mateja, Agnieszka; Krężel, Artur; Otlewski, Jacek

    2011-01-01

    Intracellular signaling cascades induced by Wnt proteins play a key role in developmental processes and are implicated in cancerogenesis. It is still unclear how the cell determines which of the three possible Wnt response mechanisms should be activated, but the decision process is most likely dependent on Dishevelled proteins. Dishevelled family members interact with many diverse targets, however, molecular mechanisms underlying these binding events have not been comprehensively described so far. Here, we investigated the specificity of the PDZ domain from human Dishevelled-2 using C-terminal phage display, which led us to identification of a leucine-rich binding motif strongly resembling the consensus sequence of a nuclear export signal. PDZ interactions with several peptide and protein motifs (including the nuclear export signal sequence from Dishevelled-2 protein) were investigated in detail using fluorescence spectroscopy, mutational analysis and immunoenzymatic assays. The experiments showed that the PDZ domain can bind the nuclear export signal sequence of the Dishevelled-2 protein. Since the intracellular localization of Dishevelled is governed by nuclear localization and nuclear export signal sequences, it is possible that the intramolecular interaction between PDZ domain and the export signal could modulate the balance between nuclear and cytoplasmic pool of the Dishevelled protein. Such a regulatory mechanism would be of utmost importance for the differential activation of Wnt signaling cascades, leading to selective promotion of the nucleus-dependent Wnt β-catenin pathway at the expense of non-canonical Wnt signaling. PMID:21666888

  18. Time-Domain Filtering of Metasurfaces

    PubMed Central

    Wakatsuchi, Hiroki

    2015-01-01

    In general electromagnetic response of each material to a continuous wave does not vary in time domain if the frequency component remains the same. Recently, it turned out that integrating several circuit elements including schottky diodes with periodically metallised surfaces, or the so-called metasurfaces, leads to selectively absorbing specific types of waveforms or pulse widths even at the same frequency. These waveform-selective metasurfaces effectively showed different absorbing performances for different widths of pulsed sine waves by gradually varying their electromagnetic responses in time domain. Here we study time-filtering effects of such circuit-based metasurfaces illuminated by continuous sine waves. Moreover, we introduce extra circuit elements to these structures to enhance the time-domain control capability. These time-varying properties are expected to give us another degree of freedom to control electromagnetic waves and thus contribute to developing new kinds of electromagnetic applications and technologies, e.g. time-windowing wireless communications and waveform conversion. PMID:26564027

  19. Domain wall motion in ferroelectrics: Barkhausen noise

    NASA Astrophysics Data System (ADS)

    Shur, V.; Rumyantsev, E.; Kozhevnikov, V.; Nikolaeva, E.; Shishkin, E.

    2002-03-01

    The switching current noise has been recorded during polarization reversal in single-crystalline gadolinium molybdate (GMO) and lithium tantalate (LT). Analysis of Barkhausen noise (BN) data allows to classify the noise types by determination of the critical indexes and fractal dimensions. BN is manifested as the short pulses during the polarization reversal. We have analyzed the BN data recorded in GMO and LT with various types of controlled domain structure. The data treatment in terms of probability distribution of duration, area and energy of individual pulses reveals the critical behavior typical for the fractal records in time. We used the Fourier transform and Hurst's rescaled range analysis for obtaining the Hurst factor, fractal dimension and classifying the noise types. We investigated by computer simulation the mechanism of sideways motion of 180O domain wall by nucleation at the wall taking into account the nuclei-nuclei interaction. It was shown that the moving domain walls display the fractal shape and their motion is accompanied by Flicker noise, which is in accord with experimental data. The research was made possible in part by Programs "Basic Research in Russian Universities" and "Priority Research in High School. Electronics", by Grant No. 01-02-17443 of RFBR, by Award No.REC-005 of CRDF.

  20. Folding and Aggregation of Mucin Domains.

    NASA Astrophysics Data System (ADS)

    Urbanc, Brigita; Bansil, Rama; Turner, Bradley

    2007-03-01

    Mucin glycoproteins consist of tandem repeating glycosylated regions flanked by non-repetitive protein domains with little glycosylation. These non-repetitive domains are involved in polymerization of mucin via disulfide bonds and play an important role in the pH dependent gelation of gastric mucin, which is essential to protecting the stomach from autodigestion. We have examined the folding and aggregation of the non-repetitive sequence of von Willebrand factor vWF-C1 domain (67 amino acids) and PGM 2X (242 amino acids) using Discrete Molecular Dynamics (four-bead protein model with hydrogen bonding and amino acid-specific hydrophobic/hydrophilic and electrostatic interactions of side chains). Simulations of vWF C1 show 4-6 β-strands separated by turns/loops with more loops at lower pH. A simulation of several vWF C1 proteins at low pH shows aggregates still with a high content of β-strands and enhanced turn/loop regions. For the PGM 2X simulation the contact map shows several salt bridges enclosing hairpin turns. The implications of these simulations for describing the aggregation/gelation of PGM will be discussed.

  1. Domain specific software design for decision aiding

    NASA Technical Reports Server (NTRS)

    Keller, Kirby; Stanley, Kevin

    1992-01-01

    McDonnell Aircraft Company (MCAIR) is involved in many large multi-discipline design and development efforts of tactical aircraft. These involve a number of design disciplines that must be coordinated to produce an integrated design and a successful product. Our interpretation of a domain specific software design (DSSD) is that of a representation or framework that is specialized to support a limited problem domain. A DSSD is an abstract software design that is shaped by the problem characteristics. This parallels the theme of object-oriented analysis and design of letting the problem model directly drive the design. The DSSD concept extends the notion of software reusability to include representations or frameworks. It supports the entire software life cycle and specifically leads to improved prototyping capability, supports system integration, and promotes reuse of software designs and supporting frameworks. The example presented in this paper is the task network architecture or design which was developed for the MCAIR Pilot's Associate program. The task network concept supported both module development and system integration within the domain of operator decision aiding. It is presented as an instance where a software design exhibited many of the attributes associated with DSSD concept.

  2. Nuclear domain 10 of the viral aspect

    PubMed Central

    Rivera-Molina, Yisel A; Martínez, Francisco Puerta; Tang, Qiyi

    2013-01-01

    Nuclear domain 10 (ND10) are spherical bodies distributed throughout the nucleoplasm and measuring around 0.2-1.0 μm. First observed under an electron microscope, they were originally described as dense bodies found in the nucleus. They are known by a number of other names, including Promyelocytic Leukemia bodies (PML bodies), Kremer bodies, and PML oncogenic domains. ND10 are frequently associated with Cajal bodies and cleavage bodies. It has been suggested that they play a role in regulating gene transcription. ND10 were originally characterized using human autoantisera, which recognizes Speckled Protein of 100 kDa, from patients with primary biliary cirrhosis. At the immunohistochemical level, ND10 appear as nuclear punctate structures, with 10 indicating the approximate number of dots per nucleus observed. ND10 do not colocalize with kinetochores, centromeres, sites of mRNA processing, or chromosomes. Resistance of ND10 antigens to nuclease digestion and salt extraction suggest that ND10 are associated with the nuclear matrix. They are often identified by immunofluorescent assay using specific antibodies against PML, Death domain-associated protein, nuclear dot protein (NDP55), and so on. The role of ND10 has long been the subject of investigation, with the specific connection of ND10 and viral infection having been a particular focus for almost 20 years. This review summarizes the relationship of ND10 and viral infection. Some future study directions are also discussed. PMID:24255882

  3. Interactions between domain walls and spin currents

    NASA Astrophysics Data System (ADS)

    Klaui, M.; Laufenberg, M.; Backes, D.; Buhrer, W.; Rudiger, U.; Vila, L.; Vouille, C.; Faini, G.

    2006-03-01

    A promising novel approach for switching magnetic nanostructures is current-induced domain wall propagation (CIDP), where due to a spin torque effect, electrons transfer angular momentum to a head-to-head domain wall and thereby push it in the direction of the electron flow without any externally applied fields. This effect has been observed with a variety of techniques including MFM [1] and spin polarized scanning electron microscopy [2] to directly observe current-induced domain wall propagation in ferromagnetic nanostructures and magnetoresistance measurements to systematically probe the critical current densities as a function of the geometry [3]. The observed wall velocities and critical current densities, where wall motion sets in at room temperature, do not agree well with theoretical 0K calculations [4]. We have therefore measured the critical current densities as a function of the sample temperature. We find that the spin torque effect becomes more efficient at low temperatures, which could account for some of the observed discrepancies between the 300K experiment and the 0K simulation. [1] A. Yamaguchi et al., Phys. Rev. Lett. 92, 77205 (2004); [2] M. Klaui et al., PRL 95, 26601 (2005); [3] M. Klaui et al., PRL 94, 106601 (2005); [4] A. Thiaville et al., EPL 69, 990 (2005); G. Tatara et al., APL 86, 252509 (2005);

  4. Energy of domain walls in ferrite films

    NASA Astrophysics Data System (ADS)

    Gomez, M. E.; Prieto, P.; Mendoza, A.; Guzman, O.

    2007-03-01

    MnZn Ferrite films were deposited by RF sputtering on (001) single crystal MgO substrates. AFM images show an increment in grain size with the film thickness. Grains with diameter between φ ˜ 70 and 700 nm have been observed. The coercive field Hc as a function of the grain size reaches a maximum value of about 80 Oe for φc˜ 300 nm. The existence of a multidomain structure associated with a critical grain size was identified by Magneto-optical Kerr effect technique (MOKE). The transition of the one-domain regime to the two-domain regime was observed at a critical grain size of Dc˜ 530 nm. This value agree with values predicted previously. The Jiles-Atherton model (JAM) was used to discuss the experimental hysteresis loops. The k pinning parameter obtained from JAM shows a maximum value of k/μo = 67 Am^2 for grains with Lc˜ 529 nm. The total energy per unit area E was correlated with k and D. We found a simple phenomenological relationship given by E α kD; where D is the magnetic domain width.

  5. Birdsong dialect patterns explained using magnetic domains

    NASA Astrophysics Data System (ADS)

    Burridge, James; Kenney, Steven

    2016-06-01

    The songs and calls of many bird species, like human speech, form distinct regional dialects. We suggest that the process of dialect formation is analogous to the physical process of magnetic domain formation. We take the coastal breeding grounds of the Puget Sound white crowned sparrow as an example. Previous field studies suggest that birds of this species learn multiple songs early in life, and when establishing a territory for the first time, retain one of these dialects in order to match the majority of their neighbors. We introduce a simple lattice model of the process, showing that this matching behavior can produce single dialect domains provided the death rate of adult birds is sufficiently low. We relate death rate to thermodynamic temperature in magnetic materials, and calculate the critical death rate by analogy with the Ising model. Using parameters consistent with the known behavior of these birds we show that coastal dialect domain shapes may be explained by viewing them as low-temperature "stripe states."

  6. Birdsong dialect patterns explained using magnetic domains.

    PubMed

    Burridge, James; Kenney, Steven

    2016-06-01

    The songs and calls of many bird species, like human speech, form distinct regional dialects. We suggest that the process of dialect formation is analogous to the physical process of magnetic domain formation. We take the coastal breeding grounds of the Puget Sound white crowned sparrow as an example. Previous field studies suggest that birds of this species learn multiple songs early in life, and when establishing a territory for the first time, retain one of these dialects in order to match the majority of their neighbors. We introduce a simple lattice model of the process, showing that this matching behavior can produce single dialect domains provided the death rate of adult birds is sufficiently low. We relate death rate to thermodynamic temperature in magnetic materials, and calculate the critical death rate by analogy with the Ising model. Using parameters consistent with the known behavior of these birds we show that coastal dialect domain shapes may be explained by viewing them as low-temperature "stripe states." PMID:27415293

  7. Lipid Bilayer Domain Fluctuations as a Probe of Membrane Viscosity

    PubMed Central

    Camley, Brian A.; Esposito, Cinzia; Baumgart, Tobias; Brown, Frank L.H.

    2010-01-01

    We argue that membrane viscosity, ηm, plays a prominent role in the thermal fluctuation dynamics of micron-scale lipid domains. A theoretical expression is presented for the timescales of domain shape relaxation, which reduces to the well-known ηm = 0 result of Stone and McConnell in the limit of large domain sizes. Experimental measurements of domain dynamics on the surface of ternary phospholipid and cholesterol vesicles confirm the theoretical results and suggest domain flicker spectroscopy as a convenient means to simultaneously measure both the line tension, σ, and the membrane viscosity, ηm, governing the behavior of individual lipid domains. PMID:20858410

  8. Antiferromagnetic Domain Wall Motion Driven by Spin-Orbit Torques.

    PubMed

    Shiino, Takayuki; Oh, Se-Hyeok; Haney, Paul M; Lee, Seo-Won; Go, Gyungchoon; Park, Byong-Guk; Lee, Kyung-Jin

    2016-08-19

    We theoretically investigate the dynamics of antiferromagnetic domain walls driven by spin-orbit torques in antiferromagnet-heavy-metal bilayers. We show that spin-orbit torques drive antiferromagnetic domain walls much faster than ferromagnetic domain walls. As the domain wall velocity approaches the maximum spin-wave group velocity, the domain wall undergoes Lorentz contraction and emits spin waves in the terahertz frequency range. The interplay between spin-orbit torques and the relativistic dynamics of antiferromagnetic domain walls leads to the efficient manipulation of antiferromagnetic spin textures and paves the way for the generation of high frequency signals from antiferromagnets. PMID:27588878

  9. Tunable conductance of magnetic nanowires with structured domain walls.

    PubMed

    Dugaev, V K; Berakdar, J; Barnaś, J

    2006-02-01

    We show that in a magnetic nanowire with double magnetic domain walls, quantum interference results in spin-split quasistationary states localized mainly between the domain walls. Spin-flip-assisted transmission through the domain structure increases strongly when these size-quantized states are tuned on resonance with the Fermi energy, e.g., upon varying the distance between the domain walls which results in resonance-type peaks of the wire conductance. This novel phenomenon is shown to be utilizable to manipulate the spin density in the domain vicinity. The domain wall parameters are readily controllable, and the predicted effect is hence exploitable in spintronic devices. PMID:16486888

  10. SARS Coronavirus-unique Domain (SUD): Three-domain Molecular Architecture in Solution and RNA Binding

    PubMed Central

    Johnson, Margaret A.; Chatterjee, Amarnath; Neuman, Benjamin W.; Wüthrich, Kurt

    2010-01-01

    The nonstructural protein 3 (nsp3) of the severe acute respiratory syndrome coronavirus (SARS-CoV) includes a “SARS-unique region” (SUD) consisting of three globular domains separated by short linker peptide segments. This paper reports NMR structure determinations of the C-terminal domain (SUD-C) and of a two-domain construct (SUD-MC) containing the middle domain (SUD-M) and the C-terminal domain, and NMR data on the conformational states of the N-terminal domain (SUD-N) and the SUD-NM two-domain construct. Both SUD-N and SUD-NM are monomeric and globular in solution, and in SUD-NM there is high mobility in the two-residue interdomain linking sequence, with no preferred relative orientation of the two domains. SUD-C adopts a frataxin-like fold and has structural similarity to DNA-binding domains of DNA-modifying enzymes. The structures of both SUD-M (previously determined) and SUD-C (from the present study) are maintained in SUD-MC, where the two domains are flexibly linked. Gel shift experiments showed that both SUD-C and SUD-MC bind to single-stranded RNA and recognize purine bases more strongly than pyrimidine bases, whereby SUD-MC binds to a more restricted set of purine-containing RNA sequences than SUD-M. NMR chemical shift perturbation experiments with observation of the 15N-labeled proteins further resulted in the delineation of the RNA binding sites, i.e., in SUD-M a positively charged surface area with a pronounced cavity, and in SUD-C several residues of an antiparallel β-sheet. Overall, the present data provide evidence for molecular mechanisms involving concerted actions of SUD-M and SUD-C, which result in specific RNA-binding that might be unique to the SUD, and thus to the SARS-CoV. PMID:20493876

  11. Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes

    PubMed Central

    Upadhyay, Amit A.; Fleetwood, Aaron D.; Adebali, Ogun; Finn, Robert D.; Zhulin, Igor B.

    2016-01-01

    Cellular receptors usually contain a designated sensory domain that recognizes the signal. Per/Arnt/Sim (PAS) domains are ubiquitous sensors in thousands of species ranging from bacteria to humans. Although PAS domains were described as intracellular sensors, recent structural studies revealed PAS-like domains in extracytoplasmic regions in several transmembrane receptors. However, these structurally defined extracellular PAS-like domains do not match sequence-derived PAS domain models, and thus their distribution across the genomic landscape remains largely unknown. Here we show that structurally defined extracellular PAS-like domains belong to the Cache superfamily, which is homologous to, but distinct from the PAS superfamily. Our newly built computational models enabled identification of Cache domains in tens of thousands of signal transduction proteins including those from important pathogens and model organisms. Furthermore, we show that Cache domains comprise the dominant mode of extracellular sensing in prokaryotes. PMID:27049771

  12. A two-domain model for the R domain of the cystic fibrosis transmembrane conductance regulator based on sequence similarities.

    PubMed

    Dulhanty, A M; Riordan, J R

    1994-04-25

    CFTR belongs to a group of proteins sharing the structural motif of six transmembrane helices and a nucleotide binding domain. Unique to CFTR is the R domain, a charged cytoplasmic domain. Comparison of R domain sequences from ten species revealed that the N-terminal third is highly conserved, while the C-terminal two-thirds is poorly conserved. The R domain shows no strong sequence similarity to known proteins; however, 14 viral pol proteins show limited similarity to fragments of the R domain. Analysis revealed a relationship between the N- and C-terminal fragments of the R domain and two discontinuous fragments of the pol protein. These observations support a two-domain model for the R domain. PMID:7513286

  13. Structure-dependent electrical conductivity of protein: its differences between alpha-domain and beta-domain structures.

    PubMed

    Zhang, X Y; Shao, Jian; Jiang, S X; Wang, Biao; Zheng, Yue

    2015-03-27

    Electron transports in the α-domain and β-domain of proteins have been comprehensively investigated. The structure-dependent electron transport of proteins has been experimentally measured and theoretically simulated, and both the theoretical and experimental results demonstrate significant differences in electrical conductivity between the α-domain and β-domain. By controlling the feedback system of the scanning tunneling microscope (STM), the conductance of a single α-domain protein hemoglobin (Hgb) and a β-domain protein superoxide dismutase enzyme (SOD) were measured, respectively. The current signal of Hgb is obviously stronger, indicating that the α-domain is more conductive. To confirm our finding, molecular orbitals of both the β-domain in SOD and α-domain in Hgb have been analyzed based on first-principles calculations. As expected, tunneling transport and hopping in the α-domain are both more efficient, indicating that it is easier for electrons to transport through the α-domain, which are in great agreement with our experimental data. In order to explain our results, molecular structures of α- and β-domains have been carefully analyzed and show that the explanation should lie in the differences in packing mode between the α-domain and β-domain. This research should be very important to application prospects in molecular electronics. PMID:25736549

  14. Structure-dependent electrical conductivity of protein: its differences between alpha-domain and beta-domain structures

    NASA Astrophysics Data System (ADS)

    Zhang, X. Y.; Shao, Jian; Jiang, S. X.; Wang, Biao; Zheng, Yue

    2015-03-01

    Electron transports in the α-domain and β-domain of proteins have been comprehensively investigated. The structure-dependent electron transport of proteins has been experimentally measured and theoretically simulated, and both the theoretical and experimental results demonstrate significant differences in electrical conductivity between the α-domain and β-domain. By controlling the feedback system of the scanning tunneling microscope (STM), the conductance of a single α-domain protein hemoglobin (Hgb) and a β-domain protein superoxide dismutase enzyme (SOD) were measured, respectively. The current signal of Hgb is obviously stronger, indicating that the α-domain is more conductive. To confirm our finding, molecular orbitals of both the β-domain in SOD and α-domain in Hgb have been analyzed based on first-principles calculations. As expected, tunneling transport and hopping in the α-domain are both more efficient, indicating that it is easier for electrons to transport through the α-domain, which are in great agreement with our experimental data. In order to explain our results, molecular structures of α- and β-domains have been carefully analyzed and show that the explanation should lie in the differences in packing mode between the α-domain and β-domain. This research should be very important to application prospects in molecular electronics.

  15. Thermomagnetic Stability in Pseudo Single Domain Grains

    NASA Astrophysics Data System (ADS)

    Nagy, Lesleis; Williams, Wyn; Muxworthy, Adrian; Fabian, Karl; Conbhuí, Pádraig Ó.

    2016-04-01

    The reliability of paleomagnetic remanences are well understood for fine grains of magnetite that are single-domain (SD, uniformly magnetized). In particular Néel's theory [1] outlined the thermal energies required to block and unblock magnetic remanences. This lead to determination of thermal stability for magnetization in fine grains as outlined in Pullaiah et. al. [2] and a comprehensive understanding of SD paleomagnetic recordings. It has been known for some time that single domain magnetite is possible only in the grain size range 30 - 80nm, which may only account for a small fraction of the grain size distribution in any rock sample. Indeed rocks are often dominated by grains in the pseudo single domain (PSD) size range, at approximately 80 - 1000nm. Toward the top end of this range multi-domain features begin to dominate. In order to determine thermomagnetic stability in PSD grains we need to identify the energy barriers between all possible pairs of local energy minima (LEM) domain states as a function of both temperature and grain size. We have attempted to do this using the nudged elastic band (NEB) method [3] which searches for minimum energy paths between any given pair of LEM states. Using this technique we have determined, for the first time, complete thermomagnetic stability curves for PSD magnetite. The work presented is at a preliminary stage. However it can be shown that PSD grains of magnetite with simple geometries (e.g. cubes or cuboctahedra) have very few low energy transition paths and the stability is likely to be similar to that observed for SD grains (as expected form experimental observations). The results will provide a basis for a much more rigorous understanding of the fidelity of paleomagnetic signals in assemblages of PSD grains and their ability to retain ancient recordings of the geomagnetic field. References: [1] Néel, Louis. "Théorie du traînage magnétique des ferromagnétiques en grains fins avec applications aux terres

  16. Ezrin NH2-terminal domain inhibits the cell extension activity of the COOH-terminal domain

    PubMed Central

    1995-01-01

    Overexpression in insect cells of the full coding sequence of the human membrane cytoskeletal linker ezrin (1-586) was compared with that of a NH2-terminal domain (ezrin 1-233) and that of a COOH-terminal domain (ezrin 310-586). Ezrin (1-586), as well as ezrin (1-233) enhanced cell adhesion of infected Sf9 cells without inducing gross morphological changes in the cell structure. Ezrin (310-586) enhanced cell adhesion and elicited membrane spreading followed by microspike and lamellipodia extensions by mobilization of Sf9 cell actin. Moreover some microspikes elongated into thin processes, up to 200 microns in length, resembling neurite outgrowths by a mechanism requiring microtubule assembly. Kinetics of videomicroscopic and drug-interference studies demonstrated that mobilization of actin was required for tubulin assembly to proceed. A similar phenotype was observed in CHO cells when a comparable ezrin domain was transiently overexpressed. The shortest domain promoting cell extension was localized between residues 373-586. Removal of residues 566-586, involved in in vitro actin binding (Turunen, O., T. Wahlstrom, and A. Vaheri. 1994. J. Cell Biol. 126:1445- 1453), suppressed the extension activity. Coexpression of ezrin (1-233) with ezrin (310-586) in the same insect cells blocked the constitutive activity of ezrin COOH-terminal domain. The inhibitory activity was mapped within ezrin 115 first NH2-terminal residues. We conclude that ezrin has properties to promote cell adhesion, and that ezrin NH2- terminal domain negatively regulates membrane spreading and elongation properties of ezrin COOH-terminal domain. PMID:7896873

  17. Translocation of the Catalytic Domain of Diphtheria Toxin across Planar Phospholipid Bilayers by Its Own T Domain

    NASA Astrophysics Data System (ADS)

    Oh, Kyoung Joon; Senzel, Lisa; Collier, R. John; Finkelstein, Alan

    1999-07-01

    The T domain of diphtheria toxin is known to participate in the pH-dependent translocation of the catalytic C domain of the toxin across the endosomal membrane, but how it does so, and whether cellular proteins are also required for this process, remain unknown. Here, we report results showing that the T domain alone is capable of translocating the entire C domain across model, planar phospholipid bilayers in the absence of other proteins. The T domain therefore contains the entire molecular machinery for mediating transfer of the catalytic domain of diphtheria toxin across membranes.

  18. Binding to retinoblastoma pocket domain does not alter the inter-domain flexibility of the J domain of SV40 large T antigen.

    PubMed

    Williams, Christina K; Vaithiyalingam, Sivaraja; Hammel, Michal; Pipas, James; Chazin, Walter J

    2012-02-15

    Simian Virus 40 uses the large T antigen (Tag) to bind and inactivate retinoblastoma tumor suppressor proteins (Rb), which can result in cellular transformation. Tag is a modular protein with four domains connected by flexible linkers. The N-terminal J domain of Tag is necessary for Rb inactivation. Binding of Rb is mediated by an LXCXE consensus motif immediately C-terminal to the J domain. Nuclear magnetic resonance (NMR) and small angle X-ray scattering (SAXS) were used to study the structural dynamics and interaction of Rb with the LXCXE motif, the J domain and a construct (N(260)) extending from the J domain through the origin binding domain (OBD). NMR and SAXS data revealed substantial flexibility between the domains in N(260). Binding of pRb to a construct containing the LXCXE motif and the J domain revealed weak interactions between pRb and the J domain. Analysis of the complex of pRb and N(260) indicated that the OBD is not involved and retains its dynamic independence from the remainder of Tag. These results support a 'chaperone' model in which the J domain of Tag changes its orientation as it acts upon different protein complexes. PMID:22227098

  19. Solution structure of leptospiral LigA4 Big domain.

    PubMed

    Mei, Song; Zhang, Jiahai; Zhang, Xuecheng; Tu, Xiaoming

    2015-11-13

    Pathogenic Leptospiraspecies express immunoglobulin-like proteins which serve as adhesins to bind to the extracellular matrices of host cells. Leptospiral immunoglobulin-like protein A (LigA), a surface exposed protein containing tandem repeats of bacterial immunoglobulin-like (Big) domains, has been proved to be involved in the interaction of pathogenic Leptospira with mammalian host. In this study, the solution structure of the fourth Big domain of LigA (LigA4 Big domain) from Leptospira interrogans was solved by nuclear magnetic resonance (NMR). The structure of LigA4 Big domain displays a similar bacterial immunoglobulin-like fold compared with other Big domains, implying some common structural aspects of Big domain family. On the other hand, it displays some structural characteristics significantly different from classic Ig-like domain. Furthermore, Stains-all assay and NMR chemical shift perturbation revealed the Ca(2+) binding property of LigA4 Big domain. PMID:26449456

  20. Generalization Bounds Derived IPM-Based Regularization for Domain Adaptation.

    PubMed

    Meng, Juan; Hu, Guyu; Li, Dong; Zhang, Yanyan; Pan, Zhisong

    2016-01-01

    Domain adaptation has received much attention as a major form of transfer learning. One issue that should be considered in domain adaptation is the gap between source domain and target domain. In order to improve the generalization ability of domain adaption methods, we proposed a framework for domain adaptation combining source and target data, with a new regularizer which takes generalization bounds into account. This regularization term considers integral probability metric (IPM) as the distance between the source domain and the target domain and thus can bound up the testing error of an existing predictor from the formula. Since the computation of IPM only involves two distributions, this generalization term is independent with specific classifiers. With popular learning models, the empirical risk minimization is expressed as a general convex optimization problem and thus can be solved effectively by existing tools. Empirical studies on synthetic data for regression and real-world data for classification show the effectiveness of this method. PMID:26819589

  1. Periodic magnetic domains in single-crystalline cobalt filament arrays

    NASA Astrophysics Data System (ADS)

    Chen, Fei; Wang, Fan; Jia, Fei; Li, Jingning; Liu, Kai; Huang, Sunxiang; Luan, Zhongzhi; Wu, Di; Chen, Yanbin; Zhu, Jianmin; Peng, Ru-Wen; Wang, Mu

    2016-02-01

    Magnetic structures with controlled domain wall pattern may be applied as potential building blocks for three-dimensional magnetic memory and logic devices. Using a unique electrochemical self-assembly method, we achieve regular single-crystalline cobalt filament arrays with specific geometric profile and crystallographic orientation, and the magnetic domain configuration can be conveniently tailored. We report the transition of periodic antiparallel magnetic domains to compressed vortex magnetic domains depending on the ratio of height to width of the wires. A "phase diagram" is obtained to describe the dependence of the type of magnetic domain and the geometrical profiles of the wires. Magnetoresistance of the filaments demonstrates that the contribution of a series of 180∘ domain walls is over 0.15 % of the zero-field resistance ρ (H =0 ) . These self-assembled magnetic nanofilaments, with controlled periodic domain patterns, offer an interesting platform to explore domain-wall-based memory and logic devices.

  2. Generating target system specifications from a domain model using CLIPS

    NASA Technical Reports Server (NTRS)

    Sugumaran, Vijayan; Gomaa, Hassan; Kerschberg, Larry

    1991-01-01

    The quest for reuse in software engineering is still being pursued and researchers are actively investigating the domain modeling approach to software construction. There are several domain modeling efforts reported in the literature and they all agree that the components that are generated from domain modeling are more conducive to reuse. Once a domain model is created, several target systems can be generated by tailoring the domain model or by evolving the domain model and then tailoring it according to the specified requirements. This paper presents the Evolutionary Domain Life Cycle (EDLC) paradigm in which a domain model is created using multiple views, namely, aggregation hierarchy, generalization/specialization hierarchies, object communication diagrams and state transition diagrams. The architecture of the Knowledge Based Requirements Elicitation Tool (KBRET) which is used to generate target system specifications is also presented. The preliminary version of KBRET is implemented in the C Language Integrated Production System (CLIPS).

  3. Domain structure of black hole space-times

    SciTech Connect

    Harmark, Troels

    2009-07-15

    We introduce the domain structure for stationary black hole space-times. The domain structure lives on the submanifold of fixed points of the Killing vector fields. Depending on which Killing vector field has fixed points the submanifold is naturally divided into domains. The domain structure provides invariants of the space-time, both topological and continuous. It is defined for any space-time dimension and any number of Killing vector fields. We examine the domain structure for asymptotically flat space-times and find a canonical form for the metric of such space-times. The domain structure generalizes the rod structure introduced for space-times with D-2 commuting Killing vector fields. We analyze in detail the domain structure for Minkowski space, the Schwarzschild-Tangherlini black hole and the Myers-Perry black hole in six and seven dimensions. Finally, we consider the possible domain structures for asymptotically flat black holes in six and seven dimensio0008.

  4. Generalization Bounds Derived IPM-Based Regularization for Domain Adaptation

    PubMed Central

    Meng, Juan; Hu, Guyu; Zhang, Yanyan

    2016-01-01

    Domain adaptation has received much attention as a major form of transfer learning. One issue that should be considered in domain adaptation is the gap between source domain and target domain. In order to improve the generalization ability of domain adaption methods, we proposed a framework for domain adaptation combining source and target data, with a new regularizer which takes generalization bounds into account. This regularization term considers integral probability metric (IPM) as the distance between the source domain and the target domain and thus can bound up the testing error of an existing predictor from the formula. Since the computation of IPM only involves two distributions, this generalization term is independent with specific classifiers. With popular learning models, the empirical risk minimization is expressed as a general convex optimization problem and thus can be solved effectively by existing tools. Empirical studies on synthetic data for regression and real-world data for classification show the effectiveness of this method. PMID:26819589

  5. Apoplastic domains and sub-domains in the shoots of etiolated corn seedlings

    NASA Technical Reports Server (NTRS)

    Epel, B. L.; Bandurski, R. S.

    1990-01-01

    Light Green, an apoplastic probe, was applied to the cut mesocotyl base or to the cut coleoptile apex of etiolated seedlings of Zea mays L. cv. Silver Queen. Probe transport was measured and its tissue distribution determined. In the mesocotyl, there is an apoplastic barrier between cortex and stele. This barrier creates two apoplastic domains which are non-communicating. A kinetic barrier exists between the apoplast of the mesocotyl stele and that of the coleoptile. This kinetic barrier is not absolute and there is limited communication between the apoplasts of the two regions. This kinetic barrier effectively creates two sub-domains. In the coleoptile, there is communication between the apoplast of the vascular strands and that of the surrounding cortical tissue. No apoplastic communication was observed between the coleoptile cortex and the mesocotyl cortex. Thus, the apoplastic space of the coleoptile cortex is a sub-domain of the integrated coleoptile domain and is separate from that of the apoplastic domain of the mesocotyl cortex.

  6. Prediction of Domain Behavior through Dynamic Well-Being Domain Model Analysis

    PubMed Central

    Bosems, Steven; van Sinderen, Marten

    2015-01-01

    As the concept of context-awareness is becoming more popular the demand for improved quality of context-aware systems increases too. Due to the inherent challenges posed by context-awareness, it is harder to predict what the behavior of the systems and their context will be once provided to the end-user than is the case for non-context-aware systems. A domain where such upfront knowledge is highly important is that of well-being. In this paper, we introduce a method to model the well-being domain and to predict the effects the system will have on its context when implemented. This analysis can be performed at design time. Using these predictions, the design can be fine-tuned to increase the chance that systems will have the desired effect. The method has been tested using three existing well-being applications. For these applications, domain models were created in the Dynamic Well-being Domain Model language. This language allows for causal reasoning over the application domain. The models created were used to perform the analysis and behavior prediction. The analysis results were compared to existing application end-user evaluation studies. Results showed that our analysis could accurately predict success and possible problems in the focus of the systems, although certain limitation regarding the predictions should be kept into consideration. PMID:26351660

  7. Entropy production by domain wall decay in the NMSSM

    NASA Astrophysics Data System (ADS)

    Hattori, Hironori; Kobayashi, Tatsuo; Omoto, Naoya; Seto, Osamu

    2015-11-01

    We consider domain walls in the Z3 symmetric next-to-minimal supersymmetric standard model. The spontaneous Z3 discrete symmetry breaking produces domain walls, and the stable domain walls are problematic. Thus, we assume the Z3 symmetry is slightly but explicitly broken and the domain walls decay. Such a decay causes a large late-time entropy production. We study its cosmological implications on unwanted relics such as the moduli, gravitino, lightest superparticle, and axion.

  8. Credentialing Data Scientists: A Domain Repository Perspective

    NASA Astrophysics Data System (ADS)

    Lehnert, K. A.; Furukawa, H.

    2015-12-01

    A career in data science can have many paths: data curation, data analysis, metadata modeling - all of these in different commercial or scientific applications. Can a certification as 'data scientist' provide the guarantee that an applicant or candidate for a data science position has just the right skills? How valuable is a 'generic' certification as data scientist for an employer looking to fill a data science position? Credentials that are more specific and discipline-oriented may be more valuable to both the employer and the job candidate. One employment sector for data scientists are the data repositories that provide discipline-specific data services for science communities. Data science positions within domain repositories include a wide range of responsibilities in support of the full data life cycle - from data preservation and curation to development of data models, ontologies, and user interfaces, to development of data analysis and visualization tools to community education and outreach, and require a substantial degree of discipline-specific knowledge of scientific data acquisition and analysis workflows, data quality measures, and data cultures. Can there be certification programs for domain-specific data scientists that help build the urgently needed workforce for the repositories? The American Geophysical Union has recently started an initiative to develop a program for data science continuing education and data science professional certification for the Earth and space sciences. An Editorial Board has been charged to identify and develop curricula and content for these programs and to provide input and feedback in the implementation of the program. This presentation will report on the progress of this initiative and evaluate its utility for the needs of domain repositories in the Earth and space sciences.

  9. Stochastic finite-difference time-domain

    NASA Astrophysics Data System (ADS)

    Smith, Steven Michael

    2011-12-01

    This dissertation presents the derivation of an approximate method to determine the mean and the variance of electro-magnetic fields in the body using the Finite-Difference Time-Domain (FDTD) method. Unlike Monte Carlo analysis, which requires repeated FDTD simulations, this method directly computes the variance of the fields at every point in space at every sample of time in the simulation. This Stochastic FDTD simulation (S-FDTD) has at its root a new wave called the Variance wave, which is computed in the time domain along with the mean properties of the model space in the FDTD simulation. The Variance wave depends on the electro-magnetic fields, the reflections and transmission though the different dielectrics, and the variances of the electrical properties of the surrounding materials. Like the electro-magnetic fields, the Variance wave begins at zero (there is no variance before the source is turned on) and is computed in the time domain until all fields reach steady state. This process is performed in a fraction of the time of a Monte Carlo simulation and yields the first two statistical parameters (mean and variance). The mean of the field is computed using the traditional FDTD equations. Variance is computed by approximating the correlation coefficients between the constituitive properties and the use of the S-FDTD equations. The impetus for this work was the simulation time it takes to perform 3D Specific Absorption Rate (SAR) FDTD analysis of the human head model for cell phone power absorption in the human head due to the proximity of a cell phone being used. In many instances, Monte Carlo analysis is not performed due to the lengthy simulation times required. With the development of S-FDTD, these statistical analyses could be performed providing valuable statistical information with this information being provided in a small fraction of the time it would take to perform a Monte Carlo analysis.

  10. Spatial-domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Langevin, L.; Gay, D.; Piché, M.

    2008-06-01

    Optical coherence tomography (OCT) is a non-invasive imaging technique invented in 1991 and allowing the observation of biological tissues with millimeter depth of penetration and a few micrometer resolution. In the standard time-domain OCT setup (TD-OCT), a broadband light source is used with a Michelson interferometer where one of the mirrors is replaced by the sample (which is mechanically moved transversally during data acquisition) while the other is axially vibrating. By analyzing the temporal signal at the exit of the interferometer, a high resolution tomographic cut of the sample can be obtained. A number of new OCT setups have been proposed since 1991 in order to improve the data acquisition speed. In particular, Fourier-domain OCT (FD-OCT) has allowed in vivo observation of samples by eliminating the necessity of the axial motion of the reference mirror in the setup. We propose in this paper new OCT setups having the same potential without requiring numerical treatment of the signal (as it is the case in FD-OCT). Because those setups are such that the axial information of the sample becomes linearly distributed at different points of space in an interference pattern, we call them spatial-domain OCT setups (SD-OCT). SD-OCT setups use a tilted mirror in a Michelson interferometer to produce an interference pattern which is imaged on a CCD detector. The pattern contains all the information on the sample and is obtained without mechanical motion or numerical treatment of the recorded signal. In order to validate the proposed scheme, prototypes of the setups have been made in the laboratories of COPL at Laval University; biological samples such as onion peels and phloem of trees have been tested in order to produce their tomographic images. Comparisons of some of our results with those from a commercial setup with the same samples had notably confirmed the capacity of ours prototypes to effectively image biological samples.

  11. Functional domains in Fok I restriction endonuclease.

    PubMed Central

    Li, L; Wu, L P; Chandrasegaran, S

    1992-01-01

    The PCR was used to alter transcriptional and translational signals surrounding the Flavobacterium okeanokoites restriction endonuclease (fokIR) gene, so as to achieve high expression in Escherichia coli. By changing the ribosome-binding site sequence preceding the fokIR gene to match the consensus E. coli signal and by placing a positive retroregulator stem-loop sequence downstream of the gene, Fok I yield was increased to 5-8% of total cellular protein. Fok I was purified to homogeneity with phosphocellulose, DEAE-Sephadex, and gel chromatography, yielding 50 mg of pure Fok I endonuclease per liter of culture medium. The recognition and cleavage domains of Fok I were analyzed by trypsin digestion. Fok I in the absence of a DNA substrate cleaves into a 58-kDa carboxyl-terminal and 8-kDa amino-terminal fragment. The 58-kDa fragment does not bind the DNA substrate. Fok I in the presence of a DNA substrate cleaves into a 41-kDa amino-terminal fragment and a 25-kDa carboxyl-terminal fragment. On further digestion, the 41-kDa fragment degrades into 30-kDa amino-terminal and 11-kDa carboxyl-terminal fragments. The cleaved fragments both bind DNA substrates, as does the 41-kDa fragment. Gel-mobility-shift assays indicate that all the protein contacts necessary for the sequence-specific recognition of DNA substrates are encoded within the 41-kDa fragment. Thus, the 41-kDa amino-terminal fragment constitutes the Fok I recognition domain. The 25-kDa fragment, purified by using a DEAE-Sephadex column, cleaves nonspecifically both methylated (pACYCfokIM) and nonmethylated (pTZ19R) DNA substrates in the presence of MgCl2. Thus, the 25-kDa carboxyl-terminal fragment constitutes the Fok I cleavage domain. Images PMID:1584761

  12. Microseismic source imaging in a compressed domain

    NASA Astrophysics Data System (ADS)

    Vera Rodriguez, Ismael; Sacchi, Mauricio D.

    2014-08-01

    Microseismic monitoring is an essential tool for the characterization of hydraulic fractures. Fast estimation of the parameters that define a microseismic event is relevant to understand and control fracture development. The amount of data contained in the microseismic records however, poses a challenge for fast continuous detection and evaluation of the microseismic source parameters. Work inspired by the emerging field of Compressive Sensing has showed that it is possible to evaluate source parameters in a compressed domain, thereby reducing processing time. This technique performs well in scenarios where the amplitudes of the signal are above the noise level, as is often the case in microseismic monitoring using downhole tools. This paper extends the idea of the compressed domain processing to scenarios of microseismic monitoring using surface arrays, where the signal amplitudes are commonly at the same level as, or below, the noise amplitudes. To achieve this, we resort to the use of an imaging operator, which has previously been found to produce better results in detection and location of microseismic events from surface arrays. The operator in our method is formed by full-waveform elastodynamic Green's functions that are band-limited by a source time function and represented in the frequency domain. Where full-waveform Green's functions are not available, ray tracing can also be used to compute the required Green's functions. Additionally, we introduce the concept of the compressed inverse, which derives directly from the compression of the migration operator using a random matrix. The described methodology reduces processing time at a cost of introducing distortions into the results. However, the amount of distortion can be managed by controlling the level of compression applied to the operator. Numerical experiments using synthetic and real data demonstrate the reductions in processing time that can be achieved and exemplify the process of selecting the

  13. Compassion and professional care: exploring the domain.

    PubMed

    van der Cingel, Margreet

    2009-04-01

    Compassion unites people during times of suffering and distress. Unfortunately, compassion cannot take away suffering. Why then, is compassion important for people who suffer? Nurses work in a domain where human suffering is evidently present. In order to give meaning to compassion in the domain of professional care, it is necessary to describe what compassion is. The purpose of this paper is to explore questions and contradictions in the debate on compassion related to nursing care. The paper reviews classical philosophers as well as contemporary scientists' main arguments on compassion. First, I will examine the relationship between compassion and suffering. Second, how does one recognize serious suffering? This issue raises questions about the role of imagination and the need for identification. Third, literature describes compassion as an emotion. Some philosophers consider emotions uncontrollable feelings; others see a clear rational dimension in emotions. In order to determine what compassion is, it is necessary to weigh these contradictional arguments. Fourth, I will discuss motives for compassion. Is compassion an act of altruism or egoism? In this debate Nietzsche and Schopenhauer are well-known opponents. Today, analysis of their arguments leads to some surprising conclusions. Fifth, there is the issue of fault and compassion. Can we only feel compassionate when people who suffer are not to blame for their own suffering? Such a condition faces professional caretakers with a dilemma which needs a thorough analysis if compassion is to be of use in the field of professional care. Finally, I will explore the moral meaning of compassion. Compassion, described as a concept with cognitive as well as affective dimensions, also has volitional and behavioural aspects. These aspects specifically are of importance to nursing care and further research of compassion in the nursing domain. PMID:19291200

  14. New Internet Domain Name Tags on the Way.

    ERIC Educational Resources Information Center

    Searcher, 1997

    1997-01-01

    Because 825,000 Internet domain names are assigned and 85,000 new site names are registered each month, the availability of new names is limited. To ease the situation, seven new generic top-level domain names (gTLDs) have been proposed for the Internet's domain name system by the International Ad Hoc Committee established by the Internet Assigned…

  15. Cross-domain active learning for video concept detection

    NASA Astrophysics Data System (ADS)

    Li, Huan; Li, Chao; Shi, Yuan; Xiong, Zhang; Hauptmann, Alexander G.

    2011-08-01

    As video data from a variety of different domains (e.g., news, documentaries, entertainment) have distinctive data distributions, cross-domain video concept detection becomes an important task, in which one can reuse the labeled data of one domain to benefit the learning task in another domain with insufficient labeled data. In this paper, we approach this problem by proposing a cross-domain active learning method which iteratively queries labels of the most informative samples in the target domain. Traditional active learning assumes that the training (source domain) and test data (target domain) are from the same distribution. However, it may fail when the two domains have different distributions because querying informative samples according to a base learner that initially learned from source domain may no longer be helpful for the target domain. In our paper, we use the Gaussian random field model as the base learner which has the advantage of exploring the distributions in both domains, and adopt uncertainty sampling as the query strategy. Additionally, we present an instance weighting trick to accelerate the adaptability of the base learner, and develop an efficient model updating method which can significantly speed up the active learning process. Experimental results on TRECVID collections highlight the effectiveness.

  16. Conception of Learning Outcomes in the Bloom's Taxonomy Affective Domain

    ERIC Educational Resources Information Center

    Savickiene, Izabela

    2010-01-01

    The article raises a problematic issue regarding an insufficient base of the conception of learning outcomes in the Bloom's taxonomy affective domain. The search for solutions introduces the conception of teaching and learning in the affective domain as well as presents validity criteria of learning outcomes in the affective domain. The…

  17. Domain Specificity between Peer Support and Self-Concept

    ERIC Educational Resources Information Center

    Leung, Kim Chau; Marsh, Herbert W.; Craven, Rhonda G.; Yeung, Alexander S.; Abduljabbar, Adel S.

    2013-01-01

    Peer support interventions have mostly neglected the domain specificity of intervention effects. In two studies, the present investigation examined the domain specificity of peer support interventions targeting specific domains of self-concept. In Study 1, participants ("n" = 50) who had received an academically oriented peer support intervention…

  18. Frequency-Domain Methods for Characterization of Pulsed Power Diagnostics

    SciTech Connect

    White, A D; Anderson, R A; Ferriera, T J; Goerz, D A

    2009-07-27

    This paper discusses methods of frequency-domain characterization of pulsed power sensors using vector network analyzer and spectrum analyzer techniques that offer significant simplification over time-domain methods, while mitigating or minimizing the effect of the difficulties present in time domain characterization. These methods are applicable to characterization of a wide variety of sensors.

  19. Biology and Beyond: Domain Specificity in a Broader Developmental Context

    ERIC Educational Resources Information Center

    Keil, Frank C.

    2007-01-01

    The assumption of domain specificity has been invaluable to the study of the emergence of biological thought in young children. Yet, domains of thought must be understood within a broader context that explains how those domains relate to the surrounding cultures, to different kinds of cognitive constraints, to framing effects, to abilities to…

  20. A Methodology to Develop Ontologies for Emerging Domains

    ERIC Educational Resources Information Center

    Meenorngwar, Chai

    2013-01-01

    The characteristic of complex, dynamic domains, such as an emerging domain, is that the information necessary to describe them is not fully established. Standards are not yet established for these domains, and hence they are difficult to describe and present, and methods are needed that will reflect the changes that will occur as the domains…

  1. Between- and Within-Domain Relations of Students' Academic Emotions

    ERIC Educational Resources Information Center

    Goetz, Thomas; Frenzel, Anne C.; Pekrun, Reinhard; Hall, Nathan C.; Ludtke, Oliver

    2007-01-01

    The authors investigated between- and within-domain relations of academic emotions, including students' enjoyment, pride, anxiety, anger, and boredom experienced in mathematics, physics, German, and English classes (N = 542; Grades 8 and 11). Corroborating assumptions of domain specificity, the between-domains relations of these emotions were weak…

  2. Changing Your Domain Name in 25 Nail-Biting Steps

    ERIC Educational Resources Information Center

    Hassler, Carol

    2012-01-01

    When staff at the Wisconsin State Law Library began compiling a wish list for a new website, the topic of a new domain name came up almost immediately. Their old website was located at http://wsll.state.wi.us. Spelling that relatively complex domain over the phone day after day provided the impetus to explore other options. Whatever domain name…

  3. Frequency Domain Modeling of SAW Devices

    NASA Technical Reports Server (NTRS)

    Wilson, W. C.; Atkinson, G. M.

    2007-01-01

    New SAW sensors for integrated vehicle health monitoring of aerospace vehicles are being investigated. SAW technology is low cost, rugged, lightweight, and extremely low power. However, the lack of design tools for MEMS devices in general, and for Surface Acoustic Wave (SAW) devices specifically, has led to the development of tools that will enable integrated design, modeling, simulation, analysis and automatic layout generation of SAW devices. A frequency domain model has been created. The model is mainly first order, but it includes second order effects from triple transit echoes. This paper presents the model and results from the model for a SAW delay line device.

  4. Time-domain multiple-quantum NMR

    SciTech Connect

    Weitekamp, D.P.

    1982-11-01

    The development of time-domain multiple-quantum nuclear magnetic resonance is reviewed through mid 1982 and some prospects for future development are indicated. Particular attention is given to the problem of obtaining resolved, interpretable, many-quantum spectra for anisotropic magnetically isolated systems of coupled spins. New results are presented on a number of topics including the optimization of multiple-quantum-line intensities, analysis of noise in two-dimensional spectroscopy, and the use of order-selective excitation for cross polarization between nuclear-spin species.

  5. Lattice gas simulations of replicating domains

    SciTech Connect

    Dawson, S.P.; Hasslacher, B.; Pearson, J.E.

    1993-12-31

    We use the lattice gas cellular automation (LGCA) developed to simulate a process of pattern-formation recently observed in reaction-diffusion systems. We study the reaction mechanism, which is an extension of the Selkov model for glycolytic oscillations. We are able to reproduce the self-replicating domains observed in this work. We use the LGCA simulation to estimate the smallest length-scale on which this process can occur under conditions encountered in the cell. These estimates are similar to those obtained for Turing patterns in the same setting.

  6. Constricted nanowire with stabilized magnetic domain wall

    NASA Astrophysics Data System (ADS)

    Sbiaa, R.; Al Bahri, M.

    2016-08-01

    Domain wall (DW)-based magnetic memory offers the possibility for increasing the storage capacity. However, stability of DW remains the major drawback of this scheme. In this letter, we propose a stepped nanowire for pinning DW in a desirable position. From micromagnetic simulation, the proposed design applied to in-plane magnetic anisotropy materials shows that by adjusting the nanowire step size and its width it is possible to stabilize DW for a desirable current density range. In contrast, only a movement of DW could be seen for conventional nanowire. An extension to a multi-stepped nanowire could be used for multi-bit per cell magnetic memory.

  7. Magnetic Domain Confinement by Anisotropy Modulation

    NASA Astrophysics Data System (ADS)

    Li, S. P.; Lew, W. S.; Bland, J. A.; Lopez-Diaz, L.; Vaz, C. A.; Natali, M.; Chen, Y.

    2002-02-01

    The spin configuration in a magnet is in general a ``natural'' consequence of both the intrinsic properties of the material and the sample dimensions. We demonstrate that this limitation can be overcome in a homogeneous ferromagnetic film by engineering an anisotropy contrast. Substrates with laterally modulated single-crystal and polycrystalline surface regions were used to induce selective epitaxial growth of a ferromagnetic Ni film. The resulting spatially varying magnetic anisotropy leads to regular perpendicular and in-plane magnetic domains, separated by a new type of magnetic wall-the ``anisotropy constrained'' magnetic wall.

  8. Dental optical coherence domain reflectometry explorer

    DOEpatents

    Everett, Matthew J.; Colston, Jr., Billy W.; Sathyam, Ujwal S.; Da Silva, Luiz B.

    2001-01-01

    A hand-held, fiber optic based dental device with optical coherence domain reflectometry (OCDR) sensing capabilities provides a profile of optical scattering as a function of depth in the tissue at the point where the tip of the dental explorer touches the tissue. This system provides information on the internal structure of the dental tissue, which is then used to detect caries and periodontal disease. A series of profiles of optical scattering or tissue microstructure are generated by moving the explorer across the tooth or other tissue. The profiles are combined to form a cross-sectional, or optical coherence tomography (OCT), image.

  9. 3D-spectral domain computational imaging

    NASA Astrophysics Data System (ADS)

    Anderson, Trevor; Segref, Armin; Frisken, Grant; Ferra, Herman; Lorenser, Dirk; Frisken, Steven

    2016-03-01

    We present a proof-of-concept experiment utilizing a novel "snap-shot" spectral domain OCT technique that captures a phase coherent volume in a single frame. The sample is illuminated with a collimated beam of 75 μm diameter and the back-reflected light is analyzed by a 2-D matrix of spectral interferograms. A key challenge that is addressed is simultaneously maintaining lateral and spectral phase coherence over the imaged volume in the presence of sample motion. Digital focusing is demonstrated for 5.0 μm lateral resolution over an 800 μm axial range.

  10. Magnetic domain wall motion by spin transfer

    NASA Astrophysics Data System (ADS)

    Grollier, Julie; Chanthbouala, A.; Matsumoto, R.; Anane, A.; Cros, V.; Nguyen van Dau, F.; Fert, Albert

    2011-04-01

    The discovery that a spin polarized current can exert a large torque on a ferromagnet through a transfusion of spin angular momentum, offers a new way to control a magnetization by simple current injection, without the help of an applied external field. Spin transfer can be used to induce magnetization reversals and oscillations, or to control the position of a magnetic domain wall. In this review, we focus on this last mechanism, which is today the subject of an extensive research, both because the microscopic details for its origin are still debated, but also because promising applications are at stake for non-volatile magnetic memories.

  11. Solitons for optical time-domain reflectometry

    NASA Astrophysics Data System (ADS)

    Levanon, Amikam; Friberg, Stephen R.; Fujii, Yoichi

    1996-06-01

    We describe the propagation of solitons in an optical time-domain reflectometry geometry. Intense nonsolitons usually broaden nonlinearly as they propagate out to a scatterer and broaden linearly as they return to their origin. In contrast, solitons propagate with a fixed pulse width or narrow on their way out to the scatterer. Returning, they broaden or narrow depending on their chirp at the scattering point. For a fixed return-pulse timing resolution we find 2.6 times or more energy can be launched when solitons are used than for normal dispersion pulses.

  12. Block rotations, fault domains and crustal deformation

    NASA Technical Reports Server (NTRS)

    Nur, A.; Ron, H.

    1987-01-01

    Much of the earth's crust is broken by sets of parallel strike-slip faults which are organized in domains. A simple kinematic model suggests that when subject to tectonic strain, the faults, and the blocks bound by them, rotate. The rotation can be estimated from the structurally-determined fault slip and fault spacing, and independently from local deviations of paleomagnetic declinations from global values. A rigorous test of this model was carried out in northern Israel, where good agreement was found between the two rotations.

  13. A review of time-domain and frequency-domain component mode synthesis method

    NASA Technical Reports Server (NTRS)

    Craig, R. R., Jr.

    1985-01-01

    Hurty (1965) has conducted a dynamic analysis of structural systems using component modes. The component mode synthesis (CMS) procedure considered by him represents a form of substructure coupling analysis which is often utilized in structural dynamics. Time-domain CMS methods employing real modes are discussed, taking into account real component modes, normal modes, redundant constraint modes, rigid-body modes, attachment modes, inertia-relief modes, statically-complete interface mode sets, dynamic component mode supersets, component modal models, the coupling of components, and the classification of methods. Attention is also given to the experimental determination of component mode synthesis parameters, time-domain CMS methods for damped systems, and frequency-domain CMS methods for damped systems.

  14. Numerical methods for time-domain and frequency-domain analysis: applications in engineering

    NASA Astrophysics Data System (ADS)

    Tamas, R. D.

    2015-11-01

    Numerical methods are widely used for modeling different physical phenomena in engineering, especially when an analytic approach is not possible. Time-domain or frequency- domain type variations are generally investigated, depending on the nature of the process under consideration. Some methods originate from mechanics, although most of their applications belong to other fields, such as electromagnetism. Conversely, other methods were firstly developed for electromagnetism, but their field of application was extended to other fields. This paper presents some results that we have obtained by using a general purpose method for solving linear equations, i.e., the method of moments (MoM), and a time-domain method derived for electromagnetism, i.e., the Transmission Line Matrix method (TLM).

  15. Advanced atomic force microscopy studies of ferroelectric domains and domain walls

    NASA Astrophysics Data System (ADS)

    Paruch, Patrycja

    2010-03-01

    The nanoscale resolution of atomic force microscopy (AFM) makes it a powerful tool for local studies of ferroelectric domain nucleation and growth. In particular, domain walls provide a useful model elastic disordered system: their behavior is governed by the competition between their elastic energy, which tends to minimize the domain wall surface, and the randomly varying potential landscape due to disorder present in the samples, which allows pinning. The domain walls present a characteristic static roughness, and a complex dynamic response when subjected to a driving force (electric field), with non-linear creep observed for small forces [1]. In addition, as a result of different symmetries and electronic structure, as well as possible defect migration, these intrinsically nanoscale interfaces often show additional properties, beyond those of their already multifunctional parent material, opening new perspectives for device applications. I will present results of our AFM studies of the static and dynamic behavior of domain walls in epitaxially grown thin films of Pb(Zr0.2Ti0.8)O3 focusing in particular on thermal effects, and on the observation of a lateral piezoresponse signal specifically due to the shear displacement of 180^o domain walls in this purely out-of-plane-polarized material [2], potentially useful for surface acoustic wave devices. I will also show how this same response can be more generally observed, necessitating care in the interpretation of lateral piezoresponse imaging in materials such as BiFeO3, where it is superimposed on signal due to the in-plane polarization components. Finally, I will present our studies of the switching mechanisms in this latter material under the influence of the electric field applied by the AFM tip. [4pt] [1] P. Paruch et al., Phys. Rev. Lett 94, 197601 (2005); J. Appl. Phys. 100, 051608 (2006); T. Tybell et al, Phys. Rev. Lett. 89, 097601 (2002)[0pt] [2] J. Guyonnet et al., Appl. Phys. Lett. 95 132902 (2009)

  16. Time domain and frequency domain design techniques for model reference adaptive control systems

    NASA Technical Reports Server (NTRS)

    Boland, J. S., III

    1971-01-01

    Some problems associated with the design of model-reference adaptive control systems are considered and solutions to these problems are advanced. The stability of the adapted system is a primary consideration in the development of both the time-domain and the frequency-domain design techniques. Consequentially, the use of Liapunov's direct method forms an integral part of the derivation of the design procedures. The application of sensitivity coefficients to the design of model-reference adaptive control systems is considered. An application of the design techniques is also presented.

  17. Interconnect modeling using integrated time-domain and frequency-domain techniques

    SciTech Connect

    You, Hong; Yeh, Chune-Sin; Gadepally, B.

    1995-12-31

    This paper presents an integrated time- and-frequency-domain technique for characterization and modeling of parasitic effects associated with interconnects. This technique enables direct measurements of critical transient as well as frequency responses of interconnects; accurate and efficient SPICE model extraction for coupled lines; and cross-domain verification of the measured data as well as the extracted models. To illustrate its application this technique is applied to characterize and extract the equivalent circuit model of the I/O bus on a real-world printed circuit board.

  18. PREFACE: Domain wall dynamics in nanostructures Domain wall dynamics in nanostructures

    NASA Astrophysics Data System (ADS)

    Marrows, C. H.; Meier, G.

    2012-01-01

    Domain structures in magnetic materials are ubiquitous and have been studied for decades. The walls that separate them are topological defects in the magnetic order parameter and have a wide variety of complex forms. In general, their investigation is difficult in bulk materials since only the domain structure on the surface of a specimen is visible. Cutting the sample to reveal the interior causes a rearrangement of the domains into a new form. As with many other areas of magnetism, the study of domain wall physics has been revitalised by the advent of nanotechnology. The ability to fabricate nanoscale structures has permitted the formation of simplified and controlled domain patterns; the development of advanced microscopy methods has permitted them to be imaged and then modelled; subjecting them to ultrashort field and current pulses has permitted their dynamics to be explored. The latest results from all of these advances are described in this special issue. Not only has this led to results of great scientific beauty, but also to concepts of great applicability to future information technologies. In this issue the reader will find the latest results for these domain wall dynamics and the high-speed processes of topological structures such as domain walls and magnetic vortices. These dynamics can be driven by the application of magnetic fields, or by flowing currents through spintronic devices using the novel physics of spin-transfer torque. This complexity has been studied using a wide variety of experimental techniques at the edge of the spatial and temporal resolution currently available, and can be described using sophisticated analytical theory and computational modelling. As a result, the dynamics can be engineered to give rise to finely controlled memory and logic devices with new functionality. Moreover, the field is moving to study not only the conventional transition metal ferromagnets, but also complex heterostructures, novel magnets and even other

  19. Cellulose-binding domains: biotechnological applications.

    PubMed

    Levy, Ilan; Shoseyov, Oded

    2002-11-01

    Many researchers have acknowledged the fact that there exists an immense potential for the application of the cellulose-binding domains (CBDs) in the field of biotechnology. This becomes apparent when the phrase "cellulose-binding domain" is used as the key word for a computerized patent search; more then 150 hits are retrieved. Cellulose is an ideal matrix for large-scale affinity purification procedures. This chemically inert matrix has excellent physical properties as well as low affinity for nonspecific protein binding. It is available in a diverse range of forms and sizes, is pharmaceutically safe, and relatively inexpensive. Present studies into the application of CBDs in industry have established that they can be applied in the modification of physical and chemical properties of composite materials and the development of modified materials with improved properties. In agro-biotechnology, CBDs can be used to modify polysaccharide materials both in vivo and in vitro. The CBDs exert nonhydrolytic fiber disruption on cellulose-containing materials. The potential applications of "CBD technology" range from modulating the architecture of individual cells to the modification of an entire organism. Expressing these genes under specific promoters and using appropriate trafficking signals, can be used to alter the nutritional value and texture of agricultural crops and their final products. PMID:14550028

  20. Inflationary power asymmetry from primordial domain walls

    SciTech Connect

    Jazayeri, Sadra; Akrami, Yashar; Firouzjahi, Hassan; Solomon, Adam R.; Wang, Yi E-mail: yashar.akrami@astro.uio.no E-mail: a.r.solomon@damtp.cam.ac.uk

    2014-11-01

    We study the asymmetric primordial fluctuations in a model of inflation in which translational invariance is broken by a domain wall. We calculate the corrections to the power spectrum of curvature perturbations; they are anisotropic and contain dipole, quadrupole, and higher multipoles with non-trivial scale-dependent amplitudes. Inspired by observations of these multipole asymmetries in terms of two-point correlations and variance in real space, we demonstrate that this model can explain the observed anomalous power asymmetry of the cosmic microwave background (CMB) sky, including its characteristic feature that the dipole dominates over higher multipoles. We test the viability of the model and place approximate constraints on its parameters by using observational values of dipole, quadrupole, and octopole amplitudes of the asymmetry measured by a local-variance estimator. We find that a configuration of the model in which the CMB sphere does not intersect the domain wall during inflation provides a good fit to the data. We further derive analytic expressions for the corrections to the CMB temperature covariance matrix, or angular power spectra, which can be used in future statistical analysis of the model in spherical harmonic space.

  1. RING domains: master builders of molecular scaffolds?

    PubMed

    Borden, K L

    2000-02-01

    Intense interest in the RING domain has arisen because of its widespread occurrence and involvement in human disease. Several intriguing characteristics evident from the study of this cysteine-rich, zinc-binding domain have made it difficult to establish a single defining biochemical function for RINGs. These proteins are found throughout the cell and mediate diverse cellular processes, e.g. oncogenesis, apoptosis, development and viral infection. Recent developments indicate that RING-mediated protein interactions are critical for transcriptional repression and for ubiquitination. These data are in addition to previously established functions for RINGs in RNA processing, cell-cycle control and peroxisomal biogenesis, to name a few. At first glance, there appears to be little to link such disparate actions. Collectively, these results suggest that RINGs function in formation and architecture of large protein complexes that contribute to diverse cellular processes. Here, new developments, in the context of previous results, are discussed in an attempt to establish a unifying theory for RING function. PMID:10653689

  2. Single-domain antibodies and their utility.

    PubMed

    Baral, Toya Nath; MacKenzie, Roger; Arbabi Ghahroudi, Mehdi

    2013-01-01

    Engineered monoclonal antibody fragments have gained market attention due to their versatility and tailor-made potential and are now considered to be an important part of future immunobiotherapeutics. Single-domain antibodies (sdAbs), also known as nanobodies, are derived from VHHs [variable domains (V) of heavy-chain-only antibodies (HCAb)] of camelid heavy-chain antibodies. These nature-made sdAbs are well suited for various applications due to their favorable characteristics such as small size, ease of genetic manipulation, high affinity and solubility, overall stability, resistance to harsh conditions (e.g., low pH, high temperature), and low immunogenicity. Most importantly, sdAbs have the feature of penetrating into cavities and recognizing hidden epitopes normally inaccessible to conventional antibodies, mainly due to their protruding CDR3/H3 loops. In this unit, we will present and discuss comprehensive and step-by-step protocols routinely practiced in our laboratory for isolating sdAbs from immunized llamas (or other members of the Camelidae family) against target antigens using phage-display technology. Expression, purification, and characterization of the isolated sdAbs will then be described, followed by presentation of several examples of applications of sdAbs previously characterized in our laboratory and elsewhere. PMID:24510545

  3. Spectral fusing Gabor domain optical coherence microscopy.

    PubMed

    Meemon, Panomsak; Widjaja, Joewono; Rolland, Jannick P

    2016-02-01

    Gabor domain optical coherence microscopy (GD-OCM) is one of many variations of optical coherence tomography (OCT) techniques that aims for invariant high resolution across a 3D field of view by utilizing the ability to dynamically refocus the imaging optics in the sample arm. GD-OCM acquires multiple cross-sectional images at different focus positions of the objective lens, and then fuses them to obtain an invariant high-resolution 3D image of the sample, which comes with the intrinsic drawback of a longer processing time as compared to conventional Fourier domain OCT. Here, we report on an alternative Gabor fusing algorithm, the spectral-fusion technique, which directly processes each acquired spectrum and combines them prior to the Fourier transformation to obtain a depth profile. The implementation of the spectral-fusion algorithm is presented and its performance is compared to that of the prior GD-OCM spatial-fusion approach. The spectral-fusion approach shows twice the speed of the spatial-fusion approach for a spectrum size of less than 2000 point sampling, which is a commonly used spectrum size in OCT imaging, including GD-OCM. PMID:26907410

  4. Inference evaluation in a finite evidence domain

    NASA Astrophysics Data System (ADS)

    Ratway, Michael J.; Bellomo, Carryn

    2000-08-01

    Modeling of a target starts with a subject matter expert (SME) analysis of the available sensor(s) data. The SME then forms relationships between the data and known target attributes, called evidence, to support modeling of different types of targets or target activity. Speeds in the interval 10 to 30 knots and ranges less than 30 nautical miles are two samples of target evidence derived from sensor data. Evidence is then organized into sets to define the activities of a target and/or to distinguish different types of targets. For example, near an airport, target activities of takeoff, landing, and holding need to be evaluated in addition to target classification of civilian or commercial aircraft. This paper discusses a method for evaluation of the inferred activities over the finite evidence domain formed from the collection of models under consideration. The methodology accounts for repeated use of evidence in different models. For example, 'near an airport' is a required piece of evidence used repeatedly in the takeoff, landing, and holding models of a wide area sensor. Properties of the activity model evaluator methodology are discussed in terms of model construction and informal results are presented in a Boolean evidence type of problem domain.

  5. Shape Statistics for Random Domains and Particles

    NASA Astrophysics Data System (ADS)

    Stoyan, Dietrich; Davtyan, Ashot; Turetayev, Daulet

    This paper surveys ideas of statistical analysis of planar images of particles such as powder particles or sand grains, domains such as monolayer domains on water or water droplets on planar surfaces and biological cells or vesicles. For a simple and fast discrimination between collectives of particles, shape ratios or indices such as `area:perimeter' ratio are powerful tools. A more detailed description is possible by means of various functions such as radius-vector function, tangent-angle function and erosion function. A deeper understanding of particle shape and size is possible by studying the relevant physical processes which generate them, such as fracture, abrasion and growth by aggregation. The second part of the paper discusses a particular stochastic model, called Gibbs pixel-particle. It produces two-dimensional connected lattice figures, often called lattice animals, the distribution of which depends on an energy function which is controled by particle area and boundary length and roughness. These pixel-particles vary in a broad spectrum of possible shapes and sizes.

  6. Frequency Domain Calculations Of Acoustic Propagation

    NASA Technical Reports Server (NTRS)

    Lockard, David P.

    2004-01-01

    Two complex geometry problems are solved using the linearized Euler equations. The impedance mismatch method1 is used to impose the solid surfaces without the need to use a body-fitted grid. The problem is solved in the frequency domain to avoid long run times. Although the harmonic assumption eliminates all time dependence, a pseudo-time term is added to allow conventional iterative methods to be employed. A Jameson type, Runge-Kutta scheme is used to advance the solution in pseudo time. The spatial operator is based on a seven-point, sixth-order finite difference. Constant coefficient, sixth-derivative artificial dissipation is used throughout the domain. A buffer zone technique employing a complex frequency to damp all waves near the boundaries is used to minimize reflections. The results show that the method is capable of capturing the salient features of the scattering, but an excessive number of grid points are required to resolve the phenomena in the vicinity of the solid bodies because the wavelength of the acoustics is relatively short compared with the size of the bodies. Smoothly transitioning into the immersed boundary condition alleviates the difficulties, but a fine mesh is still required.

  7. Birth order effects on autism symptom domains.

    PubMed

    Reichenberg, Abraham; Smith, Christopher; Schmeidler, James; Silverman, Jeremy M

    2007-03-30

    Autism is predominantly genetically determined. Evidence supports familiality of the main sets of behavioral characteristics that define the syndrome of autism; however, possible non-genetic effects have also been suggested. The present study compared levels of autism symptom domains, as measured by the Autism Diagnostic Interview, and useful phrase speech scores between 106 pairs of first- and second-born siblings from multiply affected families. In addition, the intercorrelations between the measures were compared between siblings. The overall mean repetitive behavior total score was significantly higher (worse) in first-born than in second-born siblings. In contrast, first-born siblings had significantly lower (better) useful phrase speech than their younger siblings. Autism social and non-verbal communication scores were significantly correlated in first- and in second-born siblings. However, there was a significant difference in the coefficients between first- and second-born siblings. Performance on the non-verbal communication domain was also significantly and positively correlated with useful phrase speech score in both first- and second-born siblings. It is unclear at this time whether these results are of biologic origin. Nevertheless, the findings suggest that genetic studies in autism using specific levels of familial autism traits as phenotypes should take into account their intercorrelations and birth order effects embedded in the instrument. PMID:17289158

  8. Architectures for Time-domain Astronomy

    NASA Astrophysics Data System (ADS)

    Seaman, R.; Allan, A.; Pierfederici, F.; Williams, R.

    2009-09-01

    Wonder at the changing sky predates recorded history. Empirical studies of time-varying celestial phenomena date back to Galileo and Tycho. Telegrams conveying news of transient and recurrent events have been key astronomical infrastructure since the nineteenth century. Recent micro-lensing, supernova and gamma-ray burst studies have lead to a succession of exciting discoveries, but massive new time-domain surveys will soon overwhelm our nineteenth century transient response technologies. Meeting this challenge demands new autonomous architectures for astronomy. These Architectures should reach from proposing new research, through experimental design and the scheduling of telescope operations, to the archiving and pipeline-processing of data to discover new transients, to the publishing of these events, through automated follow-up via robotic and ToO assets, and to the display and analysis of observational results. All will lead to adaptive adjustment of time-domain investigations. The IVOA VOEvent protocol provides an engine for purpose-built astronomical architectures.

  9. Confinement and localization on domain walls

    NASA Astrophysics Data System (ADS)

    Auzzi, R.; Bolognesi, S.; Shifman, M.; Yung, A.

    2009-02-01

    We continue the studies of localization of the U(1) gauge fields on domain walls. Depending on dynamics of the bulk theory the gauge field localized on the domain wall can be either in the Coulomb phase or squeezed into flux tubes implying (Abelian) confinement of probe charges on the wall along the wall surface. First, we consider a simple toy model with one flavor in the bulk at weak coupling (a minimal model) realizing the latter scenario. We then suggest a model presenting an extension of the Seiberg-Witten theory which is at strong coupling, but all theoretical constructions are under full control if we base our analysis on a dual effective action. Finally, we compare our findings with the wall in a “nonminimal” theory with two distinct quark flavors that had been studied previously. In this case the U(1) gauge field trapped on the wall is exactly massless because it is the Goldstone boson of a U(1) symmetry in the bulk spontaneously broken on the wall. The theory on the wall is in the Coulomb phase. We explain why the mechanism of confinement discussed in the first part of the paper does not work in this case, and strings are not formed on the walls.

  10. Frequency domain analysis of knock images

    NASA Astrophysics Data System (ADS)

    Qi, Yunliang; He, Xin; Wang, Zhi; Wang, Jianxin

    2014-12-01

    High speed imaging-based knock analysis has mainly focused on time domain information, e.g. the spark triggered flame speed, the time when end gas auto-ignition occurs and the end gas flame speed after auto-ignition. This study presents a frequency domain analysis on the knock images recorded using a high speed camera with direct photography in a rapid compression machine (RCM). To clearly visualize the pressure wave oscillation in the combustion chamber, the images were high-pass-filtered to extract the luminosity oscillation. The luminosity spectrum was then obtained by applying fast Fourier transform (FFT) to three basic colour components (red, green and blue) of the high-pass-filtered images. Compared to the pressure spectrum, the luminosity spectra better identify the resonant modes of pressure wave oscillation. More importantly, the resonant mode shapes can be clearly visualized by reconstructing the images based on the amplitudes of luminosity spectra at the corresponding resonant frequencies, which agree well with the analytical solutions for mode shapes of gas vibration in a cylindrical cavity.

  11. Disrupting membrane raft domains by alkylphospholipids.

    PubMed

    Gomide, A B; Thomé, C H; dos Santos, G A; Ferreira, G A; Faça, V M; Rego, E M; Greene, L J; Stabeli, R G; Ciancaglini, P; Itri, R

    2013-05-01

    Using phase contrast and fluorescence microscopy we study the influence of the alkylphospholipid, ALP, 10-(octyloxy) decyl-2-(trimethylammonium) ethyl phosphate, ODPC, in giant unilamellar vesicles, GUVs, composed of DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine), brain sphingomyelin (SM) and cholesterol (Chol). The results show that adding 100μM ODPC (below CMC) to the outer solution of GUVs promotes DOPC membrane disruption over a period of 1h of continuous observation. On the other hand, the presence of SM and Chol in homogeneous fluid lipid bilayers protects the membrane from disruption. Interestingly, by adding 100μM ODPC to GUVs containing DOPC:SM:Chol (1:1:1), which display liquid ordered (Lo)-liquid disordered (Ld) phase coexistence, the domains rapidly disappear in less than 1min of ODPC contact with the membrane. The lipids are subsequently redistributed to liquid domains within a time course of 14-18min, reflecting that the homogenous phase was not thermodynamically stable, followed by rupture of the GUVs. A similar mechanism of action is also observed for perifosine, although to a larger extent. Therefore, the initial stage of lipid raft disruption by both ODPC and perifosine, and maybe other ALPS, by promoting lipid mixing, may be correlated with their toxicity upon neoplastic cells, since selective (dis)association of essential proteins within lipid raft microdomains must take place in the plasma membrane. PMID:23376656

  12. Speckle size in optical Fourier domain imaging

    NASA Astrophysics Data System (ADS)

    Lamouche, G.; Vergnole, S.; Bisaillon, C.-E.; Dufour, M.; Maciejko, R.; Monchalin, J.-P.

    2007-06-01

    As in conventional time-domain optical coherence tomography (OCT), speckle is inherent to any Optical Fourier Domain Imaging (OFDI) of biological tissue. OFDI is also known as swept-source OCT (SS-OCT). The axial speckle size is mainly determined by the OCT resolution length and the transverse speckle size by the focusing optics illuminating the sample. There is also a contribution from the sample related to the number of scatterers contained within the probed volume. In the OFDI data processing, there is some liberty in selecting the range of wavelengths used and this allows variation in the OCT resolution length. Consequently the probed volume can be varied. By performing measurements on an optical phantom with a controlled density of discrete scatterers and by changing the probed volume with different range of wavelengths in the OFDI data processing, there is an obvious change in the axial speckle size, but we show that there is also a less obvious variation in the transverse speckle size. This work contributes to a better understanding of speckle in OCT.

  13. Domain effects and financial risk attitudes.

    PubMed

    Vlaev, Ivo; Kusev, Petko; Stewart, Neil; Aldrovandi, Silvio; Chater, Nick

    2010-09-01

    We investigated whether financial risk preferences are dependent on the financial domain (i.e., the context) in which the risky choice options are presented. Previous studies have demonstrated that risk attitudes change when gambles are framed as gains, losses, or as insurance. Our study explores this directly by offering choices between identical gambles, framed in terms of seven financial domains. Three factors were extracted, explaining 68.6% of the variance: Factor 1 (Positive)-opportunity to win, pension provision, and job salary change; Factor 2 (Positive-Complex)-investments and mortgage buying; Factor 3 (Negative)-possibility of loss and insurance. Inspection of the solution revealed context effects on risk perceptions across the seven scenarios. We also found that the commonly accepted assumption that women are more risk averse cannot be confirmed with the context structure suggested in this research; however, it is acknowledged that in the students' population the variance across genders might be considerably less. These results suggest that our financial risk attitude measures may be tapping into a stable aspect of "context dependence" of relevance to real-world decision making. PMID:20840489

  14. Establishment and Maintenance of a Heterochromatin Domain

    NASA Astrophysics Data System (ADS)

    Hall, Ira M.; Shankaranarayana, Gurumurthy D.; Noma, Ken-ichi; Ayoub, Nabieh; Cohen, Amikam; Grewal, Shiv I. S.

    2002-09-01

    The higher-order assembly of chromatin imposes structural organization on the genetic information of eukaryotes and is thought to be largely determined by posttranslational modification of histone tails. Here, we study a 20-kilobase silent domain at the mating-type region of fission yeast as a model for heterochromatin formation. We find that, although histone H3 methylated at lysine 9 (H3 Lys9) directly recruits heterochromatin protein Swi6/HP1, the critical determinant for H3 Lys9 methylation to spread in cis and to be inherited through mitosis and meiosis is Swi6 itself. We demonstrate that a centromere-homologous repeat (cenH) present at the silent mating-type region is sufficient for heterochromatin formation at an ectopic site, and that its repressive capacity is mediated by components of the RNA interference (RNAi) machinery. Moreover, cenH and the RNAi machinery cooperate to nucleate heterochromatin assembly at the endogenous mat locus but are dispensable for its subsequent inheritance. This work defines sequential requirements for the initiation and propagation of regional heterochromatic domains.

  15. Frequency Domain Sampling Using Biomedical Imaging Physics

    NASA Astrophysics Data System (ADS)

    Seo, Gun Ha; Chung, Minji; Kyung, Richard

    2015-04-01

    In magnetic resonance image analysis using physical and computational method, the process of transformation from frequency domain to image domain requires significant amount time because Inverse Fourier Transformation (IFT) takes every frequency points to determine the final output image. This paper shows the mechanisms and physics of image formation using the selectivity of proper k-space by removing different amounts of high or low frequencies to create the most optimal magnetic resonance image of a human tibial bone. Originally, square unit step function, N/2-N/10:N/2 + N/10 = 1, was used during the Fourier Transformations. And Gaussian filter, y = exp(-t2/40n) , where t = h-L/2, h = [0,M], L =2*7*N/40, the size of frequency matrix (M, N) = (365,557) was tested. Also circle equations as a filter, r = sqrt((x-M/2)2 + (y-N/2)2) , were tested in creating the images of the human tibial bone to find an efficient filter. The best efficiency occurred when the exponent n in the proposed Gaussian filter equation is in between 3 and 8, and therefore, a new algorithm is needed to find the exact number since the number is not only an integer.

  16. Accelerating advances in continental domain hydrologic modeling

    NASA Astrophysics Data System (ADS)

    Archfield, Stacey A.; Clark, Martyn; Arheimer, Berit; Hay, Lauren E.; McMillan, Hilary; Kiang, Julie E.; Seibert, Jan; Hakala, Kirsti; Bock, Andrew; Wagener, Thorsten; Farmer, William H.; Andréassian, Vazken; Attinger, Sabine; Viglione, Alberto; Knight, Rodney; Markstrom, Steven; Over, Thomas

    2015-12-01

    In the past, hydrologic modeling of surface water resources has mainly focused on simulating the hydrologic cycle at local to regional catchment modeling domains. There now exists a level of maturity among the catchment, global water security, and land surface modeling communities such that these communities are converging toward continental domain hydrologic models. This commentary, written from a catchment hydrology community perspective, provides a review of progress in each community toward this achievement, identifies common challenges the communities face, and details immediate and specific areas in which these communities can mutually benefit one another from the convergence of their research perspectives. Those include: (1) creating new incentives and infrastructure to report and share model inputs, outputs, and parameters in data services and open access, machine-independent formats for model replication or reanalysis; (2) ensuring that hydrologic models have: sufficient complexity to represent the dominant physical processes and adequate representation of anthropogenic impacts on the terrestrial water cycle, a process-based approach to model parameter estimation, and appropriate parameterizations to represent large-scale fluxes and scaling behavior; (3) maintaining a balance between model complexity and data availability as well as uncertainties; and (4) quantifying and communicating significant advancements toward these modeling goals.

  17. Radar Interferometry with Public Domain Tools

    NASA Astrophysics Data System (ADS)

    Kampes, B. M.; Hanssen, R. F.; Perski, Z.

    2004-06-01

    The development of public-domain software in the scientific community has stimulated a fast and free dissemination of ideas. Here we present latest contributions to public-domain radar interferometry software to create interferometric products and to analyze and visualize these products. We present the feasibility of the Doris radar interferometric software of Delft University of Technology to create ENVISAT interferometric products such as DEMs and deformation maps. A stepwise description of the creation of an ENVISAT DEM of the Las Vegas area is presented, using besides Doris the ESA BEAM toolbox, the statistical cost phase unwrapper SNAPHU (Stanford University), the Generic Mapping Tools (University of Hawaii), and the PROJ.4 package (USGS). Finally, the GRASS GIS software is used to drape a LandSAT image on top of the computed DEM in order to show the analysis and visualization capabilities of this free GIS package. These packages are also described briefly in this paper. Both advantages as well as drawbacks of these tools are discussed. It is the intention of this paper to demonstrate how a larger scientific community can benefit from freely available tools, and which contributions need to be solicited for.

  18. Hydrology Domain Cyberinfrastructures: Successes, Challenges, and Opportunities

    NASA Astrophysics Data System (ADS)

    Horsburgh, J. S.

    2015-12-01

    Anticipated changes to climate, human population, land use, and urban form will alter the hydrology and availability of water within the water systems on which the world's population relies. Understanding the effects of these changes will be paramount in sustainably managing water resources, as well as maintaining associated capacity to provide ecosystem services (e.g., regulating flooding, maintaining instream flow during dry periods, cycling nutrients, and maintaining water quality). It will require better information characterizing both natural and human mediated hydrologic systems and enhanced ability to generate, manage, store, analyze, and share growing volumes of observational data. Over the past several years, a number of hydrology domain cyberinfrastructures have emerged or are currently under development that are focused on providing integrated access to and analysis of data for cross-domain synthesis studies. These include the Consortium of Universities for the Advancement of Hydrologic Science, Inc. (CUAHSI) Hydrologic Information System (HIS), the Critical Zone Observatory Information System (CZOData), HyroShare, the BiG CZ software system, and others. These systems have focused on sharing, integrating, and analyzing hydrologic observations data. This presentation will describe commonalities and differences in the cyberinfrastructure approaches used by these projects and will highlight successes and lessons learned in addressing the challenges of big and complex data. It will also identify new challenges and opportunities for next generation cyberinfrastructure and a next generation of cyber-savvy scientists and engineers as developers and users.

  19. Domain-General and Domain-Specific Creative-Thinking Tests: Effects of Gender and Item Content on Test Performance

    ERIC Educational Resources Information Center

    Hong, Eunsook; Peng, Yun; O'Neil, Harold F., Jr.; Wu, Junbin

    2013-01-01

    The study examined the effects of gender and item content of domain-general and domain-specific creative-thinking tests on four subscale scores of creative-thinking (fluency, flexibility, originality, and elaboration). Chinese tenth-grade students (234 males and 244 females) participated in the study. Domain-general creative thinking was measured…

  20. The dynamics of the asymmetric motion of domain walls of sandwich domain structure in a Fe-based amorphous ribbon

    NASA Astrophysics Data System (ADS)

    Zhmetko, D. N.; Zhmetko, S. D.; Troschenkov, Y. N.; Matsura, A. V.

    2013-08-01

    The frequency dependence of asymmetry of the domain walls velocity relative to the middle plane of amorphous ribbon is investigated. An additional pressure of the same direction acting on each domain wall caused by dependence of eddy current damping on the coordinate of the domain wall is revealed. The microscopic mechanisms of this additional pressure are considered.

  1. Peer Review-Based Scripted Collaboration to Support Domain-Specific and Domain-General Knowledge Acquisition in Computer Science

    ERIC Educational Resources Information Center

    Demetriadis, Stavros; Egerter, Tina; Hanisch, Frank; Fischer, Frank

    2011-01-01

    This study investigates the effectiveness of using peer review in the context of scripted collaboration to foster both domain-specific and domain-general knowledge acquisition in the computer science domain. Using a one-factor design with a script and a control condition, students worked in small groups on a series of computer science problems…

  2. A Unified Approach to Intra-Domain Security

    SciTech Connect

    Shue, Craig A; Kalafut, Andrew J.; Gupta, Prof. Minaxi

    2009-01-01

    While a variety of mechanisms have been developed for securing individual intra-domain protocols, none address the issue in a holistic manner. We develop a unified framework to secure prominent networking protocols within a single domain. We begin with a secure version of the DHCP protocol, which has the additional feature of providing each host with a certificate. We then leverage these certificates to secure ARP, prevent spoofing within the domain, and secure SSH and VPN connections between the domain and hosts which have previously interacted with it locally. In doing so, we also develop an incrementally deployable public key infrastructure which can later be leveraged to support inter-domain authentication.

  3. Single-domain epitaxial silicene on diboride thin films

    NASA Astrophysics Data System (ADS)

    Fleurence, A.; Gill, T. G.; Friedlein, R.; Sadowski, J. T.; Aoyagi, K.; Copel, M.; Tromp, R. M.; Hirjibehedin, C. F.; Yamada-Takamura, Y.

    2016-04-01

    Epitaxial silicene, which forms spontaneously on ZrB2(0001) thin films grown on Si(111) wafers, has a periodic stripe domain structure. By adsorbing additional Si atoms on this surface, we find that the domain boundaries vanish, and a single-domain silicene sheet can be prepared without altering its buckled honeycomb structure. The amount of Si required to induce this change suggests that the domain boundaries are made of a local distortion of the silicene honeycomb lattice. The realization of a single domain sheet with structural and electronic properties close to those of the original striped state demonstrates the high structural flexibility of silicene.

  4. Soliton-dependent plasmon reflection at bilayer graphene domain walls

    NASA Astrophysics Data System (ADS)

    Jiang, Lili; Shi, Zhiwen; Zeng, Bo; Wang, Sheng; Kang, Ji-Hun; Joshi, Trinity; Jin, Chenhao; Ju, Long; Kim, Jonghwan; Lyu, Tairu; Shen, Yuen-Ron; Crommie, Michael; Gao, Hong-Jun; Wang, Feng

    2016-08-01

    Layer-stacking domain walls in bilayer graphene are emerging as a fascinating one-dimensional system that features stacking solitons structurally and quantum valley Hall boundary states electronically. The interactions between electrons in the 2D graphene domains and the one-dimensional domain-wall solitons can lead to further new quantum phenomena. Domain-wall solitons of varied local structures exist along different crystallographic orientations, which can exhibit distinct electrical, mechanical and optical properties. Here we report soliton-dependent 2D graphene plasmon reflection at different 1D domain-wall solitons in bilayer graphene using near-field infrared nanoscopy. We observe various domain-wall structures in mechanically exfoliated graphene bilayers, including network-forming triangular lattices, individual straight or bent lines, and even closed circles. The near-field infrared contrast of domain-wall solitons arises from plasmon reflection at domain walls, and exhibits markedly different behaviours at the tensile- and shear-type domain-wall solitons. In addition, the plasmon reflection at domain walls exhibits a peculiar dependence on electrostatic gating. Our study demonstrates the unusual and tunable coupling between 2D graphene plasmons and domain-wall solitons.

  5. Functional domains of the human epididymal protease inhibitor, eppin.

    PubMed

    McCrudden, Maelíosa T C; Dafforn, Tim R; Houston, David F; Turkington, Philip T; Timson, David J

    2008-04-01

    Eppin has two potential protease inhibitory domains: a whey acid protein or four disulfide core domain and a Kunitz domain. The protein is also reported to have antibacterial activity against Gram-negative bacteria. Eppin and its whey acid protein and Kunitz domains were expressed in Escherichia coli and their ability to inhibit proteases and kill bacteria compared. The Kunitz domain inhibits elastase (EC 3.4.21.37) to a similar extent as intact eppin, whereas the whey acid protein domain has no such activity. None of these fragments inhibits trypsin (EC 3.4.21.4) or chymotrypsin (EC 3.4.21.1) at the concentrations tested. In a colony forming unit assay, both domains have some antibacterial activity against E. coli, but this was not to the same degree as intact eppin or the two domains together. When bacterial respiratory electron transport was measured using a 2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide assay, eppin and its domains caused an increase in the rate of respiration. This suggests that the mechanism of cell killing may be partly through the permeablization of the bacterial inner membrane, resulting in uncoupling of respiratory electron transport and consequent collapse of the proton motive force. Thus, we conclude that although both of eppin's domains are involved in the protein's antibacterial activity, only the Kunitz domain is required for selective protease inhibition. PMID:18331357

  6. The HBM domain: Introducing bimodularity to bacterial sensing

    PubMed Central

    Ortega, Álvaro; Krell, Tino

    2014-01-01

    We have recently reported the three dimensional structure of the McpS chemoreceptor sensor domain in complex with its cognate ligands. The domain was characterized by a bimodular architecture, where ligand binding to each module caused a chemotactic response. This is a novel small molecule binding domain, which, however, is un-annotated in relevant databases. We report here the domain signature of the family of McpS-like sensor domains, which was termed helical bimodular (HBM) domain. The HBM domain was identified in Bacteria and Archaea and forms part of chemoreceptors and histidine kinases. The conservation of amino acids in the ligand binding sites of both modules suggests that HBM family members recognize similar ligands. PMID:24347303

  7. Combinatorial geometry domain decomposition strategies for Monte Carlo simulations

    SciTech Connect

    Li, G.; Zhang, B.; Deng, L.; Mo, Z.; Liu, Z.; Shangguan, D.; Ma, Y.; Li, S.; Hu, Z.

    2013-07-01

    Analysis and modeling of nuclear reactors can lead to memory overload for a single core processor when it comes to refined modeling. A method to solve this problem is called 'domain decomposition'. In the current work, domain decomposition algorithms for a combinatorial geometry Monte Carlo transport code are developed on the JCOGIN (J Combinatorial Geometry Monte Carlo transport INfrastructure). Tree-based decomposition and asynchronous communication of particle information between domains are described in the paper. Combination of domain decomposition and domain replication (particle parallelism) is demonstrated and compared with that of MERCURY code. A full-core reactor model is simulated to verify the domain decomposition algorithms using the Monte Carlo particle transport code JMCT (J Monte Carlo Transport Code), which has being developed on the JCOGIN infrastructure. Besides, influences of the domain decomposition algorithms to tally variances are discussed. (authors)

  8. A diode for ferroelectric domain-wall motion

    PubMed Central

    Whyte, J.R.; Gregg, J.M.

    2015-01-01

    For over a decade, controlling domain-wall injection, motion and annihilation along nanowires has been the preserve of the nanomagnetics research community. Revolutionary technologies have resulted, like racetrack memory and domain-wall logic. Until recently, equivalent research in analogous ferroic materials did not seem important. However, with the discovery of sheet conduction, the control of domain walls in ferroelectrics has become vital for the future of what has been termed ‘domain-wall electronics'. Here we report the creation of a ferroelectric domain-wall diode, which allows a single direction of motion for all domain walls, irrespective of their polarity, under a series of alternating electric field pulses. The diode's sawtooth morphology is central to its function. Domain walls can move readily in the direction in which thickness increases gradually, but are prevented from moving in the other direction by the sudden thickness increase at the sawtooth edge. PMID:26059779

  9. Domain Decomposition By the Advancing-Partition Method

    NASA Technical Reports Server (NTRS)

    Pirzadeh, Shahyar Z.

    2008-01-01

    A new method of domain decomposition has been developed for generating unstructured grids in subdomains either sequentially or using multiple computers in parallel. Domain decomposition is a crucial and challenging step for parallel grid generation. Prior methods are generally based on auxiliary, complex, and computationally intensive operations for defining partition interfaces and usually produce grids of lower quality than those generated in single domains. The new technique, referred to as "Advancing Partition," is based on the Advancing-Front method, which partitions a domain as part of the volume mesh generation in a consistent and "natural" way. The benefits of this approach are: 1) the process of domain decomposition is highly automated, 2) partitioning of domain does not compromise the quality of the generated grids, and 3) the computational overhead for domain decomposition is minimal. The new method has been implemented in NASA's unstructured grid generation code VGRID.

  10. Conformational instability of the MARK3 UBA domain compromises ubiquitin recognition and promotes interaction with the adjacent kinase domain

    SciTech Connect

    Murphy, James M.; Korzhnev, Dmitry M.; Ceccarelli, Derek F.; Briant, Douglas J.; Zarrine-Afsar, Arash; Sicheri, Frank; Kay, Lewis E.; Pawson, Tony

    2012-10-23

    The Par-1/MARK protein kinases play a pivotal role in establishing cellular polarity. This family of kinases contains a unique domain architecture, in which a ubiquitin-associated (UBA) domain is located C-terminal to the kinase domain. We have used a combination of x-ray crystallography and NMR dynamics experiments to understand the interaction of the human (h) MARK3 UBA domain with the adjacent kinase domain as compared with ubiquitin. The x-ray crystal structure of the linked hMARK3 kinase and UBA domains establishes that the UBA domain forms a stable intramolecular interaction with the N-terminal lobe of the kinase domain. However, solution-state NMR studies of the isolated UBA domain indicate that it is highly dynamic, undergoing conformational transitions that can be explained by a folding-unfolding equilibrium. NMR titration experiments indicated that the hMARK3 UBA domain has a detectable but extremely weak affinity for mono ubiquitin, which suggests that conformational instability of the isolated hMARK3 UBA domain attenuates binding to ubiquitin despite the presence of residues typically involved in ubiquitin recognition. Our data identify a molecular mechanism through which the hMARK3 UBA domain has evolved to bind the kinase domain, in a fashion that stabilizes an open conformation of the N- and C-terminal lobes, at the expense of its capacity to engage ubiquitin. These results may be relevant more generally to the 30% of UBA domains that lack significant ubiquitin-binding activity, and they suggest a unique mechanism by which interaction domains may evolve new binding properties.

  11. Domain-and species-specific monoclonal antibodies recognize the Von Willebrand Factor-C domain of CCN5.

    PubMed

    Wei, Lan; McKeon, Frank; Russo, Joshua W; Lemire, Joan; Castellot, John

    2009-03-01

    The CCN family of proteins typically consists of four distinct peptide domains: an insulin-like growth factor binding protein-type (IGFBP) domain, a Von Willebrand Factor C (VWC) domain, a thrombospondin type 1 repeat (TSP1) domain, and a carboxy-terminal (CT) domain. The six family members participate in many processes, including proliferation, motility, cell-matrix signaling, angiogenesis, and wound healing. Accumulating evidence suggests that truncated and alternatively spliced isoforms are responsible for the diverse functions of CCN proteins in both normal and pathophysiologic states. Analysis of the properties and functions of individual CCN domains further corroborates this idea. CCN5 is unique among the CCN family members because it lacks the CT-domain. To dissect the domain functions of CCN5, we are developing domain-specific mouse monoclonal antibodies. Monoclonal antibodies have the advantages of great specificity, reproducibility, and ease of long-term storage and production. In this communication, we injected mixtures of GST-fused rat CCN5 domains into mice to generate monoclonal antibodies. To identify the domains recognized by the antibodies, we constructed serial expression plasmids that express dual-tagged rat CCN5 domains. All of the monoclonal antibodies generated to date recognize the VWC domain, indicating it is the most highly immunogenic of the CCN5 domains. We characterized one particular clone, 22H10, and found that it recognizes mouse and rat CCN5, but not human recombinant CCN5. Purified 22H10 was successfully applied in Western Blot analysis, immunofluorescence of cultured cells and tissues, and immunoprecipitation, indicating that it will be a useful tool for domain analysis and studies of mouse-human tumor models. PMID:19401828

  12. Domain wall dynamics of periodic magnetic domain patterns in Co2MnGe-Heusler microstripes

    NASA Astrophysics Data System (ADS)

    Gross, K.; Westerholt, K.; Zabel, H.

    2016-03-01

    Highly symmetric periodic domain patterns were obtained in Co2MnGe-Heusler microstripes as a result of the competition between growth-induced in-plane magnetic anisotropy and shape anisotropy. Zero field magnetic configurations and magnetic field-induced domain wall (DW) motion were studied by magnetic force microscopy-image technique for two different cases: dominant uniaxial- and dominant cubic in-plane anisotropy. We implemented a magneto-optical Kerr effect susceptometer to investigate the DW dynamics of periodic domain structures by measuring the in-phase and out-of-phase components of the Kerr signal as a function of magnetic field frequency and amplitude. The DW dynamics for fields applied transversally to the long stripe axis was found to be dominated by viscous slide motion. We used the inherent symmetry/periodicity properties of the magnetic domain structure to fit the experimental results with a theoretical model allowing to extract the DW mobility for the case of transverse DWs (μ TDW = 1.1 m s-1 Oe-1) as well as for vortex-like DWs (μ VDW = 8.7 m s-1 Oe-1). Internal spin structure transformations may cause a reduction of DW mobility in TDWs as observed by OMMFF simulations.

  13. Domain or not domain? That is the question: longitudinal semantic deterioration in Alzheimer's disease.

    PubMed

    Moreno-Martínez, F Javier; Goñi-Imízcoz, Miguel; Spitznagel, Mary Beth

    2011-10-01

    Category specific semantic impairment (e.g. living versus nonliving things) has been reported in association with various pathologies, including herpes simplex encephalitis and semantic dementia. However, evidence is inconsistent regarding whether this effect exists in diseases progressively impacting diverse cortical regions, such as Alzheimer's disease (AD). Ceiling effects producing non-Gaussian distributions and poor control for confounds such as nuisance variables (e.g. familiarity) may contribute to this discrepancy. Fourteen AD patients were longitudinally studied examining category effects on three semantic tasks (picture naming, naming to description and word to picture matching) matched across domain on all known nuisance variables (NV). To address non-Gaussian distributions, we run bootstrap analyses to determine whether NV, semantic domain or control performance best predicted AD patient performance. Multiple hierarchical regression analyses revealed that, whilst NV accounted for most of the explained variance in patients in the three tasks, the influence of semantic domain was substantially lower. Individual logistic regression demonstrated a significant category effect in only a few patients and healthy controls. No significant qualitative changes were observed in patients over time. Our results confirm the importance of NVs as predictors of AD patient performance, suggesting that the role of semantic domain is not a useful predictor of the progressive deterioration in AD. PMID:21696875

  14. Examining the Domain-Specificity of Metacognition Using Academic Domains and Task-Specific Individual Differences

    ERIC Educational Resources Information Center

    Scott, Brianna M.; Berman, Ashleigh F.

    2013-01-01

    Metacognition refers to students' knowledge and regulation of cognition, as well as their accuracy in predicting their academic performance. This study addressed two major questions: 1) how do metacognitive knowledge, regulation and accuracy differ across domains?, and 2) how do students' individual differences relate to their reported…

  15. The Aretaic Domain and Its Relation to the Deontic Domain in Moral Reasoning.

    ERIC Educational Resources Information Center

    Lourenco, Orlando

    2000-01-01

    Investigates the ways in which young adults make judgments about two contrasting kinds of rights: moral worthiness (the aretaic) and moral obligation (the deontic), reflecting on how thinking in these areas may be coordinated with responsibility judgments and behavior. Discusses what might be gained if the aretaic domain were taken into account in…

  16. A frequency domain method for the generation of partially coherent normal stationary time domain signals

    SciTech Connect

    Smallwood, D.O.; Paez, T.L.

    1991-01-01

    A procedure for generating vectors of time domain signals which are partially coherent in a prescribed manner is described. The procedure starts with the spectral density matrix, (G{sub xx}(f)), that relates pairs of elements of the vector random process (x(t), {minus}{infinity} < t < {infinity}). The spectral density matrix is decomposed into the form (G{sub xx}(f)) = (U(f)) (S(f)) (U(f)){prime} where (U(f)) is a matrix of complex frequency response functions, and (S(f)) is a diagonal matrix of real functions which can vary with frequency. The factors of the spectral density matrix, (U(f)) and (S(f)), are then used to generate a frame of random data in the frequency domain. The data is transformed into the time domain using an inverse FFT to generate a frame of data in the time domain. Successive frames of data are then windowed, overlapped, and added to form a vector of normal stationary sampled time histories, (x(t)), of arbitrary length. 11 refs., 4 figs., 1 tab.

  17. Domain-Independent Scientific Function Finding

    NASA Astrophysics Data System (ADS)

    Schaffer, Cullen R.

    1990-01-01

    Programs such as Bacon, Abacus, Coper, Kepler and others are designed to find functional relationships of scientific significance in quantitative data without relying on the deep domain knowledge scientists normally bring to bear in analytic work. Whether these systems actually perform as intended is an open question, however. To date, they have been supported only by anecdotal evidence --reports that a desirable answer has been found in one or more selected and often artificial cases. In this dissertation, I thus attempt to develop, not only new approaches to domain -independent scientific function finding, but, equally, a rigorous methodology under which research into such methods can be conducted. A fundamental problem with previous work is that it has investigated scientific data analysis in the abstract --without referring to actual scientific data. By contrast, the work reported here is founded on a collection of 352 real scientific data sets. This empirical base supports a number of strong conclusions. First, while researchers working with artificial data have targeted complex multivariate relations, real data provides powerful evidence that even the simplest bivariate relationships are difficult to identify reliably. Second, despite its ubiquitous presence in previous work, the notion of heuristic search of a potentially explosive space of formulas appears to help very little with the problem of reliably identifying basic bivariate relationships. Instead, third, substantial performance improvement results from viewing function finding as a decision problem, the problem of classifying data sets reliably within a fixed--and quite limited--system of functional categories. This dissertation presents what I believe to be the strongest domain-independent scientific function-finding algorithm currently in existence and, certainly, the only one which has been rigorously demonstrated. At the same time, it suggests fundamental limitations in the power of such

  18. Scanning secondary-electron microscopy on ferroelectric domains and domain walls in YMnO{sub 3}

    SciTech Connect

    Li, J.; Yang, H. X.; Tian, H. F.; Ma, C.; Li, J. Q.; Zhang, S.; Zhao, Y. G.

    2012-04-09

    Ferroelectric domain structures in YMnO{sub 3} single crystals on the hexagonal polar surface have been investigated by scanning electron microscopy in secondary electron emission mode. The experimental results demonstrate that the domain, as well as domain walls, can be clearly revealed under the operation voltages ranging from 0.6 to 3 kV. Evolution of domain contrasts arising from electron-beam irradiation can be mainly explained by the pyroelectric effect and related charging process. A rich variety of microstructure features of ferroelectric domains can be clearly revealed in YMnO{sub 3} by this high-resolution technique.

  19. Using domain knowledge and domain-inspired discourse model for coreference resolution for clinical narratives

    PubMed Central

    Roth, Dan

    2013-01-01

    Objective This paper presents a coreference resolution system for clinical narratives. Coreference resolution aims at clustering all mentions in a single document to coherent entities. Materials and methods A knowledge-intensive approach for coreference resolution is employed. The domain knowledge used includes several domain-specific lists, a knowledge intensive mention parsing, and task informed discourse model. Mention parsing allows us to abstract over the surface form of the mention and represent each mention using a higher-level representation, which we call the mention's semantic representation (SR). SR reduces the mention to a standard form and hence provides better support for comparing and matching. Existing coreference resolution systems tend to ignore discourse aspects and rely heavily on lexical and structural cues in the text. The authors break from this tradition and present a discourse model for “person” type mentions in clinical narratives, which greatly simplifies the coreference resolution. Results This system was evaluated on four different datasets which were made available in the 2011 i2b2/VA coreference challenge. The unweighted average of F1 scores (over B-cubed, MUC and CEAF) varied from 84.2% to 88.1%. These experiments show that domain knowledge is effective for different mention types for all the datasets. Discussion Error analysis shows that most of the recall errors made by the system can be handled by further addition of domain knowledge. The precision errors, on the other hand, are more subtle and indicate the need to understand the relations in which mentions participate for building a robust coreference system. Conclusion This paper presents an approach that makes an extensive use of domain knowledge to significantly improve coreference resolution. The authors state that their system and the knowledge sources developed will be made publicly available. PMID:22781192

  20. Photo-induced poly-domain to mono-domain switching in ultrathin PbTiO3 films

    NASA Astrophysics Data System (ADS)

    Vailionis, A.; Meyer, R.; McIntyre, P. C.

    2010-03-01

    Ferroelectric (FE) domain structures play a crucial role in polarization switching dynamics, ferroelectric random access memory (FRAM) data retention and polarization fatigue and it is therefore of practical importance to gain a more fundamental understanding of the origin of the transition between poly-domain and mono-domain states. Methods that promote the mono-domain state in the FE films are also of interest for model studies of ferroelectricity and its dimensional scaling. We investigate a novel poly-domain to mono-domain (P-M) switching mechanism in thin ferroelectric PbTiO3 (PTO) films induced by ultraviolet (UV) light illumination. The switching occurs within minutes if a sample is irradiated with light of wavelength < 390 nm which corresponds to a photon energy that is roughly equivalent to the band gap of PbTiO3 (3.2 eV). Based on a developed electrostatic model, we show that the observed phenomenon is related to photo generation of free carriers at the PbTiO3/SrTiO3 interface which effectively screens the PTO polarization charge at the interface and therefore promotes the transition of the ferroelectric film from a poly-domain to a mono-domain state. The model successfully describes not only the observed illumination effects on PTO stripe domain patterns but also a longer-term poly-domain to mono-domain (P-M) transition that occurs without intentional illumination.