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Sample records for coiled-coil interaction mode

  1. Conserved residues in the coiled-coil pocket of human immunodeficiency virus type 1 gp41 are essential for viral replication and interhelical interaction

    International Nuclear Information System (INIS)

    Mo Hongmei; Konstantinidis, Alex K.; Stewart, Kent D.; Dekhtyar, Tatyana; Ng, Teresa; Swift, Kerry; Matayoshi, Edmund D.; Kati, Warren; Kohlbrenner, William; Molla, Akhteruzzaman

    2004-01-01

    The human immunodeficiency virus type 1 (HIV-1) gp41 plays an important role in mediating the fusion of HIV with host cells. During the fusion process, three N-terminal helices and three C-terminal helices pack in an anti-parallel direction to form a six-helix bundle. X-ray crystallographic analysis of the gp41 core demonstrated that within each coiled-coil interface, there is a deep and large pocket, formed by a cluster of residues in the N-helix coiled-coil. In this report, we systematically analyzed the role of seven conserved residues that are either lining or packing this pocket on the infectivity and interhelical interaction using novel approaches. Our results show that residues L568, V570, W571, and K574 of the N-helix that are lining the side chain and right wall of the pocket are important for establishing a productive infection. Mutations V570A and W571A completely abolished replication, while replication of the L568A and K574A mutants was significantly attenuated relative to wild type. Similarly, residues W628, W631, and I635 of the C-helix that insert into the pocket are essential for infectivity. The impaired infectivity of these seven mutants is in part attributed to the loss in binding affinity of the interhelical interaction. Molecular modeling of the crystal structure of the coiled-coil further shows that alanine substitution of those residues disrupts the hydrophobic interaction between the N- and C-helix. These results suggest that the conserved residues in the coiled-coil domain play a key role in HIV infection and this coiled-coil pocket is a good target for development of inhibitors against HIV. In addition, our data indicate that the novel fluorescence polarization assay described in this study could be valuable in screening for inhibitors that block the interhelical interaction and HIV entry

  2. CCBuilder: an interactive web-based tool for building, designing and assessing coiled-coil protein assemblies.

    Science.gov (United States)

    Wood, Christopher W; Bruning, Marc; Ibarra, Amaurys Á; Bartlett, Gail J; Thomson, Andrew R; Sessions, Richard B; Brady, R Leo; Woolfson, Derek N

    2014-11-01

    The ability to accurately model protein structures at the atomistic level underpins efforts to understand protein folding, to engineer natural proteins predictably and to design proteins de novo. Homology-based methods are well established and produce impressive results. However, these are limited to structures presented by and resolved for natural proteins. Addressing this problem more widely and deriving truly ab initio models requires mathematical descriptions for protein folds; the means to decorate these with natural, engineered or de novo sequences; and methods to score the resulting models. We present CCBuilder, a web-based application that tackles the problem for a defined but large class of protein structure, the α-helical coiled coils. CCBuilder generates coiled-coil backbones, builds side chains onto these frameworks and provides a range of metrics to measure the quality of the models. Its straightforward graphical user interface provides broad functionality that allows users to build and assess models, in which helix geometry, coiled-coil architecture and topology and protein sequence can be varied rapidly. We demonstrate the utility of CCBuilder by assembling models for 653 coiled-coil structures from the PDB, which cover >96% of the known coiled-coil types, and by generating models for rarer and de novo coiled-coil structures. CCBuilder is freely available, without registration, at http://coiledcoils.chm.bris.ac.uk/app/cc_builder/. © The Author 2014. Published by Oxford University Press.

  3. Salt effects on hydrophobic interaction and charge screening in the folding of a negatively charged peptide to a coiled coil (leucine zipper).

    Science.gov (United States)

    Jelesarov, I; Dürr, E; Thomas, R M; Bosshard, H R

    1998-05-19

    The stability of a coiled coil or leucine zipper is controlled by hydrophobic interactions and electrostatic forces between the constituent helices. We have designed a 30-residue peptide with the repeating seven-residue pattern of a coiled coil, (abcdefg)n, and with Glu in positions e and g of each heptad. The glutamate side chains prevented folding at pH values above 6 because of electrostatic repulsion across the helix dimer interface as well as within the individual helices. Protonation of the carboxylates changed the conformation from a random coil monomer to a coiled coil dimer. Folding at alkaline pH where the peptide had a net charge of -7e was promoted by the addition of salts. The nature of the charge screening cation was less important than that of the anion. The high salt concentrations (>1 M) necessary to induce folding indicated that the salt-induced folding resulted from alterations in the protein-water interaction. Folding was promoted by the kosmotropic anions sulfate and fluoride and to a lesser extent by the weak kosmotrope formate, whereas chloride and the strong chaotrope perchlorate were ineffective. Kosmotropes are excluded from the protein surface, which is preferentially hydrated, and this promotes folding by strengthening hydrophobic interactions at the coiled coil interface. Although charge neutralization also contributed to folding, it was effective only when the screening cation was partnered by a good kosmotropic anion. Folding conformed to a two-state transition from random coil monomer to coiled coil dimer and was enthalpy driven and characterized by a change in the heat capacity of unfolding of 3.9 +/- 1.2 kJ mol-1 K-1. The rate of folding was analyzed by fluorescence stopped-flow measurements. Folding occurred in a biphasic reaction in which the rapid formation of an initial dimer (kf = 2 x 10(7) M-1 s-1) was followed by an equally rapid concentration-independent rearrangement to the folded dimer (k > 100 s-1).

  4. BECN2 interacts with ATG14 through a metastable coiled-coil to mediate autophagy: BECN2 CCD Structure and Interaction with ATG14

    Energy Technology Data Exchange (ETDEWEB)

    Su, Minfei; Li, Yue; Wyborny, Shane; Neau, David; Chakravarthy, Srinivas; Levine, Beth; Colbert, Christopher L.; Sinha, Sangita C. (NDSU); (IIT); (Cornell); (UTSMC)

    2017-03-12

    ATG14 binding to BECN/Beclin homologs is essential for autophagy, a critical catabolic homeostasis pathway. Here, we show that the α-helical, coiled-coil domain (CCD) of BECN2, a recently identified mammalian BECN1 paralog, forms an antiparallel, curved homodimer with seven pairs of nonideal packing interactions, while the BECN2 CCD and ATG14 CCD form a parallel, curved heterodimer stabilized by multiple, conserved polar interactions. Compared to BECN1, the BECN2 CCD forms a weaker homodimer, but binds more tightly to the ATG14 CCD. Mutation of nonideal BECN2 interface residues to more ideal pairs improves homodimer self-association and thermal stability. Unlike BECN1, all BECN2 CCD mutants bind ATG14, although more weakly than wild type. Thus, polar BECN2 CCD interface residues result in a metastable homodimer, facilitating dissociation, but enable better interactions with polar ATG14 residues stabilizing the BECN2:ATG14 heterodimer. These structure-based mechanistic differences in BECN1 and BECN2 homodimerization and heterodimerization likely dictate competitive ATG14 recruitment.

  5. Structural analysis of intermolecular interactions in the kinesin adaptor complex fasciculation and elongation protein zeta 1/ short coiled-coil protein (FEZ1/SCOCO.

    Directory of Open Access Journals (Sweden)

    Marcos Rodrigo Alborghetti

    Full Text Available Cytoskeleton and protein trafficking processes, including vesicle transport to synapses, are key processes in neuronal differentiation and axon outgrowth. The human protein FEZ1 (fasciculation and elongation protein zeta 1 / UNC-76, in C. elegans, SCOCO (short coiled-coil protein / UNC-69 and kinesins (e.g. kinesin heavy chain / UNC116 are involved in these processes. Exploiting the feature of FEZ1 protein as a bivalent adapter of transport mediated by kinesins and FEZ1 protein interaction with SCOCO (proteins involved in the same path of axonal growth, we investigated the structural aspects of intermolecular interactions involved in this complex formation by NMR (Nuclear Magnetic Resonance, cross-linking coupled with mass spectrometry (MS, SAXS (Small Angle X-ray Scattering and molecular modelling. The topology of homodimerization was accessed through NMR (Nuclear Magnetic Resonance studies of the region involved in this process, corresponding to FEZ1 (92-194. Through studies involving the protein in its monomeric configuration (reduced and dimeric state, we propose that homodimerization occurs with FEZ1 chains oriented in an anti-parallel topology. We demonstrate that the interaction interface of FEZ1 and SCOCO defined by MS and computational modelling is in accordance with that previously demonstrated for UNC-76 and UNC-69. SAXS and literature data support a heterotetrameric complex model. These data provide details about the interaction interfaces probably involved in the transport machinery assembly and open perspectives to understand and interfere in this assembly and its involvement in neuronal differentiation and axon outgrowth.

  6. The Chloroplastic Protein THF1 Interacts with the Coiled-Coil Domain of the Disease Resistance Protein N′ and Regulates Light-Dependent Cell Death1[OPEN

    Science.gov (United States)

    Sekine, Ken-Taro; Wallon, Thérèse; Sugiwaka, Yuji; Kobayashi, Kappei

    2016-01-01

    One branch of plant immunity is mediated through nucleotide-binding/Leu-rich repeat (NB-LRR) family proteins that recognize specific effectors encoded by pathogens. Members of the I2-like family constitute a well-conserved subgroup of NB-LRRs from Solanaceae possessing a coiled-coil (CC) domain at their N termini. We show here that the CC domains of several I2-like proteins are able to induce a hypersensitive response (HR), a form of programmed cell death associated with disease resistance. Using yeast two-hybrid screens, we identified the chloroplastic protein Thylakoid Formation1 (THF1) as an interacting partner for several I2-like CC domains. Co-immunoprecipitations and bimolecular fluorescence complementation assays confirmed that THF1 and I2-like CC domains interact in planta and that these interactions take place in the cytosol. Several HR-inducing I2-like CC domains have a negative effect on the accumulation of THF1, suggesting that the latter is destabilized by active CC domains. To confirm this model, we investigated N′, which recognizes the coat protein of most Tobamoviruses, as a prototypical member of the I2-like family. Transient expression and gene silencing data indicated that THF1 functions as a negative regulator of cell death and that activation of full-length N′ results in the destabilization of THF1. Consistent with the known function of THF1 in maintaining chloroplast homeostasis, we show that the HR induced by N′ is light-dependent. Together, our results define, to our knowledge, novel molecular mechanisms linking light and chloroplasts to the induction of cell death by a subgroup of NB-LRR proteins. PMID:26951433

  7. The Chloroplastic Protein THF1 Interacts with the Coiled-Coil Domain of the Disease Resistance Protein N' and Regulates Light-Dependent Cell Death.

    Science.gov (United States)

    Hamel, Louis-Philippe; Sekine, Ken-Taro; Wallon, Thérèse; Sugiwaka, Yuji; Kobayashi, Kappei; Moffett, Peter

    2016-05-01

    One branch of plant immunity is mediated through nucleotide-binding/Leu-rich repeat (NB-LRR) family proteins that recognize specific effectors encoded by pathogens. Members of the I2-like family constitute a well-conserved subgroup of NB-LRRs from Solanaceae possessing a coiled-coil (CC) domain at their N termini. We show here that the CC domains of several I2-like proteins are able to induce a hypersensitive response (HR), a form of programmed cell death associated with disease resistance. Using yeast two-hybrid screens, we identified the chloroplastic protein Thylakoid Formation1 (THF1) as an interacting partner for several I2-like CC domains. Co-immunoprecipitations and bimolecular fluorescence complementation assays confirmed that THF1 and I2-like CC domains interact in planta and that these interactions take place in the cytosol. Several HR-inducing I2-like CC domains have a negative effect on the accumulation of THF1, suggesting that the latter is destabilized by active CC domains. To confirm this model, we investigated N', which recognizes the coat protein of most Tobamoviruses, as a prototypical member of the I2-like family. Transient expression and gene silencing data indicated that THF1 functions as a negative regulator of cell death and that activation of full-length N' results in the destabilization of THF1. Consistent with the known function of THF1 in maintaining chloroplast homeostasis, we show that the HR induced by N' is light-dependent. Together, our results define, to our knowledge, novel molecular mechanisms linking light and chloroplasts to the induction of cell death by a subgroup of NB-LRR proteins. © 2016 American Society of Plant Biologists. All Rights Reserved.

  8. Investigation of the network of preferred interactions in an artificial coiled-coil association using the peptide array technique

    Directory of Open Access Journals (Sweden)

    Raheleh Rezaei Araghi

    2012-04-01

    Full Text Available We screened a randomized library and identified natural peptides that bound selectively to a chimeric peptide containing α-, β- and γ-amino acids. The SPOT arrays provide a means for the systematic study of the possible interaction space accessible to the αβγ-chimera. The mutational analysis reveals the dependence of the binding affinities of α-peptides to the αβγ-chimera, on the hydrophobicity and bulkiness of the side chains at the corresponding hydrophobic interface. The stability of the resulting heteroassemblies was further confirmed in solution by CD and thermal denaturation.

  9. Multicoil2: predicting coiled coils and their oligomerization states from sequence in the twilight zone.

    Directory of Open Access Journals (Sweden)

    Jason Trigg

    Full Text Available The alpha-helical coiled coil can adopt a variety of topologies, among the most common of which are parallel and antiparallel dimers and trimers. We present Multicoil2, an algorithm that predicts both the location and oligomerization state (two versus three helices of coiled coils in protein sequences. Multicoil2 combines the pairwise correlations of the previous Multicoil method with the flexibility of Hidden Markov Models (HMMs in a Markov Random Field (MRF. The resulting algorithm integrates sequence features, including pairwise interactions, through multinomial logistic regression to devise an optimized scoring function for distinguishing dimer, trimer and non-coiled-coil oligomerization states; this scoring function is used to produce Markov Random Field potentials that incorporate pairwise correlations localized in sequence. Multicoil2 significantly improves both coiled-coil detection and dimer versus trimer state prediction over the original Multicoil algorithm retrained on a newly-constructed database of coiled-coil sequences. The new database, comprised of 2,105 sequences containing 124,088 residues, includes reliable structural annotations based on experimental data in the literature. Notably, the enhanced performance of Multicoil2 is evident when tested in stringent leave-family-out cross-validation on the new database, reflecting expected performance on challenging new prediction targets that have minimal sequence similarity to known coiled-coil families. The Multicoil2 program and training database are available for download from http://multicoil2.csail.mit.edu.

  10. Biomaterials Made from Coiled-Coil Peptides.

    Science.gov (United States)

    Conticello, Vincent; Hughes, Spencer; Modlin, Charles

    The development of biomaterials designed for specific applications is an important objective in personalized medicine. While the breadth and prominence of biomaterials have increased exponentially over the past decades, critical challenges remain to be addressed, particularly in the development of biomaterials that exhibit highly specific functions. These functional properties are often encoded within the molecular structure of the component molecules. Proteins, as a consequence of their structural specificity, represent useful substrates for the construction of functional biomaterials through rational design. This chapter provides an in-depth survey of biomaterials constructed from coiled-coils, one of the best-understood protein structural motifs. We discuss the utility of this structurally diverse and functionally tunable class of proteins for the creation of novel biomaterials. This discussion illustrates the progress that has been made in the development of coiled-coil biomaterials by showcasing studies that bridge the gap between the academic science and potential technological impact.

  11. Four signature motifs define the first class of structurally related large coiled-coil proteins in plants.

    Directory of Open Access Journals (Sweden)

    Meier Iris

    2002-04-01

    Full Text Available Abstract Background Animal and yeast proteins containing long coiled-coil domains are involved in attaching other proteins to the large, solid-state components of the cell. One subgroup of long coiled-coil proteins are the nuclear lamins, which are involved in attaching chromatin to the nuclear envelope and have recently been implicated in inherited human diseases. In contrast to other eukaryotes, long coiled-coil proteins have been barely investigated in plants. Results We have searched the completed Arabidopsis genome and have identified a family of structurally related long coiled-coil proteins. Filament-like plant proteins (FPP were identified by sequence similarity to a tomato cDNA that encodes a coiled-coil protein which interacts with the nuclear envelope-associated protein, MAF1. The FPP family is defined by four novel unique sequence motifs and by two clusters of long coiled-coil domains separated by a non-coiled-coil linker. All family members are expressed in a variety of Arabidopsis tissues. A homolog sharing the structural features was identified in the monocot rice, indicating conservation among angiosperms. Conclusion Except for myosins, this is the first characterization of a family of long coiled-coil proteins in plants. The tomato homolog of the FPP family binds in a yeast two-hybrid assay to a nuclear envelope-associated protein. This might suggest that FPP family members function in nuclear envelope biology. Because the full Arabidopsis genome does not appear to contain genes for lamins, it is of interest to investigate other long coiled-coil proteins, which might functionally replace lamins in the plant kingdom.

  12. Molecular basis of coiled-coil oligomerization-state specificity.

    Science.gov (United States)

    Ciani, Barbara; Bjelic, Saša; Honnappa, Srinivas; Jawhari, Hatim; Jaussi, Rolf; Payapilly, Aishwarya; Jowitt, Thomas; Steinmetz, Michel O; Kammerer, Richard A

    2010-11-16

    Coiled coils are extensively and successfully used nowadays to rationally design multistranded structures for applications, including basic research, biotechnology, nanotechnology, materials science, and medicine. The wide range of applications as well as the important functions these structures play in almost all biological processes highlight the need for a detailed understanding of the factors that control coiled-coil folding and oligomerization. Here, we address the important and unresolved question why the presence of particular oligomerization-state determinants within a coiled coil does frequently not correlate with its topology. We found an unexpected, general link between coiled-coil oligomerization-state specificity and trigger sequences, elements that are indispensable for coiled-coil formation. By using the archetype coiled-coil domain of the yeast transcriptional activator GCN4 as a model system, we show that well-established trimer-specific oligomerization-state determinants switch the peptide's topology from a dimer to a trimer only when inserted into the trigger sequence. We successfully confirmed our results in two other, unrelated coiled-coil dimers, ATF1 and cortexillin-1. We furthermore show that multiple topology determinants can coexist in the same trigger sequence, revealing a delicate balance of the resulting oligomerization state by position-dependent forces. Our experimental results should significantly improve the prediction of the oligomerization state of coiled coils. They therefore should have major implications for the rational design of coiled coils and consequently many applications using these popular oligomerization domains.

  13. Extending the self-assembly of coiled-coil hybrids

    NARCIS (Netherlands)

    Robson Marsden, Hana

    2009-01-01

    Of the various biomolecular building blocks in use in nature, coiled-coil forming peptides are amongst those with the most potential as building blocks for the synthetic self-assembly of nanostructures. Native coiled coils have the ability to function in, and influence, complex systems composed of

  14. A periodic table of coiled-coil protein structures.

    Science.gov (United States)

    Moutevelis, Efrosini; Woolfson, Derek N

    2009-01-23

    Coiled coils are protein structure domains with two or more alpha-helices packed together via interlacing of side chains known as knob-into-hole packing. We analysed and classified a large set of coiled-coil structures using a combination of automated and manual methods. This led to a systematic classification that we termed a "periodic table of coiled coils," which we have made available at http://coiledcoils.chm.bris.ac.uk/ccplus/search/periodic_table. In this table, coiled-coil assemblies are arranged in columns with increasing numbers of alpha-helices and in rows of increased complexity. The table provides a framework for understanding possibilities in and limits on coiled-coil structures and a basis for future prediction, engineering and design studies.

  15. Historical review: another 50th anniversary--new periodicities in coiled coils.

    Science.gov (United States)

    Gruber, Markus; Lupas, Andrei N

    2003-12-01

    In 1953, Francis Crick and Linus Pauling both proposed models of supercoiled alpha helices ('coiled coils') for the structure of keratin. These were the first attempts at modelling the tertiary structure of a protein. Crick emphasized the packing mode of the side-chains ('knobs-into-holes'), which required a periodicity of seven residues over two helical turns (7/2) and a supercoil in the opposite sense of the constituent helices. By contrast, Pauling envisaged a broader set of periodicities (4/1, 7/2, 18/5, 15/4, 11/3) and supercoils of both senses. Crick's model became canonical and the 'heptad repeat' essentially synonymous with coiled coils, but 50 years later new crystal structures and protein sequences show that the less common periodicities envisaged by Pauling also occur in coiled coils, adding a variant packing mode ('knobs-to-knobs') to the standard model. Pauling's laboratory notebooks suggest that he searched unsuccessfully for this packing mode in 1953.

  16. Strong contributions from vertical triads to helix-partner preferences in parallel coiled coils.

    Science.gov (United States)

    Steinkruger, Jay D; Bartlett, Gail J; Woolfson, Derek N; Gellman, Samuel H

    2012-09-26

    Pairing preferences in heterodimeric coiled coils are determined by complementarities among side chains that pack against one another at the helix-helix interface. However, relationships between dimer stability and interfacial residue identity are not fully understood. In the context of the "knobs-into-holes" (KIH) packing pattern, one can identify two classes of interactions between side chains from different helices: "lateral", in which a line connecting the adjacent side chains is perpendicular to the helix axes, and "vertical", in which the connecting line is parallel to the helix axes. We have previously analyzed vertical interactions in antiparallel coiled coils and found that one type of triad constellation (a'-a-a') exerts a strong effect on pairing preferences, while the other type of triad (d'-d-d') has relatively little impact on pairing tendencies. Here, we ask whether vertical interactions (d'-a-d') influence pairing in parallel coiled-coil dimers. Our results indicate that vertical interactions can exert a substantial impact on pairing specificity, and that the influence of the d'-a-d' triad depends on the lateral a' contact within the local KIH motif. Structure-informed bioinformatic analyses of protein sequences reveal trends consistent with the thermodynamic data derived from our experimental model system in suggesting that heterotriads involving Leu and Ile are preferred over homotriads involving Leu and Ile.

  17. Structure of bacteriophage T4 fibritin: a segmented coiled coil and the role of the C-terminal domain.

    Science.gov (United States)

    Tao, Y; Strelkov, S V; Mesyanzhinov, V V; Rossmann, M G

    1997-06-15

    Oligomeric coiled-coil motifs are found in numerous protein structures; among them is fibritin, a structural protein of bacteriophage T4, which belongs to a class of chaperones that catalyze a specific phage-assembly process. Fibritin promotes the assembly of the long tail fibers and their subsequent attachment to the tail baseplate; it is also a sensing device that controls the retraction of the long tail fibers in adverse environments and, thus, prevents infection. The structure of fibritin had been predicted from sequence and biochemical analyses to be mainly a triple-helical coiled coil. The determination of its structure at atomic resolution was expected to give insights into the assembly process and biological function of fibritin, and the properties of modified coiled-coil structures in general. The three-dimensional structure of fibritin E, a deletion mutant of wild-type fibritin, was determined to 2.2 A resolution by X-ray crystallography. Three identical subunits of 119 amino acid residues form a trimeric parallel coiled-coil domain and a small globular C-terminal domain about a crystallographic threefold axis. The coiled-coil domain is divided into three segments that are separated by insertion loops. The C-terminal domain, which consists of 30 residues from each subunit, contains a beta-propeller-like structure with a hydrophobic interior. The residues within the C-terminal domain make extensive hydrophobic and some polar intersubunit interactions. This is consistent with the C-terminal domain being important for the correct assembly of fibritin, as shown earlier by mutational studies. Tight interactions between the C-terminal residues of adjacent subunits counteract the latent instability that is suggested by the structural properties of the coiled-coil segments. Trimerization is likely to begin with the formation of the C-terminal domain which subsequently initiates the assembly of the coiled coil. The interplay between the stabilizing effect of the C

  18. GBNV encoded movement protein (NSm) remodels ER network via C-terminal coiled coil domain

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Pratibha; Savithri, H.S., E-mail: bchss@biochem.iisc.ernet.in

    2015-08-15

    Plant viruses exploit the host machinery for targeting the viral genome–movement protein complex to plasmodesmata (PD). The mechanism by which the non-structural protein m (NSm) of Groundnut bud necrosis virus (GBNV) is targeted to PD was investigated using Agrobacterium mediated transient expression of NSm and its fusion proteins in Nicotiana benthamiana. GFP:NSm formed punctuate structures that colocalized with mCherry:plasmodesmata localized protein 1a (PDLP 1a) confirming that GBNV NSm localizes to PD. Unlike in other movement proteins, the C-terminal coiled coil domain of GBNV NSm was shown to be involved in the localization of NSm to PD, as deletion of this domain resulted in the cytoplasmic localization of NSm. Treatment with Brefeldin A demonstrated the role of ER in targeting GFP NSm to PD. Furthermore, mCherry:NSm co-localized with ER–GFP (endoplasmic reticulum targeting peptide (HDEL peptide fused with GFP). Co-expression of NSm with ER–GFP showed that the ER-network was transformed into vesicles indicating that NSm interacts with ER and remodels it. Mutations in the conserved hydrophobic region of NSm (residues 130–138) did not abolish the formation of vesicles. Additionally, the conserved prolines at positions 140 and 142 were found to be essential for targeting the vesicles to the cell membrane. Further, systematic deletion of amino acid residues from N- and C-terminus demonstrated that N-terminal 203 amino acids are dispensable for the vesicle formation. On the other hand, the C-terminal coiled coil domain when expressed alone could also form vesicles. These results suggest that GBNV NSm remodels the ER network by forming vesicles via its interaction through the C-terminal coiled coil domain. Interestingly, NSm interacts with NP in vitro and coexpression of these two proteins in planta resulted in the relocalization of NP to PD and this relocalization was abolished when the N-terminal unfolded region of NSm was deleted. Thus, the NSm

  19. Coiled-Coil Proteins Facilitated the Functional Expansion of the Centrosome

    Science.gov (United States)

    Kuhn, Michael; Hyman, Anthony A.; Beyer, Andreas

    2014-01-01

    Repurposing existing proteins for new cellular functions is recognized as a main mechanism of evolutionary innovation, but its role in organelle evolution is unclear. Here, we explore the mechanisms that led to the evolution of the centrosome, an ancestral eukaryotic organelle that expanded its functional repertoire through the course of evolution. We developed a refined sequence alignment technique that is more sensitive to coiled coil proteins, which are abundant in the centrosome. For proteins with high coiled-coil content, our algorithm identified 17% more reciprocal best hits than BLAST. Analyzing 108 eukaryotic genomes, we traced the evolutionary history of centrosome proteins. In order to assess how these proteins formed the centrosome and adopted new functions, we computationally emulated evolution by iteratively removing the most recently evolved proteins from the centrosomal protein interaction network. Coiled-coil proteins that first appeared in the animal–fungi ancestor act as scaffolds and recruit ancestral eukaryotic proteins such as kinases and phosphatases to the centrosome. This process created a signaling hub that is crucial for multicellular development. Our results demonstrate how ancient proteins can be co-opted to different cellular localizations, thereby becoming involved in novel functions. PMID:24901223

  20. The coiled coil motif in polymer drug delivery systems

    Czech Academy of Sciences Publication Activity Database

    Pechar, Michal; Pola, Robert

    2013-01-01

    Roč. 31, č. 1 (2013), s. 90-96 ISSN 0734-9750 R&D Projects: GA ČR GA203/08/0543; GA MŠk 1M0505 Institutional research plan: CEZ:AV0Z40500505 Keywords : coiled coil * hydrophilic polymer * recombinant protein Subject RIV: CD - Macromolecular Chemistry Impact factor: 8.905, year: 2013

  1. Structural mapping of the coiled-coil domain of a bacterial condensin and comparative analyses across all domains of life suggest conserved features of SMC proteins.

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    Waldman, Vincent M; Stanage, Tyler H; Mims, Alexandra; Norden, Ian S; Oakley, Martha G

    2015-06-01

    The structural maintenance of chromosomes (SMC) proteins form the cores of multisubunit complexes that are required for the segregation and global organization of chromosomes in all domains of life. These proteins share a common domain structure in which N- and C- terminal regions pack against one another to form a globular ATPase domain. This "head" domain is connected to a central, globular, "hinge" or dimerization domain by a long, antiparallel coiled coil. To date, most efforts for structural characterization of SMC proteins have focused on the globular domains. Recently, however, we developed a method to map interstrand interactions in the 50-nm coiled-coil domain of MukB, the divergent SMC protein found in γ-proteobacteria. Here, we apply that technique to map the structure of the Bacillus subtilis SMC (BsSMC) coiled-coil domain. We find that, in contrast to the relatively complicated coiled-coil domain of MukB, the BsSMC domain is nearly continuous, with only two detectable coiled-coil interruptions. Near the middle of the domain is a break in coiled-coil structure in which there are three more residues on the C-terminal strand than on the N-terminal strand. Close to the head domain, there is a second break with a significantly longer insertion on the same strand. These results provide an experience base that allows an informed interpretation of the output of coiled-coil prediction algorithms for this family of proteins. A comparison of such predictions suggests that these coiled-coil deviations are highly conserved across SMC types in a wide variety of organisms, including humans. © 2015 Wiley Periodicals, Inc.

  2. CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information

    DEFF Research Database (Denmark)

    Bartoli, Lisa; Fariselli, Piero; Krogh, Anders

    2009-01-01

    tools are available for predicting coiled-coil domains in protein sequences, including those based on position-specific score matrices and machine learning methods. RESULTS: In this article, we introduce a hidden Markov model (CCHMM_PROF) that exploits the information contained in multiple sequence...... alignments (profiles) to predict coiled-coil regions. The new method discriminates coiled-coil sequences with an accuracy of 97% and achieves a true positive rate of 79% with only 1% of false positives. Furthermore, when predicting the location of coiled-coil segments in protein sequences, the method reaches...

  3. Structural basis for cargo binding and autoinhibition of Bicaudal-D1 by a parallel coiled-coil with homotypic registry

    Energy Technology Data Exchange (ETDEWEB)

    Terawaki, Shin-ichi, E-mail: terawaki@gunma-u.ac.jp [Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515 (Japan); SPring-8 Center, RIKEN, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148 (Japan); Yoshikane, Asuka [Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515 (Japan); SPring-8 Center, RIKEN, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148 (Japan); Higuchi, Yoshiki [Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297 (Japan); Department of Picobiology, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297 (Japan); SPring-8 Center, RIKEN, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148 (Japan); Wakamatsu, Kaori [Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515 (Japan); SPring-8 Center, RIKEN, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148 (Japan)

    2015-05-01

    Bicaudal-D1 (BICD1) is an α-helical coiled-coil protein mediating the attachment of specific cargo to cytoplasmic dynein. It plays an essential role in minus end-directed intracellular transport along microtubules. The third C-terminal coiled-coil region of BICD1 (BICD1 CC3) has an important role in cargo sorting, including intracellular vesicles associating with the small GTPase Rab6 and the nuclear pore complex Ran binding protein 2 (RanBP2), and inhibiting the association with cytoplasmic dynein by binding to the first N-terminal coiled-coil region (CC1). The crystal structure of BICD1 CC3 revealed a parallel homodimeric coiled-coil with asymmetry and complementary knobs-into-holes interactions, differing from Drosophila BicD CC3. Furthermore, our binding study indicated that BICD1 CC3 possesses a binding surface for two distinct cargos, Rab6 and RanBP2, and that the CC1-binding site overlaps with the Rab6-binding site. These findings suggest a molecular basis for cargo recognition and autoinhibition of BICD proteins during dynein-dependent intracellular retrograde transport. - Highlights: • BICD1 CC3 is a parallel homodimeric coiled-coil with axial asymmetry. • The coiled-coil packing of BICD1 CC3 is adapted to the equivalent heptad position. • BICD1 CC3 has distinct binding sites for two classes of cargo, Rab6 and RanBP2. • The CC1-binding site of BICD1 CC3 overlaps with the Rab6-binding site.

  4. Structural basis for cargo binding and autoinhibition of Bicaudal-D1 by a parallel coiled-coil with homotypic registry

    International Nuclear Information System (INIS)

    Terawaki, Shin-ichi; Yoshikane, Asuka; Higuchi, Yoshiki; Wakamatsu, Kaori

    2015-01-01

    Bicaudal-D1 (BICD1) is an α-helical coiled-coil protein mediating the attachment of specific cargo to cytoplasmic dynein. It plays an essential role in minus end-directed intracellular transport along microtubules. The third C-terminal coiled-coil region of BICD1 (BICD1 CC3) has an important role in cargo sorting, including intracellular vesicles associating with the small GTPase Rab6 and the nuclear pore complex Ran binding protein 2 (RanBP2), and inhibiting the association with cytoplasmic dynein by binding to the first N-terminal coiled-coil region (CC1). The crystal structure of BICD1 CC3 revealed a parallel homodimeric coiled-coil with asymmetry and complementary knobs-into-holes interactions, differing from Drosophila BicD CC3. Furthermore, our binding study indicated that BICD1 CC3 possesses a binding surface for two distinct cargos, Rab6 and RanBP2, and that the CC1-binding site overlaps with the Rab6-binding site. These findings suggest a molecular basis for cargo recognition and autoinhibition of BICD proteins during dynein-dependent intracellular retrograde transport. - Highlights: • BICD1 CC3 is a parallel homodimeric coiled-coil with axial asymmetry. • The coiled-coil packing of BICD1 CC3 is adapted to the equivalent heptad position. • BICD1 CC3 has distinct binding sites for two classes of cargo, Rab6 and RanBP2. • The CC1-binding site of BICD1 CC3 overlaps with the Rab6-binding site

  5. Rice Cellulose SynthaseA8 Plant-Conserved Region Is a Coiled-Coil at the Catalytic Core Entrance

    Energy Technology Data Exchange (ETDEWEB)

    Rushton, Phillip S.; Olek, Anna T.; Makowski, Lee; Badger, John; Steussy, C. Nicklaus; Carpita, Nicholas C.; Stauffacher, Cynthia V. (NEU); (Purdue)

    2016-11-22

    The crystallographic structure of a rice (Oryza sativa) cellulose synthase, OsCesA8, plant-conserved region (P-CR), one of two unique domains in the catalytic domain of plant CesAs, was solved to 2.4 Å resolution. Two antiparallel α-helices form a coiled-coil domain linked by a large extended connector loop containing a conserved trio of aromatic residues. The P-CR structure was fit into a molecular envelope for the P-CR domain derived from small-angle X-ray scattering data. The P-CR structure and molecular envelope, combined with a homology-based chain trace of the CesA8 catalytic core, were modeled into a previously determined CesA8 small-angle X-ray scattering molecular envelope to produce a detailed topological model of the CesA8 catalytic domain. The predicted position for the P-CR domain from the molecular docking models places the P-CR connector loop into a hydrophobic pocket of the catalytic core, with the coiled-coil aligned near the entrance of the substrate UDP-glucose into the active site. In this configuration, the P-CR coiled-coil alone is unlikely to regulate substrate access to the active site, but it could interact with other domains of CesA, accessory proteins, or other CesA catalytic domains to control substrate delivery.

  6. Plasmodium vivax antigen discovery based on alpha-helical coiled coil protein motif

    DEFF Research Database (Denmark)

    Céspedes, Nora; Habel, Catherine; Lopez-Perez, Mary

    2014-01-01

    Protein α-helical coiled coil structures that elicit antibody responses, which block critical functions of medically important microorganisms, represent a means for vaccine development. By using bioinformatics algorithms, a total of 50 antigens with α-helical coiled coil motifs orthologous to Pla...

  7. Conformational switching in the coiled-coil domains of a proteasomal ATPase regulates substrate processing.

    Science.gov (United States)

    Snoberger, Aaron; Brettrager, Evan J; Smith, David M

    2018-06-18

    Protein degradation in all domains of life requires ATPases that unfold and inject proteins into compartmentalized proteolytic chambers. Proteasomal ATPases in eukaryotes and archaea contain poorly understood N-terminally conserved coiled-coil domains. In this study, we engineer disulfide crosslinks in the coiled-coils of the archaeal proteasomal ATPase (PAN) and report that its three identical coiled-coil domains can adopt three different conformations: (1) in-register and zipped, (2) in-register and partially unzipped, and (3) out-of-register. This conformational heterogeneity conflicts with PAN's symmetrical OB-coiled-coil crystal structure but resembles the conformational heterogeneity of the 26S proteasomal ATPases' coiled-coils. Furthermore, we find that one coiled-coil can be conformationally constrained even while unfolding substrates, and conformational changes in two of the coiled-coils regulate PAN switching between resting and active states. This switching functionally mimics similar states proposed for the 26S proteasome from cryo-EM. These findings thus build a mechanistic framework to understand regulation of proteasome activity.

  8. Routine phasing of coiled-coil protein crystal structures with AMPLE

    Directory of Open Access Journals (Sweden)

    Jens M. H. Thomas

    2015-03-01

    Full Text Available Coiled-coil protein folds are among the most abundant in nature. These folds consist of long wound α-helices and are architecturally simple, but paradoxically their crystallographic structures are notoriously difficult to solve with molecular-replacement techniques. The program AMPLE can solve crystal structures by molecular replacement using ab initio search models in the absence of an existent homologous protein structure. AMPLE has been benchmarked on a large and diverse test set of coiled-coil crystal structures and has been found to solve 80% of all cases. Successes included structures with chain lengths of up to 253 residues and resolutions down to 2.9 Å, considerably extending the limits on size and resolution that are typically tractable by ab initio methodologies. The structures of two macromolecular complexes, one including DNA, were also successfully solved using their coiled-coil components. It is demonstrated that both the ab initio modelling and the use of ensemble search models contribute to the success of AMPLE by comparison with phasing attempts using single structures or ideal polyalanine helices. These successes suggest that molecular replacement with AMPLE should be the method of choice for the crystallographic elucidation of a coiled-coil structure. Furthermore, AMPLE may be able to exploit the presence of a coiled coil in a complex to provide a convenient route for phasing.

  9. Self-assembly of coiled coil peptides into nanoparticles vs 2-d plates: effects of assembly pathway

    Science.gov (United States)

    Kim, Kyunghee; Pochan, Darrin

    Molecular solution assembly, or self-assembly, is a process by which ordered nanostructures or patterns are formed by non-covalent interactions during assembly. Biomimicry, the use of bioinspired molecules or biologically relevant materials, is an important area of self-assembly research with peptides serving a critical role as molecular tools. The morphology of peptide assemblies can be controlled by adjusting solution conditions such as the concentration of peptides, the temperature, and pH. Herein, spherical nanostructures, which have potential for creating an encapsulation system, are formed by self-assembly when coiled coil peptides are combined in solution. These peptides are homotrimeric and heterodimeric coiled-coil bundles and the homotrimer is connected with each of heterodimer through their external surfaces via disulfide bonds. The resultant covalent constructs could co-assemble into complementary trimeric hubs, respectively. The two peptide constructs are directly mixed and assembled in solution in order to produce either spherical particles or 2-d plates depending on the solution conditions and kinetic pathway of assembly. In particular, structural changes of the self-assembled peptides are explored by control of the thermal history of the assembly solution.

  10. Two coiled-coil domains of Chlamydia trachomatis IncA affect membrane fusion events during infection.

    Science.gov (United States)

    Ronzone, Erik; Paumet, Fabienne

    2013-01-01

    Chlamydia trachomatis replicates in a parasitophorous membrane-bound compartment called an inclusion. The inclusions corrupt host vesicle trafficking networks to avoid the degradative endolysosomal pathway but promote fusion with each other in order to sustain higher bacterial loads in a process known as homotypic fusion. The Chlamydia protein IncA (Inclusion protein A) appears to play central roles in both these processes as it participates to homotypic fusion and inhibits endocytic SNARE-mediated membrane fusion. How IncA selectively inhibits or activates membrane fusion remains poorly understood. In this study, we analyzed the spatial and molecular determinants of IncA's fusogenic and inhibitory functions. Using a cell-free membrane fusion assay, we found that inhibition of SNARE-mediated fusion requires IncA to be on the same membrane as the endocytic SNARE proteins. IncA displays two coiled-coil domains showing high homology with SNARE proteins. Domain swap and deletion experiments revealed that although both these domains are capable of independently inhibiting SNARE-mediated fusion, these two coiled-coil domains cooperate in mediating IncA multimerization and homotypic membrane interaction. Our results support the hypothesis that Chlamydia employs SNARE-like virulence factors that positively and negatively affect membrane fusion and promote infection.

  11. Two coiled-coil domains of Chlamydia trachomatis IncA affect membrane fusion events during infection.

    Directory of Open Access Journals (Sweden)

    Erik Ronzone

    Full Text Available Chlamydia trachomatis replicates in a parasitophorous membrane-bound compartment called an inclusion. The inclusions corrupt host vesicle trafficking networks to avoid the degradative endolysosomal pathway but promote fusion with each other in order to sustain higher bacterial loads in a process known as homotypic fusion. The Chlamydia protein IncA (Inclusion protein A appears to play central roles in both these processes as it participates to homotypic fusion and inhibits endocytic SNARE-mediated membrane fusion. How IncA selectively inhibits or activates membrane fusion remains poorly understood. In this study, we analyzed the spatial and molecular determinants of IncA's fusogenic and inhibitory functions. Using a cell-free membrane fusion assay, we found that inhibition of SNARE-mediated fusion requires IncA to be on the same membrane as the endocytic SNARE proteins. IncA displays two coiled-coil domains showing high homology with SNARE proteins. Domain swap and deletion experiments revealed that although both these domains are capable of independently inhibiting SNARE-mediated fusion, these two coiled-coil domains cooperate in mediating IncA multimerization and homotypic membrane interaction. Our results support the hypothesis that Chlamydia employs SNARE-like virulence factors that positively and negatively affect membrane fusion and promote infection.

  12. Regulatory coiled-coil domains promote head-to-head assemblies of AAA+ chaperones essential for tunable activity control.

    Science.gov (United States)

    Carroni, Marta; Franke, Kamila B; Maurer, Michael; Jäger, Jasmin; Hantke, Ingo; Gloge, Felix; Linder, Daniela; Gremer, Sebastian; Turgay, Kürşad; Bukau, Bernd; Mogk, Axel

    2017-11-22

    Ring-forming AAA+ chaperones exert ATP-fueled substrate unfolding by threading through a central pore. This activity is potentially harmful requiring mechanisms for tight repression and substrate-specific activation. The AAA+ chaperone ClpC with the peptidase ClpP forms a bacterial protease essential to virulence and stress resistance. The adaptor MecA activates ClpC by targeting substrates and stimulating ClpC ATPase activity. We show how ClpC is repressed in its ground state by determining ClpC cryo-EM structures with and without MecA. ClpC forms large two-helical assemblies that associate via head-to-head contacts between coiled-coil middle domains (MDs). MecA converts this resting state to an active planar ring structure by binding to MD interaction sites. Loss of ClpC repression in MD mutants causes constitutive activation and severe cellular toxicity. These findings unravel an unexpected regulatory concept executed by coiled-coil MDs to tightly control AAA+ chaperone activity.

  13. Immunogenicity of coiled-coil based drug-free macromolecular therapeutics

    Czech Academy of Sciences Publication Activity Database

    Kverka, Miloslav; Hartley, J.M.; Chu, T.W.; Yang, J.; Heidchen, R.; Kopeček, J.

    2014-01-01

    Roč. 35, č. 2 (2014), s. 5886-5896 ISSN 1616-0177 R&D Projects: GA MŠk(CZ) EE2.3.30.0003 Grant - others:NIH(US) GM095606 Institutional support: RVO:61388971 Keywords : coiled-coil * enantiomers * HPMA copolymer Subject RIV: EC - Immunology

  14. Golgi coiled-coil proteins contain multiple binding sites for Rab family G proteins

    NARCIS (Netherlands)

    Sinka, Rita; Gillingham, Alison K.; Kondylis, Vangelis; Munro, Sean

    2008-01-01

    Vesicles and other carriers destined for the Golgi apparatus must be guided to the correct cisternae. Golgins, long coiled-coil proteins that localize to particular Golgi subdomains via their C termini, are candidate regulators of vesicle sorting. In this study, we report that the GRIP domain

  15. Automated de novo phasing and model building of coiled-coil proteins.

    Science.gov (United States)

    Rämisch, Sebastian; Lizatović, Robert; André, Ingemar

    2015-03-01

    Models generated by de novo structure prediction can be very useful starting points for molecular replacement for systems where suitable structural homologues cannot be readily identified. Protein-protein complexes and de novo-designed proteins are examples of systems that can be challenging to phase. In this study, the potential of de novo models of protein complexes for use as starting points for molecular replacement is investigated. The approach is demonstrated using homomeric coiled-coil proteins, which are excellent model systems for oligomeric systems. Despite the stereotypical fold of coiled coils, initial phase estimation can be difficult and many structures have to be solved with experimental phasing. A method was developed for automatic structure determination of homomeric coiled coils from X-ray diffraction data. In a benchmark set of 24 coiled coils, ranging from dimers to pentamers with resolutions down to 2.5 Å, 22 systems were automatically solved, 11 of which had previously been solved by experimental phasing. The generated models contained 71-103% of the residues present in the deposited structures, had the correct sequence and had free R values that deviated on average by 0.01 from those of the respective reference structures. The electron-density maps were of sufficient quality that only minor manual editing was necessary to produce final structures. The method, named CCsolve, combines methods for de novo structure prediction, initial phase estimation and automated model building into one pipeline. CCsolve is robust against errors in the initial models and can readily be modified to make use of alternative crystallographic software. The results demonstrate the feasibility of de novo phasing of protein-protein complexes, an approach that could also be employed for other small systems beyond coiled coils.

  16. Thermodynamic analysis of cavity creating mutations in an engineered leucine zipper and energetics of glycerol-induced coiled coil stabilization.

    Science.gov (United States)

    Dürr, E; Jelesarov, I

    2000-04-18

    Protein stability in vitro can be influenced either by introduction of mutations or by changes in the chemical composition of the solvent. Recently, we have characterized the thermodynamic stability and the rate of folding of the engineered dimeric leucine zipper A(2), which has a strengthened hydrophobic core [Dürr, E., Jelesarov, I., and Bosshard, H. R. (1999) Biochemistry 38, 870-880]. Here we report on the energetic consequences of a cavity introduced by Leu/Ala substitution at the tightly packed dimeric interface and how addition of 30% glycerol affects the folding thermodynamics of A(2) and the cavity mutants. Folding could be described by a two-state transition from two unfolded monomers to a coiled coil dimer. Removal of six methylene groups by Leu/Ala substitutions destabilized the dimeric coiled coil by 25 kJ mol(-1) at pH 3.5 and 25 degrees C in aqueous buffer. Destabilization was purely entropic at around room temperature and became increasingly enthalpic at elevated temperatures. Mutations were accompanied by a decrease of the unfolding heat capacity by 0.5 kJ K(-1) mol(-1). Addition of 30% glycerol increased the free energy of folding of A(2) and the cavity mutants by 5-10 kJ mol(-1) and lowered the unfolding heat capacity by 25% for A(2) and by 50% for the Leu/Ala mutants. The origin of the stabilizing effect of glycerol varied with temperature. Stabilization of the parent leucine zipper A(2) was enthalpic with an unfavorable entropic component between 0 and 100 degrees C. In the case of cavity mutants, glycerol induced enthalpic stabilization below 50 degrees C and entropic stabilization above 50 degrees C. The effect of glycerol could not be accounted for solely by the enthalpy and entropy of transfer or protein surface from water to glycerol/water mixture. We propose that in the presence of glycerol the folded coiled coil dimer is better packed and displays less intramolecular fluctuations, leading to enhanced enthalpic interactions and to an

  17. Plasmodium vivax antigen discovery based on alpha-helical coiled coil protein motif.

    Directory of Open Access Journals (Sweden)

    Nora Céspedes

    Full Text Available Protein α-helical coiled coil structures that elicit antibody responses, which block critical functions of medically important microorganisms, represent a means for vaccine development. By using bioinformatics algorithms, a total of 50 antigens with α-helical coiled coil motifs orthologous to Plasmodium falciparum were identified in the P. vivax genome. The peptides identified in silico were chemically synthesized; circular dichroism studies indicated partial or high α-helical content. Antigenicity was evaluated using human sera samples from malaria-endemic areas of Colombia and Papua New Guinea. Eight of these fragments were selected and used to assess immunogenicity in BALB/c mice. ELISA assays indicated strong reactivity of serum samples from individuals residing in malaria-endemic regions and sera of immunized mice, with the α-helical coiled coil structures. In addition, ex vivo production of IFN-γ by murine mononuclear cells confirmed the immunogenicity of these structures and the presence of T-cell epitopes in the peptide sequences. Moreover, sera of mice immunized with four of the eight antigens recognized native proteins on blood-stage P. vivax parasites, and antigenic cross-reactivity with three of the peptides was observed when reacted with both the P. falciparum orthologous fragments and whole parasites. Results here point to the α-helical coiled coil peptides as possible P. vivax malaria vaccine candidates as were observed for P. falciparum. Fragments selected here warrant further study in humans and non-human primate models to assess their protective efficacy as single components or assembled as hybrid linear epitopes.

  18. Coiled-coil forming peptides for the induction of silver nanoparticles

    International Nuclear Information System (INIS)

    Božič Abram, Sabina; Aupič, Jana; Dražić, Goran; Gradišar, Helena; Jerala, Roman

    2016-01-01

    Biopolymers with defined sequence patterns offer an attractive alternative for the formation of silver nanoparticle (AgNP). A set of coiled-coil dimer forming peptides was tested for their AgNP formation ability. Seventeen of those peptides mediated the formation of AgNPs in aqueous solution at neutral pH, while the formation of a coiled-coil dimer inhibited the nanoparticle generation. A QSAR regression model on the relationship between sequence and function suggests that in this peptide type the patterns KXQQ and KXEE are favorable, whereas Ala residues appear to have an inhibitory effect. UV–VIS spectra of the obtained nanoparticles gave a peak at around 420 nm, typical for AgNPs in the size range around 40 nm, which was confirmed by dynamic light scattering and transmission electron microscopy. Peptide-induced AgNPs exhibited good antibacterial activity, even after a 15 min contact time, while they had low toxicity to human cells at the same concentrations. These results show that our designed peptides generate AgNPs with antibacterial activity at mild conditions and might be used for antibacterial coatings. - Highlights: • 17 of the 30 tested coiled-coil forming peptides induce AgNP formation. • Coiled-coil dimer formation suppresses AgNP generation of individual peptides. • Size of the peptide-induced silver nanoparticles is around 40 nm. • QSAR analysis points to the importance of KXQQ and KXEE motifs for AgNP generation. • Peptide-induced silver nanoparticles exhibit antibacterial activity.

  19. CCBuilder 2.0: Powerful and accessible coiled-coil modeling.

    Science.gov (United States)

    Wood, Christopher W; Woolfson, Derek N

    2018-01-01

    The increased availability of user-friendly and accessible computational tools for biomolecular modeling would expand the reach and application of biomolecular engineering and design. For protein modeling, one key challenge is to reduce the complexities of 3D protein folds to sets of parametric equations that nonetheless capture the salient features of these structures accurately. At present, this is possible for a subset of proteins, namely, repeat proteins. The α-helical coiled coil provides one such example, which represents ≈ 3-5% of all known protein-encoding regions of DNA. Coiled coils are bundles of α helices that can be described by a small set of structural parameters. Here we describe how this parametric description can be implemented in an easy-to-use web application, called CCBuilder 2.0, for modeling and optimizing both α-helical coiled coils and polyproline-based collagen triple helices. This has many applications from providing models to aid molecular replacement for X-ray crystallography, in silico model building and engineering of natural and designed protein assemblies, and through to the creation of completely de novo "dark matter" protein structures. CCBuilder 2.0 is available as a web-based application, the code for which is open-source and can be downloaded freely. http://coiledcoils.chm.bris.ac.uk/ccbuilder2. We have created CCBuilder 2.0, an easy to use web-based application that can model structures for a whole class of proteins, the α-helical coiled coil, which is estimated to account for 3-5% of all proteins in nature. CCBuilder 2.0 will be of use to a large number of protein scientists engaged in fundamental studies, such as protein structure determination, through to more-applied research including designing and engineering novel proteins that have potential applications in biotechnology. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

  20. Coiled-coil forming peptides for the induction of silver nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Božič Abram, Sabina [Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana (Slovenia); Graduate School of Biomedicine, University of Ljubljana, Ljubljana 1000 (Slovenia); Aupič, Jana [Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana (Slovenia); Doctoral Programme in Chemical Sciences, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana 1000 (Slovenia); Dražić, Goran [Laboratory for Materials Chemistry, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana (Slovenia); Gradišar, Helena [Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana (Slovenia); EN-FIST, Centre of Excellence, Trg Osvobodilne fronte 13, Ljubljana 1000 (Slovenia); Jerala, Roman, E-mail: roman.jerala@ki.si [Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana (Slovenia); EN-FIST, Centre of Excellence, Trg Osvobodilne fronte 13, Ljubljana 1000 (Slovenia)

    2016-04-08

    Biopolymers with defined sequence patterns offer an attractive alternative for the formation of silver nanoparticle (AgNP). A set of coiled-coil dimer forming peptides was tested for their AgNP formation ability. Seventeen of those peptides mediated the formation of AgNPs in aqueous solution at neutral pH, while the formation of a coiled-coil dimer inhibited the nanoparticle generation. A QSAR regression model on the relationship between sequence and function suggests that in this peptide type the patterns KXQQ and KXEE are favorable, whereas Ala residues appear to have an inhibitory effect. UV–VIS spectra of the obtained nanoparticles gave a peak at around 420 nm, typical for AgNPs in the size range around 40 nm, which was confirmed by dynamic light scattering and transmission electron microscopy. Peptide-induced AgNPs exhibited good antibacterial activity, even after a 15 min contact time, while they had low toxicity to human cells at the same concentrations. These results show that our designed peptides generate AgNPs with antibacterial activity at mild conditions and might be used for antibacterial coatings. - Highlights: • 17 of the 30 tested coiled-coil forming peptides induce AgNP formation. • Coiled-coil dimer formation suppresses AgNP generation of individual peptides. • Size of the peptide-induced silver nanoparticles is around 40 nm. • QSAR analysis points to the importance of KXQQ and KXEE motifs for AgNP generation. • Peptide-induced silver nanoparticles exhibit antibacterial activity.

  1. Coiled coil peptides as universal linkers for the attachment of recombinant proteins to polymer therapeutics

    Czech Academy of Sciences Publication Activity Database

    Pechar, Michal; Pola, Robert; Laga, Richard; Ulbrich, Karel; Bednárová, Lucie; Maloň, Petr; Sieglová, Irena; Král, Vlastimil; Fábry, Milan; Vaněk, O.

    2011-01-01

    Roč. 12, č. 10 (2011), s. 3645-3655 ISSN 1525-7797 R&D Projects: GA ČR GA203/08/0543; GA MŠk 1M0505 Institutional research plan: CEZ:AV0Z40500505; CEZ:AV0Z40550506; CEZ:AV0Z50520514 Keywords : coiled coil * polymer the rapeutics * drug targeting Subject RIV: CC - Organic Chemistry Impact factor: 5.479, year: 2011

  2. Fine-tuning of protein domain boundary by minimizing potential coiled coil regions

    International Nuclear Information System (INIS)

    Iwaya, Naoko; Goda, Natsuko; Unzai, Satoru; Fujiwara, Kenichiro; Tanaka, Toshiki; Tomii, Kentaro; Tochio, Hidehito; Shirakawa, Masahiro; Hiroaki, Hidekazu

    2007-01-01

    Structural determination of individual protein domains isolated from multidomain proteins is a common approach in the post-genomic era. Novel and thus uncharacterized domains liberated from intact proteins often self-associate due to incorrectly defined domain boundaries. Self-association results in missing signals, poor signal dispersion and a low signal-to-noise ratio in 1 H- 15 N HSQC spectra. We have found that a putative, non-canonical coiled coil region close to a domain boundary can cause transient hydrophobic self-association and monomer-dimer equilibrium in solution. Here we propose a rational method to predict putative coiled coil regions adjacent to the globular core domain using the program COILS. Except for the amino acid sequence, no preexisting knowledge concerning the domain is required. A small number of mutant proteins with a minimized coiled coil region have been rationally designed and tested. The engineered domains exhibit decreased self-association as assessed by 1 H- 15 N HSQC spectra with improved peak dispersion and sharper cross peaks. Two successful examples of isolating novel N-terminal domains from AAA-ATPases are demonstrated. Our method is useful for the experimental determination of domain boundaries suited for structural genomics studies

  3. Fine-tuning of protein domain boundary by minimizing potential coiled coil regions.

    Science.gov (United States)

    Iwaya, Naoko; Goda, Natsuko; Unzai, Satoru; Fujiwara, Kenichiro; Tanaka, Toshiki; Tomii, Kentaro; Tochio, Hidehito; Shirakawa, Masahiro; Hiroaki, Hidekazu

    2007-01-01

    Structural determination of individual protein domains isolated from multidomain proteins is a common approach in the post-genomic era. Novel and thus uncharacterized domains liberated from intact proteins often self-associate due to incorrectly defined domain boundaries. Self-association results in missing signals, poor signal dispersion and a low signal-to-noise ratio in (1)H-(15)N HSQC spectra. We have found that a putative, non-canonical coiled coil region close to a domain boundary can cause transient hydrophobic self-association and monomer-dimer equilibrium in solution. Here we propose a rational method to predict putative coiled coil regions adjacent to the globular core domain using the program COILS. Except for the amino acid sequence, no preexisting knowledge concerning the domain is required. A small number of mutant proteins with a minimized coiled coil region have been rationally designed and tested. The engineered domains exhibit decreased self-association as assessed by (1)H-(15)N HSQC spectra with improved peak dispersion and sharper cross peaks. Two successful examples of isolating novel N-terminal domains from AAA-ATPases are demonstrated. Our method is useful for the experimental determination of domain boundaries suited for structural genomics studies.

  4. Exploring the conserved water site and hydration of a coiled-coil trimerisation motif: a MD simulation study.

    Science.gov (United States)

    Dolenc, Jozica; Baron, Riccardo; Missimer, John H; Steinmetz, Michel O; van Gunsteren, Wilfred F

    2008-07-21

    The solvent structure and dynamics around ccbeta-p, a 17-residue peptide that forms a parallel three-stranded alpha-helical coiled coil in solution, was analysed through 10 ns explicit solvent molecular dynamics (MD) simulations at 278 and 330 K. Comparison with two corresponding simulations of the monomeric form of ccbeta-p was used to investigate the changes of hydration upon coiled-coil formation. Pronounced peaks in the solvent density distribution between residues Arg8 and Glu13 of neighbouring helices show the presence of water bridges between the helices of the ccbeta-p trimer; this is in agreement with the water sites observed in X-ray crystallography experiments. Interestingly, this water site is structurally conserved in many three-stranded coiled coils and, together with the Arg and Glu residues, forms part of a motif that determines three-stranded coiled-coil formation. Our findings show that little direct correlation exists between the solvent density distribution and the temporal ordering of water around the trimeric coiled coil. The MD-calculated effective residence times of up to 40 ps show rapid exchange of surface water molecules with the bulk phase, and indicate that the solvent distribution around biomolecules requires interpretation in terms of continuous density distributions rather than in terms of discrete molecules of water. Together, our study contributes to understanding the principles of three-stranded coiled-coil formation.

  5. Unraveling double stranded alpha-helical coiled coils: an x-ray diffraction study on hard alpha-keratin fibers.

    Science.gov (United States)

    Kreplak, L; Doucet, J; Briki, F

    2001-04-15

    Transformations of proteins secondary and tertiary structures are generally studied in globular proteins in solution. In fibrous proteins, such as hard alpha-keratin, that contain long and well-defined double stranded alpha-helical coiled coil domains, such study can be directly done on the native fibrous tissue. In order to assess the structural behavior of the coiled coil domains under an axial mechanical stress, wide angle x-ray scattering and small angle x-ray scattering experiments have been carried out on stretched horse hair fibers at relative humidity around 30%. Our observations of the three major axial spacings as a function of the applied macroscopic strain have shown two rates. Up to 4% macroscopic strain the coiled coils were slightly distorted but retained their overall conformation. Above 4% the proportion of coiled coil domains progressively decreased. The main and new result of our study is the observation of the transition from alpha-helical coiled coils to disordered chains instead of the alpha-helical coiled coil to beta-sheet transition that occurs in wet fibers.

  6. Polymer therapeutics with a coiled coil motif targeted against murine BCL1 leukemia

    Czech Academy of Sciences Publication Activity Database

    Pola, Robert; Laga, Richard; Ulbrich, Karel; Sieglová, Irena; Král, Vlastimil; Fábry, Milan; Kabešová, Martina; Kovář, Marek; Pechar, Michal

    2013-01-01

    Roč. 14, č. 3 (2013), s. 881-889 ISSN 1525-7797 R&D Projects: GA ČR GAP301/11/0325; GA AV ČR IAAX00500803 Institutional research plan: CEZ:AV0Z50520514 Institutional support: RVO:61389013 ; RVO:61388971 ; RVO:68378050 Keywords : coiled coil * polymer therapeutics * scFv Subject RIV: CD - Macromolecular Chemistry; EC - Immunology (MBU-M); EB - Genetics ; Molecular Biology (UMG-J) Impact factor: 5.788, year: 2013

  7. Polymer cancerostatics with a coiled coil motif targeted against murine leukemia

    Czech Academy of Sciences Publication Activity Database

    Pechar, Michal; Pola, Robert; Janoušková, Olga; Sieglová, Irena; Král, Vlastimil; Fábry, Milan; Tomalová, Barbora; Kovář, Marek

    2017-01-01

    Roč. 6, 4 (Suppl) (2017), s. 36 ISSN 2325-9604. [International Conference and Exhibition on Nanomedicine and Drug Delivery. 29.05.2017-31.05.2017, Osaka] R&D Projects: GA ČR(CZ) GA16-17207S Institutional support: RVO:61389013 ; RVO:68378050 ; RVO:61388971 Keywords : coiled coil * polymer cancerostatics * active targeting Subject RIV: CD - Macromolecular Chemistry; EC - Immunology (MBU-M) https://www.scitechnol.com/conference-abstracts/scientific-tracks-abstracts/nanodelivery-2017-proceedings.html

  8. An analysis of 3D solvation structure in biomolecules: application to coiled coil serine and bacteriorhodopsin.

    Science.gov (United States)

    Hirano, Kenji; Yokogawa, Daisuke; Sato, Hirofumi; Sakaki, Shigeyoshi

    2010-06-17

    Three-dimensional (3D) solvation structure around coiled coil serine (Coil-Ser) and inner 3D hydration structure in bacteriorhodopsin (bR) were studied using a recently developed method named multicenter molecular Ornstein-Zernike equation (MC-MOZ) theory. In addition, a procedure for analyzing the 3D solvent distribution was proposed. The method enables us to calculate the coordination number of solvent water as well as the strength of hydrogen bonding between the water molecule and the protein. The results for Coil-Ser and bR showed very good agreement with the experimental observations.

  9. The heterotrimeric laminin coiled-coil domain exerts anti-adhesive effects and induces a pro-invasive phenotype.

    Directory of Open Access Journals (Sweden)

    Patricia Santos-Valle

    Full Text Available Laminins are large heterotrimeric cross-shaped extracellular matrix glycoproteins with terminal globular domains and a coiled-coil region through which the three chains are assembled and covalently linked. Laminins are key components of basement membranes, and they serve as attachment sites for cell adhesion, migration and proliferation. In this work, we produced a recombinant fragment comprising the entire laminin coiled-coil of the α1-, β1-, and γ1-chains that assemble into a stable heterotrimeric coiled-coil structure independently of the rest of the molecule. This domain was biologically active and not only failed to serve as a substrate for cell attachment, spreading and focal adhesion formation but also inhibited cell adhesion to laminin when added to cells in a soluble form at the time of seeding. Furthermore, gene array expression profiling in cells cultured in the presence of the laminin coiled-coil domain revealed up-regulation of genes involved in cell motility and invasion. These findings were confirmed by real-time quantitative PCR and zymography assays. In conclusion, this study shows for the first time that the laminin coiled-coil domain displays anti-adhesive functions and has potential implications for cell migration during matrix remodeling.

  10. Fifty years of coiled-coils and alpha-helical bundles: a close relationship between sequence and structure.

    Science.gov (United States)

    Parry, David A D; Fraser, R D Bruce; Squire, John M

    2008-09-01

    alpha-Helical coiled coils are remarkable for the diversity of related conformations that they adopt in both fibrous and globular proteins, and for the range of functions that they exhibit. The coiled coils are based on a heptad (7-residue), hendecad (11-residue) or a related quasi-repeat of apolar residues in the sequences of the alpha-helical regions involved. Most of these, however, display one or more sequence discontinuities known as stutters or stammers. The resulting coiled coils vary in length, in the number of chains participating, in the relative polarity of the contributing alpha-helical regions (parallel or antiparallel), and in the pitch length and handedness of the supercoil (left- or right-handed). Functionally, the concept that a coiled coil can act only as a static rod is no longer valid, and the range of roles that these structures have now been shown to exhibit has expanded rapidly in recent years. An important development has been the recognition that the delightful simplicity that exists between sequence and structure, and between structure and function, allows coiled coils with specialized features to be designed de novo.

  11. Invited review the coiled coil silk of bees, ants, and hornets.

    Science.gov (United States)

    Sutherland, Tara D; Weisman, Sarah; Walker, Andrew A; Mudie, Stephen T

    2012-06-01

    In this article, we review current knowledge about the silk produced by the larvae of bees, ants, and hornets [Apoidea and Vespoidea: Hymenoptera]. Different species use the silk either alone or in composites for a variety of purposes including mechanical reinforcement, thermal regulation, or humidification. The characteristic molecular structure of this silk is α-helical proteins assembled into tetrameric coiled coils. Gene sequences from seven species are available, and each species possesses a copy of each of four related silk genes that encode proteins predicted to form coiled coils. The proteins are ordered at multiple length scales within the labial gland of the final larval instar before spinning. The insects control the morphology of the silk during spinning to produce either fibers or sheets. The silk proteins are small and non repetitive and have been produced artificially at high levels by fermentation in E. coli. The artificial silk proteins can be fabricated into materials with structural and mechanical properties similar to those of native silks. Copyright © 2011 Wiley Periodicals, Inc.

  12. d-Cysteine Ligands Control Metal Geometries within De Novo Designed Three-Stranded Coiled Coils

    DEFF Research Database (Denmark)

    Ruckthong, Leela; Peacock, Anna F.A.; Pascoe, Cherilyn E.

    2017-01-01

    Although metal ion binding to naturally occurring l-amino acid proteins is well documented, understanding the impact of the opposite chirality (d-)amino acids on the structure and stereochemistry of metals is in its infancy. We examine the effect of a d-configuration cysteine within a designed l......-amino acid three-stranded coiled coil in order to enforce a precise coordination number on a metal center. The d chirality does not alter the native fold, but the side-chain re-orientation modifies the sterics of the metal binding pocket. l-Cys side chains within the coiled-coil structure have previously...... by comparison of the structure of ZnIICl(CSL16DC)3 2- to the published structure of ZnII(H2O)(GRAND-CSL12AL16LC)3 -. Moreover, spectroscopic analysis indicates that the CdII geometry observed by using l-Cys ligands (a mixture of three- and four-coordinate CdII) is altered to a single four-coordinate species...

  13. Structure and Misfolding of the Flexible Tripartite Coiled-Coil Domain of Glaucoma-Associated Myocilin

    Energy Technology Data Exchange (ETDEWEB)

    Hill, Shannon E.; Nguyen, Elaine; Donegan, Rebecca K.; Patterson-Orazem, Athéna C.; Hazel, Anthony; Gumbart, James C.; Lieberman, Raquel L.

    2017-11-01

    Glaucoma-associated myocilin is a member of the olfactomedins, a protein family involved in neuronal development and human diseases. Molecular studies of the myocilin N-terminal coiled coil demonstrate a unique tripartite architecture: a Y-shaped parallel dimer-of-dimers with distinct tetramer and dimer regions. The structure of the dimeric C-terminal 7-heptad repeats elucidates an unexpected repeat pattern involving inter-strand stabilization by oppositely charged residues. Molecular dynamics simulations reveal an alternate accessible conformation in which the terminal inter-strand disulfide limits the extent of unfolding and results in a kinked configuration. By inference, full-length myocilin is also branched, with two pairs of C-terminal olfactomedin domains. Selected variants within the N-terminal region alter the apparent quaternary structure of myocilin but do so without compromising stability or causing aggregation. In addition to increasing our structural knowledge of naturally occurring extracellular coiled coils and biomedically important olfactomedins, this work broadens the scope of protein misfolding in the pathogenesis of myocilin-associated glaucoma.

  14. Structure and Misfolding of the Flexible Tripartite Coiled-Coil Domain of Glaucoma-Associated Myocilin.

    Science.gov (United States)

    Hill, Shannon E; Nguyen, Elaine; Donegan, Rebecca K; Patterson-Orazem, Athéna C; Hazel, Anthony; Gumbart, James C; Lieberman, Raquel L

    2017-11-07

    Glaucoma-associated myocilin is a member of the olfactomedins, a protein family involved in neuronal development and human diseases. Molecular studies of the myocilin N-terminal coiled coil demonstrate a unique tripartite architecture: a Y-shaped parallel dimer-of-dimers with distinct tetramer and dimer regions. The structure of the dimeric C-terminal 7-heptad repeats elucidates an unexpected repeat pattern involving inter-strand stabilization by oppositely charged residues. Molecular dynamics simulations reveal an alternate accessible conformation in which the terminal inter-strand disulfide limits the extent of unfolding and results in a kinked configuration. By inference, full-length myocilin is also branched, with two pairs of C-terminal olfactomedin domains. Selected variants within the N-terminal region alter the apparent quaternary structure of myocilin but do so without compromising stability or causing aggregation. In addition to increasing our structural knowledge of naturally occurring extracellular coiled coils and biomedically important olfactomedins, this work broadens the scope of protein misfolding in the pathogenesis of myocilin-associated glaucoma. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Magnetic field alignment of coil-coil diblock copolymers and blends via intrinsic chain anisotropy

    Science.gov (United States)

    Rokhlenko, Yekaterina; Majewski, Pawel; Larson, Steven; Yager, Kevin; Gopalan, Padma; Avgeropoulos, Apostolos; Chan, Edwin; Osuji, Chinedum

    Magnetic fields can control alignment of self-assembled soft materials such as block copolymers provided there is a suitably large magnetic susceptibility anisotropy present in the system. Recent results have highlighted the existence of a non-trivial intrinsic anisotropy in coil-coil diblock copolymers, specifically in lamellar-forming PS-b-P4VP, which enables alignment at field strengths of a few tesla in systems lacking mesogenic components. Alignment is predicated on correlation in the orientation of end-end vectors implied by the localization of block junctions at the microdomain interface and is observed on cooling across the order-disorder transition in the presence of the field. For appropriate combinations of field strength and grain size, we can leverage intrinsic chain anisotropy to magnetically direct self-assembly of many non-mesogenic systems, including other coil-coil BCPs like PS-b-PDMS and PS-b-PMMA, blends of BCPs of disparate morphologies and MWs, and blends of BCPs with homopolymers. This is noteworthy as blends of PS-b-P4VP with PEO provide a route to form functional materials such as nanoporous films by dissolution of PEO, or aligned ion conduction materials. We survey these various systems using TEM and in-situ X-ray scattering to study the phase behavior and temperature-, time- and field- dependent dynamics of alignment.

  16. Structure of a designed, right-handed coiled-coil tetramer containing all biological amino acids.

    Science.gov (United States)

    Sales, Mark; Plecs, Joseph J; Holton, James M; Alber, Tom

    2007-10-01

    The previous design of an unprecedented family of two-, three-, and four-helical, right-handed coiled coils utilized nonbiological amino acids to efficiently pack spaces in the oligomer cores. Here we show that a stable, right-handed parallel tetrameric coiled coil, called RH4B, can be designed entirely using biological amino acids. The X-ray crystal structure of RH4B was determined to 1.1 Angstrom resolution using a designed metal binding site to coordinate a single Yb(2+) ion per 33-amino acid polypeptide chain. The resulting experimental phases were particularly accurate, and the experimental electron density map provided an especially clear, unbiased view of the molecule. The RH4B structure closely matched the design, with equivalent core rotamers and an overall root-mean-square deviation for the N-terminal repeat of the tetramer of 0.24 Angstrom. The clarity and resolution of the electron density map, however, revealed alternate rotamers and structural differences between the three sequence repeats in the molecule. These results suggest that the RH4B structure populates an unanticipated variety of structures.

  17. Sme4 coiled-coil protein mediates synaptonemal complex assembly, recombinosome relocalization, and spindle pole body morphogenesis.

    Science.gov (United States)

    Espagne, Eric; Vasnier, Christelle; Storlazzi, Aurora; Kleckner, Nancy E; Silar, Philippe; Zickler, Denise; Malagnac, Fabienne

    2011-06-28

    We identify a large coiled-coil protein, Sme4/PaMe4, that is highly conserved among the large group of Sordariales and plays central roles in two temporally and functionally distinct aspects of the fungal sexual cycle: first as a component of the meiotic synaptonemal complex (SC) and then, after disappearing and reappearing, as a component of the spindle pole body (SPB). In both cases, the protein mediates spatial juxtaposition of two major structures: linkage of homolog axes through the SC and a change in the SPB from a planar to a bent conformation. Corresponding mutants exhibit defects, respectively, in SC and SPB morphogenesis, with downstream consequences for recombination and astral-microtubule nucleation plus postmeiotic nuclear migration. Sme4 is also required for reorganization of recombination complexes in which Rad51, Mer3, and Msh4 foci relocalize from an on-axis position to a between-axis (on-SC) position concomitant with SC installation. Because involved recombinosome foci represent total recombinational interactions, these dynamics are irrespective of their designation for maturation into cross-overs or noncross-overs. The defined dual roles for Sme4 in two different structures that function at distinct phases of the sexual cycle also provide more functional links and evolutionary dynamics among the nuclear envelope, SPB, and SC.

  18. Antibody engineering using phage display with a coiled-coil heterodimeric Fv antibody fragment.

    Directory of Open Access Journals (Sweden)

    Xinwei Wang

    Full Text Available A Fab-like antibody binding unit, ccFv, in which a pair of heterodimeric coiled-coil domains was fused to V(H and V(L for Fv stabilization, was constructed for an anti-VEGF antibody. The anti-VEGF ccFv showed the same binding affinity as scFv but significantly improved stability and phage display level. Furthermore, phage display libraries in the ccFv format were constructed for humanization and affinity maturation of the anti-VEGF antibody. A panel of V(H frameworks and V(H-CDR3 variants, with a significant improvement in affinity and expressibility in both E. coli and yeast systems, was isolated from the ccFv phage libraries. These results demonstrate the potential application of the ccFv antibody format in antibody engineering.

  19. Low resolution crystal structure of Arenicola erythrocruorin: influence of coiled coils on the architecture of a megadalton respiratory protein.

    Science.gov (United States)

    Royer, William E; Omartian, Michael N; Knapp, James E

    2007-01-05

    Annelid erythrocruorins are extracellular respiratory complexes assembled from 180 subunits into hexagonal bilayers. Cryo-electron microscopic experiments have identified two different architectural classes. In one, designated type I, the vertices of the two hexagonal layers are partially staggered, with one hexagonal layer rotated by about 16 degrees relative to the other layer, whereas in the other class, termed type II, the vertices are essentially eclipsed. We report here the first crystal structure of a type II erythrocruorin, that from Arenicola marina, at 6.2 A resolution. The structure reveals the presence of long continuous triple-stranded coiled-coil "spokes" projecting towards the molecular center from each one-twelfth unit; interdigitation of these spokes provides the only contacts between the two hexagonal layers of the complex. This arrangement contrasts with that of a type I erythrocruorin from Lumbricus terrestris in which the spokes are broken into two triple-stranded coiled coils with a disjointed connection. The disjointed connection allows formation of a more compact structure in the type I architecture, with the two hexagonal layers closer together and additional extensive contacts between the layers. Comparison of sequences of the coiled-coil regions of various linker subunits shows that the linker subunits from type II erythrocruorins possess continuous heptad repeats, whereas a sequence gap places these repeats out of register in the type I linker subunits, consistent with a disjointed coiled-coil arrangement.

  20. Sub-20 nm Stable Micelles Based on a Mixture of Coiled-Coils: A Platform for Controlled Ligand Presentation.

    Science.gov (United States)

    Ang, JooChuan; Ma, Dan; Jung, Benson T; Keten, Sinan; Xu, Ting

    2017-11-13

    Ligand-functionalized, multivalent nanoparticles have been extensively studied for biomedical applications from imaging agents to drug delivery vehicles. However, the ligand cluster size is usually heterogeneous and the local valency is ill-defined. Here, we present a mixed micelle platform hierarchically self-assembled from a mixture of two amphiphilic 3-helix and 4-helix peptide-polyethylene glycol (PEG)-lipid hybrid conjugates. We demonstrate that the local multivalent ligand cluster size on the micelle surface can be controlled based on the coiled-coil oligomeric state. The oligomeric states of mixed peptide bundles were found to be in their individual native states. Similarly, mixed micelles indicate the orthogonal self-association of coiled-coil amphiphiles. Using differential scanning calorimetry, fluorescence recovery spectroscopy, and coarse-grained molecular dynamics simulation, we studied the distribution of coiled-coil bundles within the mixed micelles and observed migration of coiled-coils into nanodomains within the sub-20 nm mixed micelle. This report provides important insights into the assembly and formation of nanophase-separated micelles with precise control over the local multivalent state of ligands on the micelle surface.

  1. Rho-associated coiled-coil kinase (ROCK) protein controls microtubule dynamics in a novel signaling pathway that regulates cell migration.

    Science.gov (United States)

    Schofield, Alice V; Steel, Rohan; Bernard, Ora

    2012-12-21

    The two members of the Rho-associated coiled-coil kinase (ROCK1 and 2) family are established regulators of actin dynamics that are involved in the regulation of the cell cycle as well as cell motility and invasion. Here, we discovered a novel signaling pathway whereby ROCK regulates microtubule (MT) acetylation via phosphorylation of the tubulin polymerization promoting protein 1 (TPPP1/p25). We show that ROCK phosphorylation of TPPP1 inhibits the interaction between TPPP1 and histone deacetylase 6 (HDAC6), which in turn results in increased HDAC6 activity followed by a decrease in MT acetylation. As a consequence, we show that TPPP1 phosphorylation by ROCK increases cell migration and invasion via modulation of cellular acetyl MT levels. We establish here that the ROCK-TPPP1-HDAC6 signaling pathway is important for the regulation of cell migration and invasion.

  2. Missense mutation in DISC1 C-terminal coiled-coil has GSK3β signaling and sex-dependent behavioral effects in mice

    Science.gov (United States)

    Dachtler, James; Elliott, Christina; Rodgers, R. John; Baillie, George S.; Clapcote, Steven J.

    2016-01-01

    Disrupted-in-Schizophrenia 1 (DISC1) is a risk factor for schizophrenia and affective disorders. The full-length DISC1 protein consists of an N-terminal ‘head’ domain and a C-terminal tail domain that contains several predicted coiled-coils, structural motifs involved in protein-protein interactions. To probe the in vivo effects of missense mutation of DISC1’s C-terminal tail, we tested mice carrying mutation D453G within a predicted α-helical coiled-coil region. We report that, relative to wild-type littermates, female DISC1D453G mice exhibited novelty-induced hyperlocomotion, an anxiogenic profile in the elevated plus-maze and open field tests, and reduced social exploration of unfamiliar mice. Male DISC1D453G mice displayed a deficit in passive avoidance, while neither males nor females exhibited any impairment in startle reactivity or prepulse inhibition. Whole brain homogenates showed normal levels of DISC1 protein, but decreased binding of DISC1 to GSK3β, decreased phospho-inhibition of GSK3β at serine 9, and decreased levels of β-catenin in DISC1D453G mice of either sex. Interrupted GSK3β signaling may thus be part of the mechanism underlying the behavioral phenotype associated with D453G, in common with the previously described N-terminal domain mutations Q31L and L100P in mice, and the schizophrenia risk-conferring variant R264Q in humans. PMID:26728762

  3. Coiled coil peptides and polymer-peptide conjugates: synthesis, self-assembly, characterization and potential in drug delivery systems

    Czech Academy of Sciences Publication Activity Database

    Pechar, Michal; Pola, Robert; Laga, Richard; Braunová, Alena; Filippov, Sergey K.; Bogomolova, Anna; Bednárová, Lucie; Vaněk, O.; Ulbrich, Karel

    2014-01-01

    Roč. 15, č. 7 (2014), s. 2590-2599 ISSN 1525-7797 R&D Projects: GA ČR GCP207/12/J030 Grant - others:AV ČR(CZ) AP0802 Program:Akademická prémie - Praemium Academiae Institutional support: RVO:61389013 ; RVO:61388963 Keywords : coiled coil * self-assembly * hydrophilic polymer Subject RIV: CD - Macromolecular Chemistry; FR - Pharmacology ; Medidal Chemistry (UOCHB-X) Impact factor: 5.750, year: 2014

  4. Intermediate filament mechanics in vitro and in the cell: From coiled coils to filaments, fibers and networks

    OpenAIRE

    Köster, Sarah; Weitz, David; Goldman, Robert D.; Aebi, Ueli; Herrmann, Harald

    2015-01-01

    Intermediate filament proteins form filaments, fibers and networks both in the cytoplasm and the nucleus of metazoan cells. Their general structural building plan accommodates highly varying amino acid sequences to yield extended dimeric α-helical coiled coils of highly conserved design. These “rod” particles are the basic building blocks of intrinsically flexible, filamentous structures that are able to resist high mechanical stresses, i.e. bending and stretching to a considerable degree, bo...

  5. Novel Anti-Nicotine Vaccine Using a Trimeric Coiled-Coil Hapten Carrier.

    Directory of Open Access Journals (Sweden)

    Keith D Miller

    Full Text Available Tobacco addiction represents one of the largest public health problems in the world and is the leading cause of cancer and heart disease, resulting in millions of deaths a year. Vaccines for smoking cessation have shown considerable promise in preclinical models, although functional antibody responses induced in humans are only modestly effective in preventing nicotine entry into the brain. The challenge in generating serum antibodies with a large nicotine binding capacity is made difficult by the fact that this drug is non-immunogenic and must be conjugated as a hapten to a protein carrier. To circumvent the limitations of traditional carriers like keyhole limpet hemocyanin (KLH, we have synthesized a short trimeric coiled-coil peptide (TCC that creates a series of B and T cell epitopes with uniform stoichiometry and high density. Here we compared the relative activities of a TCC-nic vaccine and two control KLH-nic vaccines using Alum as an adjuvant or GLA-SE, which contains a synthetic TLR4 agonist formulated in a stable oil-in-water emulsion. The results showed that the TCC's high hapten density correlated with a better immune response in mice as measured by anti-nicotine Ab titer, affinity, and specificity, and was responsible for a reduction in anti-carrier immunogenicity. The Ab responses achieved with this synthetic vaccine resulted in a nicotine binding capacity in serum that could prevent >90% of a nicotine dose equivalent to three smoked cigarettes (0.05 mg/kg from reaching the brain.

  6. Oncogenic TPM3-ALK activation requires dimerization through the coiled-coil structure of TPM3

    International Nuclear Information System (INIS)

    Amano, Yosuke; Ishikawa, Rie; Sakatani, Toshio; Ichinose, Junji; Sunohara, Mitsuhiro; Watanabe, Kousuke; Kage, Hidenori; Nakajima, Jun; Nagase, Takahide; Ohishi, Nobuya; Takai, Daiya

    2015-01-01

    Inflammatory myofibroblastic tumor (IMT) is a mesenchymal tumor that can arise from anywhere in the body. Anaplastic lymphoma kinase (ALK) gene rearrangements, most often resulting in the tropomyosin 3 (TPM3)-ALK fusion gene, are the main causes of IMT. However, the mechanism of malignant transformation in IMT has yet to be elucidated. The purpose of this study was to clarify the role of the TPM3 region in the transformation of IMT via TPM3-ALK. Lentivirus vectors containing a TPM3-ALK fusion gene lacking various lengths of TPM3 were constructed and expressed in HEK293T and NIH3T3 cell lines. Focus formation assay revealed loss of contact inhibition in NIH3T3 cells transfected with full-length TPM3-ALK, but not with ALK alone. Blue-native polyacrylamide gel electrophoresis (BN-PAGE) revealed that TPM3-ALK dimerization increased in proportion to the length of TPM3. Western blot showed phosphorylation of ALK, ERK1/2, and STAT3 in HEK293T cells transfected with TPM3-ALK. Thus, the coiled-coil structure of TPM3 contributes to the transforming ability of the TPM3-ALK fusion protein, and longer TPM3 region leads to higher dimer formation. - Highlights: • TPM3-ALK fusion protein dimerizes through the coiled-coil structure of TPM3. • Longer coiled-coil structure of TPM3 leads to higher TPM3-ALK dimer formation. • Presence of TPM3-ALK dimer leads to ALK, STAT3, and ERK1/2 phosphorylation. • Presence of TPM3-ALK leads to loss of contact inhibition. • BN-PAGE is a simple technique for visualizing oncogenic dimerization

  7. Oncogenic TPM3-ALK activation requires dimerization through the coiled-coil structure of TPM3

    Energy Technology Data Exchange (ETDEWEB)

    Amano, Yosuke; Ishikawa, Rie; Sakatani, Toshio [Department of Respiratory Medicine, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655 (Japan); Ichinose, Junji [Department of Cardiothoracic Surgery, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655 (Japan); Sunohara, Mitsuhiro; Watanabe, Kousuke; Kage, Hidenori [Department of Respiratory Medicine, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655 (Japan); Nakajima, Jun [Department of Cardiothoracic Surgery, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655 (Japan); Nagase, Takahide; Ohishi, Nobuya [Department of Respiratory Medicine, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655 (Japan); Takai, Daiya, E-mail: dtakai-ind@umin.ac.jp [Department of Respiratory Medicine, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655 (Japan); Department of Clinical Laboratory, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655 (Japan)

    2015-02-13

    Inflammatory myofibroblastic tumor (IMT) is a mesenchymal tumor that can arise from anywhere in the body. Anaplastic lymphoma kinase (ALK) gene rearrangements, most often resulting in the tropomyosin 3 (TPM3)-ALK fusion gene, are the main causes of IMT. However, the mechanism of malignant transformation in IMT has yet to be elucidated. The purpose of this study was to clarify the role of the TPM3 region in the transformation of IMT via TPM3-ALK. Lentivirus vectors containing a TPM3-ALK fusion gene lacking various lengths of TPM3 were constructed and expressed in HEK293T and NIH3T3 cell lines. Focus formation assay revealed loss of contact inhibition in NIH3T3 cells transfected with full-length TPM3-ALK, but not with ALK alone. Blue-native polyacrylamide gel electrophoresis (BN-PAGE) revealed that TPM3-ALK dimerization increased in proportion to the length of TPM3. Western blot showed phosphorylation of ALK, ERK1/2, and STAT3 in HEK293T cells transfected with TPM3-ALK. Thus, the coiled-coil structure of TPM3 contributes to the transforming ability of the TPM3-ALK fusion protein, and longer TPM3 region leads to higher dimer formation. - Highlights: • TPM3-ALK fusion protein dimerizes through the coiled-coil structure of TPM3. • Longer coiled-coil structure of TPM3 leads to higher TPM3-ALK dimer formation. • Presence of TPM3-ALK dimer leads to ALK, STAT3, and ERK1/2 phosphorylation. • Presence of TPM3-ALK leads to loss of contact inhibition. • BN-PAGE is a simple technique for visualizing oncogenic dimerization.

  8. Interaction of tearing modes

    International Nuclear Information System (INIS)

    Satya, Y.; Schmidt, G.

    1979-01-01

    A fully developed tearing mode modifies the magnetic field profile. The effect of this profile modification on the linear growth rate of a different tearing mode in a slab and cylindrical geometry is investigated

  9. The coiled-coil domain of MURC/cavin-4 is involved in membrane trafficking of caveolin-3 in cardiomyocytes.

    Science.gov (United States)

    Naito, Daisuke; Ogata, Takehiro; Hamaoka, Tetsuro; Nakanishi, Naohiko; Miyagawa, Kotaro; Maruyama, Naoki; Kasahara, Takeru; Taniguchi, Takuya; Nishi, Masahiro; Matoba, Satoaki; Ueyama, Tomomi

    2015-12-15

    Muscle-restricted coiled-coil protein (MURC), also referred to as cavin-4, is a member of the cavin family that works cooperatively with caveolins in caveola formation and function. Cavins are cytoplasmic proteins with coiled-coil domains and form heteromeric complexes, which are recruited to caveolae in cells expressing caveolins. Among caveolins, caveolin-3 (Cav3) is exclusively expressed in muscle cells, similar to MURC/cavin-4. In the heart, Cav3 overexpression contributes to cardiac protection, and its deficiency leads to progressive cardiomyopathy. Mutations in the MURC/cavin-4 gene have been identified in patients with dilated cardiomyopathy. In the present study, we show the role of MURC/cavin-4 as a caveolar component in the heart. In H9c2 cells, MURC/cavin-4 was localized at the plasma membrane, whereas a MURC/cavin-4 mutant lacking the coiled-coil domain (ΔCC) was primarily localized to the cytoplasm. ΔCC bound to Cav3 and impaired membrane localization of Cav3 in cardiomyocytes. Additionally, although ΔCC did not alter Cav3 mRNA expression, ΔCC decreased the Cav3 protein level. MURC/cavin-4 and ΔCC similarly induced cardiomyocyte hypertrophy; however, ΔCC showed higher hypertrophy-related fetal gene expression than MURC/cavin-4. ΔCC induced ERK activation in cardiomyocytes. Transgenic mice expressing ΔCC in the heart (ΔCC-Tg mice) showed impaired cardiac function accompanied by cardiomyocyte hypertrophy and marked interstitial fibrosis. Hearts from ΔCC-Tg mice showed a reduction of the Cav3 protein level and activation of ERK. These results suggest that MURC/cavin-4 requires its coiled-coil domain to target the plasma membrane and to stabilize Cav3 at the plasma membrane of cardiomyocytes and that MURC/cavin-4 functions as a crucial caveolar component to regulate cardiac function. Copyright © 2015 the American Physiological Society.

  10. PspF-binding domain PspA1-144 and the PspA·F complex: New insights into the coiled-coil-dependent regulation of AAA+ proteins.

    Science.gov (United States)

    Osadnik, Hendrik; Schöpfel, Michael; Heidrich, Eyleen; Mehner, Denise; Lilie, Hauke; Parthier, Christoph; Risselada, H Jelger; Grubmüller, Helmut; Stubbs, Milton T; Brüser, Thomas

    2015-11-01

    Phage shock protein A (PspA) belongs to the highy conserved PspA/IM30 family and is a key component of the stress inducible Psp system in Escherichia coli. One of its central roles is the regulatory interaction with the transcriptional activator of this system, the σ(54) enhancer-binding protein PspF, a member of the AAA+ protein family. The PspA/F regulatory system has been intensively studied and serves as a paradigm for AAA+ enzyme regulation by trans-acting factors. However, the molecular mechanism of how exactly PspA controls the activity of PspF and hence σ(54) -dependent expression of the psp genes is still unclear. To approach this question, we identified the minimal PspF-interacting domain of PspA, solved its structure, determined its affinity to PspF and the dissociation kinetics, identified residues that are potentially important for PspF regulation and analyzed effects of their mutation on PspF in vivo and in vitro. Our data indicate that several characteristics of AAA+ regulation in the PspA·F complex resemble those of the AAA+ unfoldase ClpB, with both proteins being regulated by a structurally highly conserved coiled-coil domain. The convergent evolution of both regulatory domains points to a general mechanism to control AAA+ activity for divergent physiologic tasks via coiled-coil domains. © 2015 John Wiley & Sons Ltd.

  11. Design considerations in coiled-coil fusion constructs for the structural determination of a problematic region of the human cardiac myosin rod

    Energy Technology Data Exchange (ETDEWEB)

    Andreas, Michael P.; Ajay, Gautam; Gellings, Jaclyn A.; Rayment, Ivan (UW)

    2017-12-01

    X-ray structural determination of segments of the myosin rod has proved difficult because of the strong salt-dependent aggregation properties and repeating pattern of charges on the surface of the coiled-coil that lead to the formation of paracrystals. This problem has been resolved in part through the use of globular assembly domains that improve protein folding and prevent aggregation. The primary consideration now in designing coiled-coil fusion constructs for myosin is deciding where to truncate the coiled-coil and which amino acid residues to include from the folding domain. This is especially important for myosin that contains numerous regions of low predicted coiled-coil propensity. Here we describe the strategy adopted to determine the structure of the region that extends from Arg1677 – Leu1797 that included two areas that do not show a strong sequence signature of a conventional left-handed coiled coil or canonical heptad repeat. This demonstrates again that, with careful choice of fusion constructs, overlapping structures exhibit very similar conformations for the myosin rod fragments in the canonical regions. However, conformational variability is seen around Leu1706 which is a hot spot for cardiomyopathy mutations suggesting that this might be important for function.

  12. Alanine Zipper-Like Coiled-Coil Domains Are Necessary for Homotypic Dimerization of Plant GAGA-Factors in the Nucleus and Nucleolus

    Science.gov (United States)

    Bloss, Ulrich; Hecker, Andreas; Elgass, Kirstin; Hummel, Sabine; Hahn, Achim; Caesar, Katharina; Schleifenbaum, Frank; Harter, Klaus; Berendzen, Kenneth W.

    2011-01-01

    GAGA-motif binding proteins control transcriptional activation or repression of homeotic genes. Interestingly, there are no sequence similarities between animal and plant proteins. Plant BBR/BPC-proteins can be classified into two distinct groups: Previous studies have elaborated on group I members only and so little is known about group II proteins. Here, we focused on the initial characterization of AtBPC6, a group II protein from Arabidopsis thaliana. Comparison of orthologous BBR/BPC sequences disclosed two conserved signatures besides the DNA binding domain. A first peptide signature is essential and sufficient to target AtBPC6-GFP to the nucleus and nucleolus. A second domain is predicted to form a zipper-like coiled-coil structure. This novel type of domain is similar to Leucine zippers, but contains invariant alanine residues with a heptad spacing of 7 amino acids. By yeast-2-hybrid and BiFC-assays we could show that this Alanine zipper domain is essential for homotypic dimerization of group II proteins in vivo. Interhelical salt bridges and charge-stabilized hydrogen bonds between acidic and basic residues of the two monomers are predicted to form an interaction domain, which does not follow the classical knobs-into-holes zipper model. FRET-FLIM analysis of GFP/RFP-hybrid fusion proteins validates the formation of parallel dimers in planta. Sequence comparison uncovered that this type of domain is not restricted to BBR/BPC proteins, but is found in all kingdoms. PMID:21347358

  13. Insights on the structure and stability of Licanantase: a trimeric acid-stable coiled-coil lipoprotein from Acidithiobacillus thiooxidans

    Directory of Open Access Journals (Sweden)

    Fernando Abarca

    2014-08-01

    Full Text Available Licanantase (Lic is the major component of the secretome of Acidithiobacillus thiooxidans when grown in elemental sulphur. When used as an additive, Lic improves copper recovery from bioleaching processes. However, this recovery enhancement is not fully understood. In this context, our aim is to predict the 3D structure of Lic, to shed light on its structure-function relationships. Bioinformatics analyses on the amino acid sequence of Lic showed a great similarity with Lpp, an Escherichia coli Lipoprotein that can form stable trimers in solution. Lic and Lpp share the secretion motif, intracellular processing and alpha helix structure, as well as the distribution of hydrophobic residues in heptads forming a hydrophobic core, typical of coiled-coil structures. Cross-linking experiments showed the presence of Lic trimers, supporting our predictions. Taking the in vitro and in silico evidence as a whole, we propose that the most probable structure for Lic is a trimeric coiled-coil. According to this prediction, a suitable model for Lic was produced using the de novo algorithm “Rosetta Fold-and-Dock”. To assess the structural stability of our model, Molecular Dynamics (MD and Replica Exchange MD simulations were performed using the structure of Lpp and a 14-alanine Lpp mutant as controls, at both acidic and neutral pH. Our results suggest that Lic was the most stable structure among the studied proteins in both pH conditions. This increased stability can be explained by a higher number of both intermonomer hydrophobic contacts and hydrogen bonds, key elements for the stability of Lic’s secondary and tertiary structure.

  14. The Structures of Coiled-Coil Domains from Type III Secretion System Translocators Reveal Homology to Pore-Forming Toxins

    Energy Technology Data Exchange (ETDEWEB)

    Barta, Michael L.; Dickenson, Nicholas E.; Patil, Mrinalini; Keightley, Andrew; Wyckoff, Gerald J.; Picking, William D.; Picking, Wendy L.; Geisbrecht, Brian V. (UMKC); (OKLU)

    2012-03-26

    Many pathogenic Gram-negative bacteria utilize type III secretion systems (T3SSs) to alter the normal functions of target cells. Shigella flexneri uses its T3SS to invade human intestinal cells to cause bacillary dysentery (shigellosis) that is responsible for over one million deaths per year. The Shigella type III secretion apparatus is composed of a basal body spanning both bacterial membranes and an exposed oligomeric needle. Host altering effectors are secreted through this energized unidirectional conduit to promote bacterial invasion. The active needle tip complex of S. flexneri is composed of a tip protein, IpaD, and two pore-forming translocators, IpaB and IpaC. While the atomic structure of IpaD has been elucidated and studied, structural data on the hydrophobic translocators from the T3SS family remain elusive. We present here the crystal structures of a protease-stable fragment identified within the N-terminal regions of IpaB from S. flexneri and SipB from Salmonella enterica serovar Typhimurium determined at 2.1 {angstrom} and 2.8 {angstrom} limiting resolution, respectively. These newly identified domains are composed of extended-length (114 {angstrom} in IpaB and 71 {angstrom} in SipB) coiled-coil motifs that display a high degree of structural homology to one another despite the fact that they share only 21% sequence identity. Further structural comparisons also reveal substantial similarity to the coiled-coil regions of pore-forming proteins from other Gram-negative pathogens, notably, colicin Ia. This suggests that these mechanistically separate and functionally distinct membrane-targeting proteins may have diverged from a common ancestor during the course of pathogen-specific evolutionary events.

  15. Coiled-coil domain-dependent homodimerization of intracellular barley immune receptors defines a minimal functional module for triggering cell death

    NARCIS (Netherlands)

    Maekawa, T.; Cheng, W.; Spiridon, L.N.; Töller, A.; Lukasik, E.; Saijo, Y.; Liu, P.; Shen, Q.H.; Micluta, M.A.; Somssich, I.E.; Takken, F.L.W.; Petrescu, A.J.; Chai, J.; Schulze-Lefert, P.

    2011-01-01

    Plants and animals have evolved structurally related innate immune sensors, designated NLRs, to detect intracellular nonself molecules. NLRs are modular, consisting of N-terminal coiled-coil (CC) or TOLL/interleukin-1 receptor (TIR) domains, a central nucleotide-binding (NB) domain, and C-terminal

  16. Ancient Origin of the CARD–Coiled Coil/Bcl10/MALT1-Like Paracaspase Signaling Complex Indicates Unknown Critical Functions

    Directory of Open Access Journals (Sweden)

    Jens Staal

    2018-05-01

    Full Text Available The CARD–coiled coil (CC/Bcl10/MALT1-like paracaspase (CBM signaling complexes composed of a CARD–CC family member (CARD-9, -10, -11, or -14, Bcl10, and the type 1 paracaspase MALT1 (PCASP1 play a pivotal role in immunity, inflammation, and cancer. Targeting MALT1 proteolytic activity is of potential therapeutic interest. However, little is known about the evolutionary origin and the original functions of the CBM complex. Type 1 paracaspases originated before the last common ancestor of planulozoa (bilaterians and cnidarians. Notably in bilaterians, Ecdysozoa (e.g., nematodes and insects lacks Bcl10, whereas other lineages have a Bcl10 homolog. A survey of invertebrate CARD–CC homologs revealed such homologs only in species with Bcl10, indicating an ancient common origin of the entire CBM complex. Furthermore, vertebrate-like Syk/Zap70 tyrosine kinase homologs with the ITAM-binding SH2 domain were only found in invertebrate organisms with CARD–CC/Bcl10, indicating that this pathway might be related to the original function of the CBM complex. Moreover, the type 1 paracaspase sequences from invertebrate organisms that have CARD–CC/Bcl10 are more similar to vertebrate paracaspases. Functional analysis of protein–protein interactions, NF-κB signaling, and CYLD cleavage for selected invertebrate type 1 paracaspase and Bcl10 homologs supports this scenario and indicates an ancient origin of the CARD–CC/Bcl10/paracaspase signaling complex. By contrast, many of the known MALT1-associated activities evolved fairly recently, indicating that unknown functions are at the basis of the protein conservation. As a proof-of-concept, we provide initial evidence for a CBM- and NF-κB-independent neuronal function of the Caenorhabditis elegans type 1 paracaspase malt-1. In conclusion, this study shows how evolutionary insights may point at alternative functions of MALT1.

  17. Effect of modes interaction on the resistive wall mode stability

    International Nuclear Information System (INIS)

    Chen Longxi; Wu Bin

    2013-01-01

    Effects of modes interaction on the resistive wall mode (RWM) stability are studied. When considering the modes interaction effects, the linear growth rate of the most unstable (3, 1) mode decreases. After linear evolution, the RWM saturates at the nonlinear phase. The saturation can be attributed to flux piling up on the resistive wall. When some modes exist, the (3, 1) mode saturates at lower level compared with single mode evolution. Meanwhile, the magnetic energy of the (5, 2) mode increases correspondingly, but the magnetic energy saturation level of the (2, 1) mode changes weakly. (authors)

  18. Exploring the trigger sequence of the GCN4 coiled-coil: Biased molecular dynamics resolves apparent inconsistencies in NMR measurements

    Science.gov (United States)

    Missimer, John H; Dolenc, Jožica; Steinmetz, Michel O; van Gunsteren, Wilfred F

    2010-01-01

    Trigger sequences are indispensable elements for coiled-coil formation. The monomeric helical trigger sequence of the yeast transcriptional activator GCN4 has been investigated recently using several solution NMR observables including nuclear Overhauser enhancement (NOE) intensities and 3J(HN,HCα)-coupling constants, and a set of 20 model structures was proposed. Constrained to satisfy the NOE-derived distance bounds, the NMR model structures do not appear to reproduce all the measured 3J(HN-HCα)-coupling constant values, indicating that the α-helical propensity is not uniform along the GCN4 trigger sequence. A recent methodological study of unrestrained and restrained molecular dynamics (MD) simulations of the GCN4 trigger sequence in solution showed that only MD simulations incorporating time-averaged NOE distance restraints and instantaneous or local-elevation 3J-coupling restraints could satisfy the entire set of the experimental data. In this report, we assess by means of cluster analyses the model structures characteristic of the two simulations that are compatible with the measured data and compare them with the proposed 20 NMR model structures. Striking characteristics of the MD model structures are the variability of the simulated configurations and the indication of entropic stability mediated by the aromatic N-terminal residues 17Tyr and 18His, which are absent in the set of NMR model structures. PMID:20954244

  19. Requirement of the coiled-coil domain of PML-RARα oncoprotein for localization, sumoylation, and inhibition of monocyte differentiation

    International Nuclear Information System (INIS)

    Kim, Young-Eui; Kim, Dong-Yeon; Lee, Jang-Mi; Kim, Seong-Tae; Han, Tae-Hee; Ahn, Jin-Hyun

    2005-01-01

    Homo-oligomerization via a coiled-coil (C-C) domain has been shown to be necessary for the promyelocytic leukemia (PML)-retinoic acid receptor-α (RARα) fusion protein to acquire oncogenic potential in acute promyelocytic leukemia. We show here that PML(ΔC-C)-RARα, which contains a deletion in its C-C domain, is neither localized as characteristic microspeckles nor modified by small ubiquitin-like modifiers (SUMO). The absence of sumoylation of the ΔC-C mutant was due to the lack of binding to Ubc9, a SUMO conjugation enzyme. The integrity of RING finger domain was also needed for both sumoylation and microspeckle formation. In GAL4-DNA tethering assays, the ΔC-C mutant completely lost the inhibitory effect on retinoic acid (RA)-mediated transactivation. Furthermore, the expression of CD14 in U937 cells expressing the ΔC-C mutant in response to vitamin D3 was markedly higher than in cells expressing PML-RARα. However, the RA-mediated induction of C/EBPβ in cells expressing the ΔC-C mutant was comparable to that of control cells. Thus, our results suggest that the C-C domain-associated functions of sumoylation, localization as microspeckles, and the inhibition of monocyte differentiation all contribute to the oncogenic activity of PML-RARα

  20. MURC, a muscle-restricted coiled-coil protein, is involved in the regulation of skeletal myogenesis.

    Science.gov (United States)

    Tagawa, Masashi; Ueyama, Tomomi; Ogata, Takehiro; Takehara, Naofumi; Nakajima, Norio; Isodono, Koji; Asada, Satoshi; Takahashi, Tomosaburo; Matsubara, Hiroaki; Oh, Hidemasa

    2008-08-01

    Skeletal myogenesis is a multistep process by which multinucleated mature muscle fibers are formed from undifferentiated, mononucleated myoblasts. However, the molecular mechanisms of skeletal myogenesis have not been fully elucidated. Here, we identified muscle-restricted coiled-coil (MURC) protein as a positive regulator of myogenesis. In skeletal muscle, MURC was localized to the cytoplasm with accumulation in the Z-disc of the sarcomere. In C2C12 myoblasts, MURC expression occurred coincidentally with myogenin expression and preceded sarcomeric myosin expression during differentiation into myotubes. RNA interference (RNAi)-mediated knockdown of MURC impaired differentiation in C2C12 myoblasts, which was accompanied by impaired myogenin expression and ERK activation. Overexpression of MURC in C2C12 myoblasts resulted in the promotion of differentiation with enhanced myogenin expression and ERK activation during differentiation. During injury-induced muscle regeneration, MURC expression increased, and a higher abundance of MURC was observed in immature myofibers compared with mature myofibers. In addition, ERK was activated in regenerating tissue, and ERK activation was detected in MURC-expressing immature myofibers. These findings suggest that MURC is involved in the skeletal myogenesis that results from modulation of myogenin expression and ERK activation. MURC may play pivotal roles in the molecular mechanisms of skeletal myogenic differentiation.

  1. Magnetic Field Alignment of PS-P4VP: a Non-Liquid Crystalline Coil-Coil Block Copolymer

    Science.gov (United States)

    Rokhlenko, Yekaterina; Zhang, Kai; Larson, Steven; Gopalan, Padma; O'Hern, Corey; Osuji, Chinedum

    2015-03-01

    Magnetic fields provide the ability to control alignment of self-assembled soft materials such as block copolymers. Most prior work in this area has relied on the presence of ordered assemblies of anisotropic liquid crystalline species to ensure sufficient magnetic anisotropy to drive alignment. Recent experiments with poly(styrene-b-4-vinylpyridine), a non-liquid crystalline BCP, however, show field-induced alignment of a lamellar microstructure during cooling across the order-disorder transition. Using in situ x-ray scattering, we examine the roles of field strength and cooling rate on the alignment response of this low MW coil-coil BCP. Alignment is first observed at field strengths as low as 1 Tesla and improves markedly with both increasing field strength and slower cooling. We present a geometric argument to illustrate the origin of a finite, non-trivial magnetic susceptibility anisotropy for highly stretched surface-tethered polymer chains and corroborate this using coarse-grained molecular dynamics simulations. We rationalize the magnetic field response of the system in terms of the mobility afforded by the absence of entanglements, the intrinsic anisotropy resulting from the stretched polymer chains and sterically constrained conjugated rings, and the large grain size in these low molecular weight materials.

  2. An alternative conformation of the gp41 heptad repeat 1 region coiled coil exists in the human immunodeficiency virus (HIV-1) envelope glycoprotein precursor

    International Nuclear Information System (INIS)

    Mische, Claudia C.; Yuan Wen; Strack, Bettina; Craig, Stewart; Farzan, Michael; Sodroski, Joseph

    2005-01-01

    The human immunodeficiency virus (HIV-1) transmembrane envelope glycoprotein, gp41, which mediates virus-cell fusion, exists in at least three different conformations within the trimeric envelope glycoprotein complex. The structures of the prefusogenic and intermediate states are unknown; structures representing the postfusion state have been solved. In the postfusion conformation, three helical heptad repeat 2 (HR2) regions pack in an antiparallel fashion into the hydrophobic grooves on the surface of a triple-helical coiled coil formed by the heptad repeat 1 (HR1) regions. We studied the prefusogenic conformation of gp41 by mutagenic alteration of membrane-anchored and soluble forms of the HIV-1 envelope glycoproteins. Our results indicate that, in the HIV-1 envelope glycoprotein precursor, the gp41 HR1 region is in a conformation distinct from that of a trimeric coiled coil. Thus, the central gp41 coiled coil is formed during the transition of the HIV-1 envelope glycoproteins from the precursor state to the receptor-bound intermediate

  3. Spontaneous adsorption of coiled-coil model peptides K and E to a mixed lipid bilayer.

    Science.gov (United States)

    Pluhackova, Kristyna; Wassenaar, Tsjerk A; Kirsch, Sonja; Böckmann, Rainer A

    2015-03-26

    A molecular description of the lipid-protein interactions underlying the adsorption of proteins to membranes is crucial for understanding, for example, the specificity of adsorption or the binding strength of a protein to a bilayer, or for characterizing protein-induced changes of membrane properties. In this paper, we extend an automated in silico assay (DAFT) for binding studies and apply it to characterize the adsorption of the model fusion peptides E and K to a mixed phospholipid/cholesterol membrane using coarse-grained molecular dynamics simulations. In addition, we couple the coarse-grained protocol to reverse transformation to atomistic resolution, thereby allowing to study molecular interactions with high detail. The experimentally observed differential binding of the peptides E and K to membranes, as well as the increased binding affinity of helical over unstructered peptides, could be well reproduced using the polarizable Martini coarse-grained (CG) force field. Binding to neutral membranes is shown to be dominated by initial binding of the positively charged N-terminus to the phospholipid headgroup region, followed by membrane surface-aligned insertion of the peptide at the interface between the hydrophobic core of the membrane and its polar headgroup region. Both coarse-grained and atomistic simulations confirm a before hypothesized snorkeling of lysine side chains for the membrane-bound state of the peptide K. Cholesterol was found to be enriched in peptide vicinity, which is probably of importance for the mechanism of membrane fusion. The applied sequential multiscale method, using coarse-grained simulations for the slow adsorption process of peptides to membranes followed by backward transformation to atomistic detail and subsequent atomistic simulations of the preformed peptide-lipid complexes, is shown to be a versatile approach to study the interactions of peptides or proteins with biomembranes.

  4. Hypoxia activates muscle-restricted coiled-coil protein (MURC) expression via transforming growth factor-β in cardiac myocytes.

    Science.gov (United States)

    Shyu, Kou-Gi; Cheng, Wen-Pin; Wang, Bao-Wei; Chang, Hang

    2014-03-01

    The expression of MURC (muscle-restricted coiled-coil protein), a hypertrophy-regulated gene, increases during pressure overload. Hypoxia can cause myocardial hypertrophy; however, how hypoxia affects the regulation of MURC in cardiomyocytes undergoing hypertrophy is still unknown. The aim of the present study was to test the hypothesis that hypoxia induces MURC expression in cardiomyocytes during hypertrophy. The expression of MURC was evaluated in cultured rat neonatal cardiomyocytes subjected to hypoxia and in an in vivo model of AMI (acute myocardial infarction) to induce myocardial hypoxia in adult rats. MURC protein and mRNA expression were significantly enhanced by hypoxia. MURC proteins induced by hypoxia were significantly blocked after the addition of PD98059 or ERK (extracellular-signal-regulated kinase) siRNA 30 min before hypoxia. Gel-shift assay showed increased DNA-binding activity of SRF (serum response factor) after hypoxia. PD98059, ERK siRNA and an anti-TGF-β (transforming growth factor-β) antibody abolished the SRF-binding activity enhanced by hypoxia or exogenous administration of TGF-β. A luciferase promoter assay demonstrated increased transcriptional activity of SRF in cardiomyocytes by hypoxia. Increased βMHC (β-myosin heavy chain) and BNP (B-type natriuretic peptide) protein expression and increased protein synthesis was identified after hypoxia with the presence of MURC in hypertrophic cardiomyocytes. MURC siRNA inhibited the hypertrophic marker protein expression and protein synthesis induced by hypoxia. AMI in adult rats also demonstrated increased MURC protein expression in the left ventricular myocardium. In conclusion, hypoxia in cultured rat neonatal cardiomyocytes increased MURC expression via the induction of TGF-β, SRF and the ERK pathway. These findings suggest that MURC plays a role in hypoxia-induced hypertrophy in cardiomyocytes.

  5. The coiled-coil domain containing protein CCDC40 is essential for motile cilia function and left-right axis formation

    DEFF Research Database (Denmark)

    Becker-Heck, Anita; Zohn, Irene E; Okabe, Noriko

    2011-01-01

    Primary ciliary dyskinesia (PCD) is a genetically heterogeneous autosomal recessive disorder characterized by recurrent infections of the respiratory tract associated with the abnormal function of motile cilia. Approximately half of individuals with PCD also have alterations in the left-right...... organization of their internal organ positioning, including situs inversus and situs ambiguous (Kartagener's syndrome). Here, we identify an uncharacterized coiled-coil domain containing a protein, CCDC40, essential for correct left-right patterning in mouse, zebrafish and human. In mouse and zebrafish, Ccdc40...

  6. cDNA cloning of the basement membrane chondroitin sulfate proteoglycan core protein, bamacan: a five domain structure including coiled-coil motifs

    DEFF Research Database (Denmark)

    Wu, R R; Couchman, J R

    1997-01-01

    Basement membranes contain several proteoglycans, and those bearing heparan sulfate glycosaminoglycans such as perlecan and agrin usually predominate. Most mammalian basement membranes also contain chondroitin sulfate, and a core protein, bamacan, has been partially characterized. We have now....... The protein sequence has low overall homology, apart from very small NH2- and COOH-terminal motifs. At the junctions between the distal globular domains and the coiled-coil regions lie glycosylation sites, with up to three N-linked oligosaccharides and probably three chondroitin chains. Three other Ser...

  7. N-terminal aliphatic residues dictate the structure, stability, assembly, and small molecule binding of the coiled-coil region of cartilage oligomeric matrix protein.

    Science.gov (United States)

    Gunasekar, Susheel K; Asnani, Mukta; Limbad, Chandani; Haghpanah, Jennifer S; Hom, Wendy; Barra, Hanna; Nanda, Soumya; Lu, Min; Montclare, Jin Kim

    2009-09-15

    The coiled-coil domain of cartilage oligomeric matrix protein (COMPcc) assembles into a homopentamer that naturally recognizes the small molecule 1,25-dihydroxyvitamin D(3) (vit D). To identify the residues critical for the structure, stability, oligomerization, and binding to vit D as well as two other small molecules, all-trans-retinol (ATR) and curcumin (CCM), here we perform an alanine scanning mutagenesis study. Ten residues lining the hydrophobic pocket of COMPcc were mutated into alanine; of the mutated residues, the N-terminal aliphatic residues L37, L44, V47, and L51 are responsible for maintaining the structure and function. Furthermore, two polar residues, T40 and Q54, within the N-terminal region when converted into alanine improve the alpha-helical structure, stability, and self-assembly behavior. Helical stability, oligomerization, and binding appear to be linked in a manner in which mutations that abolish helical structure and assembly bind poorly to vit D, ATR, and CCM. These results provide not only insight into COMPcc and its functional role but also useful guidelines for the design of stable, pentameric coiled-coils capable of selectively storing and delivering various small molecules.

  8. Glycosaminoglycans are interactants of Langerin: comparison with gp120 highlights an unexpected calcium-independent binding mode.

    Science.gov (United States)

    Chabrol, Eric; Nurisso, Alessandra; Daina, Antoine; Vassal-Stermann, Emilie; Thepaut, Michel; Girard, Eric; Vivès, Romain R; Fieschi, Franck

    2012-01-01

    Langerin is a C-type lectin specifically expressed in Langerhans cells. As recently shown for HIV, Langerin is thought to capture pathogens and mediate their internalisation into Birbeck Granules for elimination. However, the precise functions of Langerin remain elusive, mostly because of the lack of information on its binding properties and physiological ligands. Based on recent reports that Langerin binds to sulfated sugars, we conducted here a comparative analysis of Langerin interaction with mannose-rich HIV glycoprotein gp120 and glycosaminoglycan (GAGs), a family of sulfated polysaccharides expressed at the surface of most mammalian cells. Our results first revealed that Langerin bound to these different glycans through very distinct mechanisms and led to the identification of a novel, GAG-specific binding mode within Langerin. In contrast to the canonical lectin domain, this new binding site showed no Ca(2+)-dependency, and could only be detected in entire, trimeric extracellular domains of Langerin. Interestingly binding to GAGs, did not simply rely on a net charge effect, but rather on more discrete saccharide features, such as 6-O-sulfation, or iduronic acid content. Using molecular modelling simulations, we proposed a model of Langerin/heparin complex, which located the GAG binding site at the interface of two of the three Carbohydrate-recognition domains of the protein, at the edge of the a-helix coiled-coil. To our knowledge, the binding properties that we have highlighted here for Langerin, have never been reported for C-type lectins before. These findings provide new insights towards the understanding of Langerin biological functions.

  9. Glycosaminoglycans are interactants of Langerin: comparison with gp120 highlights an unexpected calcium-independent binding mode.

    Directory of Open Access Journals (Sweden)

    Eric Chabrol

    Full Text Available Langerin is a C-type lectin specifically expressed in Langerhans cells. As recently shown for HIV, Langerin is thought to capture pathogens and mediate their internalisation into Birbeck Granules for elimination. However, the precise functions of Langerin remain elusive, mostly because of the lack of information on its binding properties and physiological ligands. Based on recent reports that Langerin binds to sulfated sugars, we conducted here a comparative analysis of Langerin interaction with mannose-rich HIV glycoprotein gp120 and glycosaminoglycan (GAGs, a family of sulfated polysaccharides expressed at the surface of most mammalian cells. Our results first revealed that Langerin bound to these different glycans through very distinct mechanisms and led to the identification of a novel, GAG-specific binding mode within Langerin. In contrast to the canonical lectin domain, this new binding site showed no Ca(2+-dependency, and could only be detected in entire, trimeric extracellular domains of Langerin. Interestingly binding to GAGs, did not simply rely on a net charge effect, but rather on more discrete saccharide features, such as 6-O-sulfation, or iduronic acid content. Using molecular modelling simulations, we proposed a model of Langerin/heparin complex, which located the GAG binding site at the interface of two of the three Carbohydrate-recognition domains of the protein, at the edge of the a-helix coiled-coil. To our knowledge, the binding properties that we have highlighted here for Langerin, have never been reported for C-type lectins before. These findings provide new insights towards the understanding of Langerin biological functions.

  10. Polymer cancerostatics targeted with an antibody fragment bound via a coiled coil motif: in vivo therapeutic efficacy against murine BCL1 leukemia

    Czech Academy of Sciences Publication Activity Database

    Pechar, Michal; Pola, Robert; Janoušková, Olga; Sieglová, Irena; Král, Vlastimil; Fábry, Milan; Tomalová, Barbora; Kovář, Marek

    2018-01-01

    Roč. 18, č. 1 (2018), s. 1-11, č. článku 1700173. ISSN 1616-5187 R&D Projects: GA MŠk(CZ) LO1507; GA MŠk(CZ) LQ1604; GA MZd(CZ) NV16-28594A; GA ČR(CZ) GA16-17207S; GA ČR GA13-12885S Institutional support: RVO:61389013 ; RVO:68378050 ; RVO:61388971 Keywords : cancer therapy * coiled coil * drug targeting Subject RIV: CD - Macromolecular Chemistry; CD - Macromolecular Chemistry (UMG-J); EE - Microbiology, Virology (MBU-M) OBOR OECD: Polymer science; Polymer science (UMG-J); Microbiology (MBU-M) Impact factor: 3.238, year: 2016

  11. Interaction Modes for Emergency Mobile Apps

    Directory of Open Access Journals (Sweden)

    Claudia Nass

    2018-01-01

    Full Text Available While seemingly irrational behaviors such as panicking or displaying antisocial behavior are the responses to emergency situations the media and movies lead us to believe, several studies show that people rather react based on decision-making such as acting altruistically and protectively. However, what can we really expect from people in a crowd in terms of participation in an emergency response system? In this paper, we present a mobile application called the RESCUER App, which allows civilians to participate in the emergency response process by providing information about the emergency to a command center and to receive instructions from this command center. We developed a human reaction model for emergencies to better understand the human–computer interaction capabilities of people in an emergency situation. Based on this model, we defined three different interaction modes: one-click interaction, guided interaction, and chat interaction. These interaction modes were implemented in an interactive prototype and evaluated in an experiment in which high cognitive load was induced to simulate a stress situation, similar to the stress experienced in an emergency. The experiment results showed that the three predefined interaction modes enabled people to interact with the RESCUER App even though they were in a stress situation.

  12. Nuclear Magnetic Resonance Structures of GCN4p Are Largely Conserved When Ion Pairs Are Disrupted at Acidic pH but Show a Relaxation of the Coiled Coil Superhelix.

    Science.gov (United States)

    Kaplan, Anne R; Brady, Megan R; Maciejewski, Mark W; Kammerer, Richard A; Alexandrescu, Andrei T

    2017-03-21

    To understand the roles ion pairs play in stabilizing coiled coils, we determined nuclear magnetic resonance structures of GCN4p at three pH values. At pH 6.6, all acidic residues are fully charged; at pH 4.4, they are half-charged, and at pH 1.5, they are protonated and uncharged. The α-helix monomer and coiled coil structures of GCN4p are largely conserved, except for a loosening of the coiled coil quaternary structure with a decrease in pH. Differences going from neutral to acidic pH include (i) an unwinding of the coiled coil superhelix caused by the loss of interchain ion pair contacts, (ii) a small increase in the separation of the monomers in the dimer, (iii) a loosening of the knobs-into-holes packing motifs, and (iv) an increased separation between oppositely charged residues that participate in ion pairs at neutral pH. Chemical shifts (HN, N, C', Cα, and Cβ) of GCN4p display a seven-residue periodicity that is consistent with α-helical structure and is invariant with pH. By contrast, periodicity in hydrogen exchange rates at neutral pH is lost at acidic pH as the exchange mechanism moves into the EX1 regime. On the basis of 1 H- 15 N nuclear Overhauser effect relaxation measurements, the α-helix monomers experience only small increases in picosecond to nanosecond backbone dynamics at acidic pH. By contrast, 13 C rotating frame T 1 relaxation (T 1ρ ) data evince an increase in picosecond to nanosecond side-chain dynamics at lower pH, particularly for residues that stabilize the coiled coil dimerization interface through ion pairs. The results on the structure and dynamics of GCNp4 over a range of pH values help rationalize why a single structure at neutral pH poorly predicts the pH dependence of the unfolding stability of the coiled coil.

  13. Conformational plasticity of the coiled-coil domain of BmrR is required for bmr operator binding: the structure of unliganded BmrR.

    Science.gov (United States)

    Kumaraswami, Muthiah; Newberry, Kate J; Brennan, Richard G

    2010-04-30

    The multidrug-binding transcription regulator BmrR from Bacillus subtilis is a MerR family member that binds to a wide array of cationic lipophilic toxins to activate the transcription of the multidrug efflux pump gene bmr. Transcription activation from the sigma(A)-dependent bmr operator requires BmrR to remodel the nonoptimal 19-bp spacer between the -10 promoter element and the -35 promoter element in order to facilitate productive RNA polymerase binding. Despite the availability of several structures of BmrR bound to DNA and drugs, the lack of a BmrR structure in its unliganded or apo (DNA free and drug free) state hinders our full understanding of the structural transitions required for DNA binding and transcription activation. Here, we report the crystal structure of the constitutively active, unliganded BmrR mutant BmrR(E253Q/R275E). Superposition of the ligand-free (apo BmrR(E253Q/R275E)) and DNA-bound BmrR structures reveals that apo BmrR must undergo significant rearrangement in order to assume the DNA-bound conformation, including an outward rotation of minor groove binding wings, an inward movement of helix-turn-helix motifs, and a downward relocation of pliable coiled-coil helices. Computational analysis of the DNA-free and DNA-bound structures reveals a flexible joint that is located at the center of the coiled-coil helices. This region, which is composed of residues 94 through 98, overlaps the helical bulge that is observed only in the apo BmrR structure. This conformational hinge is likely common to other MerR family members with large effector-binding domains, but appears to be missing from the smaller metal-binding MerR family members. Interestingly, the center-to-center distance of the recognition helices of apo BmrR is 34 A and suggests that the conformational change from the apo BmrR structure to the bmr operator-bound BmrR structure is initiated by the binding of this transcription activator to a more B-DNA-like conformation. (c) 2010 Elsevier

  14. Mode Interaction in Structures - An Overview

    DEFF Research Database (Denmark)

    Byskov, Esben

    2004-01-01

    Abstract Koiter [1] was the first to formulate an asymptotic expansion to investigate postbuckling behavior and imperfection sensitivity of elastic structures. Since then, a large number of analyses of particular structures have appeared as well as some new expansions aimed at specific problems, ...... analyses must always be preferred because asymptotic expansions are obsolete. Keywords: stability, elastic, mode interaction....

  15. Coiled-coil domain of PML is essential for the aberrant dynamics of PML-RARα, resulting in sequestration and decreased mobility of SMRT

    International Nuclear Information System (INIS)

    Huang Ying; Qiu Jihui; Chen Guoqiang; Dong Shuo

    2008-01-01

    Promyelocytic leukemia-retinoic acid receptor α (PML-RARα) is the most frequent RARα fusion protein in acute promyelocytic leukemia (APL). Our previous study has demonstrated that, compared with RARα, PML-RARα had reduced intranuclear mobility accompanied with mislocalization. To understand the molecular basis for the altered dynamics of PML-RARα fusion protein, we performed FRAP analysis at a single cell level. Results indicated that three known sumoylation site mutated PML-RARα had same intracellular localization and reduced mobility as wild-type counterpart. The coiled-coil domain of PML is responsible for the aberrant dynamics of PML-RARα. In addition, we revealed that co-repressor SMRT co-localized with PML-RARα, resulting in the immobilization of SMRT while ATRA treatment eliminated their association and reversed the immobile effect of SMRT. Furthermore, co-activator CBP, co-localized with PML-RARα in an ATRA-independent way, was demonstrated as a high dynamic intranuclear molecule. These results would shed new insights for the molecular mechanisms of PML-RARα-associated leukemogenesis

  16. MURC, a muscle-restricted coiled-coil protein that modulates the Rho/ROCK pathway, induces cardiac dysfunction and conduction disturbance.

    Science.gov (United States)

    Ogata, Takehiro; Ueyama, Tomomi; Isodono, Koji; Tagawa, Masashi; Takehara, Naofumi; Kawashima, Tsuneaki; Harada, Koichiro; Takahashi, Tomosaburo; Shioi, Tetsuo; Matsubara, Hiroaki; Oh, Hidemasa

    2008-05-01

    We identified a novel muscle-restricted putative coiled-coil protein, MURC, which is evolutionarily conserved from frog to human. MURC was localized to the cytoplasm with accumulation in the Z-line of the sarcomere in the murine adult heart. MURC mRNA expression in the heart increased during the developmental process from the embryonic stage to adulthood. In response to pressure overload, MURC mRNA expression increased in the hypertrophied heart. Using the yeast two-hybrid system, we identified the serum deprivation response (SDPR) protein, a phosphatidylserine-binding protein, as a MURC-binding protein. MURC induced activation of the RhoA/ROCK pathway, which modulated serum response factor-mediated atrial natriuretic peptide (ANP) expression and myofibrillar organization. SDPR augmented MURC-induced transactivation of the ANP promoter in cardiomyocytes, and RNA interference of SDPR attenuated the action of MURC on the ANP promoter. Transgenic mice expressing cardiac-specific MURC (Tg-MURC) exhibited cardiac contractile dysfunction and atrioventricular (AV) conduction disturbances with atrial chamber enlargement, reduced thickness of the ventricular wall, and interstitial fibrosis. Spontaneous episodes of atrial fibrillation and AV block were observed in Tg-MURC mice. These findings indicate that MURC modulates RhoA signaling and that MURC plays an important role in the development of cardiac dysfunction and conduction disturbance with increased vulnerability to atrial arrhythmias.

  17. MURC, a Muscle-Restricted Coiled-Coil Protein That Modulates the Rho/ROCK Pathway, Induces Cardiac Dysfunction and Conduction Disturbance▿

    Science.gov (United States)

    Ogata, Takehiro; Ueyama, Tomomi; Isodono, Koji; Tagawa, Masashi; Takehara, Naofumi; Kawashima, Tsuneaki; Harada, Koichiro; Takahashi, Tomosaburo; Shioi, Tetsuo; Matsubara, Hiroaki; Oh, Hidemasa

    2008-01-01

    We identified a novel muscle-restricted putative coiled-coil protein, MURC, which is evolutionarily conserved from frog to human. MURC was localized to the cytoplasm with accumulation in the Z-line of the sarcomere in the murine adult heart. MURC mRNA expression in the heart increased during the developmental process from the embryonic stage to adulthood. In response to pressure overload, MURC mRNA expression increased in the hypertrophied heart. Using the yeast two-hybrid system, we identified the serum deprivation response (SDPR) protein, a phosphatidylserine-binding protein, as a MURC-binding protein. MURC induced activation of the RhoA/ROCK pathway, which modulated serum response factor-mediated atrial natriuretic peptide (ANP) expression and myofibrillar organization. SDPR augmented MURC-induced transactivation of the ANP promoter in cardiomyocytes, and RNA interference of SDPR attenuated the action of MURC on the ANP promoter. Transgenic mice expressing cardiac-specific MURC (Tg-MURC) exhibited cardiac contractile dysfunction and atrioventricular (AV) conduction disturbances with atrial chamber enlargement, reduced thickness of the ventricular wall, and interstitial fibrosis. Spontaneous episodes of atrial fibrillation and AV block were observed in Tg-MURC mice. These findings indicate that MURC modulates RhoA signaling and that MURC plays an important role in the development of cardiac dysfunction and conduction disturbance with increased vulnerability to atrial arrhythmias. PMID:18332105

  18. Coiled-coil formation of the membrane-fusion K/E peptides viewed by electron paramagnetic resonance.

    Directory of Open Access Journals (Sweden)

    Pravin Kumar

    Full Text Available The interaction of the complementary K (Ac-(KIAALKE3-GW-NH2 and E (Ac-(EIAALEK3-GY-NH2 peptides, components of the zipper of an artificial membrane fusion system (Robson Marsden H. et al. Angew Chemie Int Ed. 2009 is investigated by electron paramagnetic resonance (EPR. By frozen solution continuous-wave EPR and double electron-electron resonance (DEER, the distance between spin labels attached to the K- and to the E-peptide is measured. Three constructs of spin-labelled K- and E-peptides are used in five combinations for low temperature investigations. The K/E heterodimers are found to be parallel, in agreement with previous studies. Also, K homodimers in parallel orientation were observed, a finding that was not reported before. Comparison to room-temperature, solution EPR shows that the latter method is less specific to detect this peptide-peptide interaction. Combining frozen solution cw-EPR for short distances (1.8 nm to 2.0 nm and DEER for longer distances thus proves versatile to detect the zipper interaction in membrane fusion. As the methodology can be applied to membrane samples, the approach presented suggests itself for in-situ studies of the complete membrane fusion process, opening up new avenues for the study of membrane fusion.

  19. Contributed Review: Absolute spectral radiance calibration of fiber-optic shock-temperature pyrometers using a coiled-coil irradiance standard lamp

    Energy Technology Data Exchange (ETDEWEB)

    Fat’yanov, O. V., E-mail: fatyan1@gps.caltech.edu; Asimow, P. D., E-mail: asimow@gps.caltech.edu [Division of Geological and Planetary Sciences 252-21, California Institute of Technology, Pasadena, California 91125 (United States)

    2015-10-15

    We describe an accurate and precise calibration procedure for multichannel optical pyrometers such as the 6-channel, 3-ns temporal resolution instrument used in the Caltech experimental geophysics laboratory. We begin with a review of calibration sources for shock temperatures in the 3000-30 000 K range. High-power, coiled tungsten halogen standards of spectral irradiance appear to be the only practical alternative to NIST-traceable tungsten ribbon lamps, which are no longer available with large enough calibrated area. However, non-uniform radiance complicates the use of such coiled lamps for reliable and reproducible calibration of pyrometers that employ imaging or relay optics. Careful analysis of documented methods of shock pyrometer calibration to coiled irradiance standard lamps shows that only one technique, not directly applicable in our case, is free of major radiometric errors. We provide a detailed description of the modified Caltech pyrometer instrument and a procedure for its absolute spectral radiance calibration, accurate to ±5%. We employ a designated central area of a 0.7× demagnified image of a coiled-coil tungsten halogen lamp filament, cross-calibrated against a NIST-traceable tungsten ribbon lamp. We give the results of the cross-calibration along with descriptions of the optical arrangement, data acquisition, and processing. We describe a procedure to characterize the difference between the static and dynamic response of amplified photodetectors, allowing time-dependent photodiode correction factors for spectral radiance histories from shock experiments. We validate correct operation of the modified Caltech pyrometer with actual shock temperature experiments on single-crystal NaCl and MgO and obtain very good agreement with the literature data for these substances. We conclude with a summary of the most essential requirements for error-free calibration of a fiber-optic shock-temperature pyrometer using a high-power coiled tungsten halogen

  20. Immune response against the coiled coil domain of Sjögren's syndrome associated autoantigen Ro52 induces salivary gland dysfunction.

    Science.gov (United States)

    Sroka, Magdalena; Bagavant, Harini; Biswas, Indranil; Ballard, Abigail; Deshmukh, Umesh S

    2018-01-31

    The structural domains of Ro52, termed the RING, B-box, coiled coil (CC) and B30.2/SPRY are targets of anti-Ro52 in multiple autoimmune disorders. In Sjögren's syndrome patients, the presence of anti-Ro52 is associated with higher disease severity, and in mice, they induce salivary gland hypofunction. This study was undertaken to investigate whether immune responses against different domains of Ro52, influences salivary gland disease in mice. Female NZM2758 mice were immunised with Ro52 domains expressed as recombinant fusion proteins with maltose binding protein (MBP) [MBP-RING-B-box, MBP-CC, MBP-CC(ΔC19), MBP-B30.2/SPRY]. Sera from immunised mice were studied for IgG antibodies to Ro52 by immunoprecipitation, and to salivary gland cells by immunofluorescence. Pilocarpine-induced saliva production was measured to evaluate salivary gland function. Submandibular glands were investigated by histopathology for inflammation and by immune-histochemistry for IgG deposition. Mice immunised with different Ro52-domains had comparable reactivity to Ro52 and to salivary gland cells. However, only mice immunised with the CC domain and its C-terminal truncated version CC(ΔC19) showed a significant drop in saliva production. None of the mice developed severe salivary gland inflammation. The salivary gland hypofunction significantly correlated with increased intra-lobar IgG deposits in the submandibular salivary glands. Our data demonstrate that epitope specificity of anti-Ro52 antibodies plays a critical role in the induction of glandular dysfunction. Clearly, screening Sjögren's syndrome patients for relative levels of Ro52 domain specific antibodies will be more informative for associating anti-Ro52 with clinical measures of the disorder.

  1. Novel Coiled-Coil Cell Division Factor ZapB Stimulates Z Ring Assembly and Cell Division

    DEFF Research Database (Denmark)

    Ebersbach, Gitte; Galli, Elizabeth; Møller-Jensen, Jakob

    2008-01-01

    Formation of the Z ring is the first known event in bacterial cell division. However, it is not yet known how the assembly and contraction of the Z ring is regulated. Here, we identify a novel cell division factor ZapB in Escherichia coli that simultaneously stimulates Z ring assembly and cell...... division. Deletion of zapB resulted in delayed cell division and the formation of ectopic Z rings and spirals whereas overexpression of ZapB resulted in nucleoid condensation and aberrant cell divisions. Localization of ZapB to the divisome depended on FtsZ but not FtsA, ZipA or FtsI and ZapB interacted...... with FtsZ in a bacterial two-hybrid analysis. The simultaneous inactivation of FtsA and ZipA prevented Z ring assembly and ZapB localization. Time lapse microscopy showed that ZapB-GFP is present at mid-cell in a pattern very similar to that of FtsZ. Cells carrying a zapB deletion and the ftsZ84ts allele...

  2. Decay modes of two repulsively interacting bosons

    International Nuclear Information System (INIS)

    Kim, Sungyun; Brand, Joachim

    2011-01-01

    We study the decay of two repulsively interacting bosons tunnelling through a delta potential barrier by a direct numerical solution of the time-dependent Schroedinger equation. The solutions are analysed according to the regions of particle presence: both particles inside the trap (in-in), one particle in and one particle out (in-out) and both particles outside (out-out). It is shown that the in-in probability is dominated by the exponential decay, and its decay rate is predicted very well from outgoing boundary conditions. Up to a certain range of interaction strength, the decay of in-out probability is dominated by the single-particle decay mode. The decay mechanisms are adequately described by simple models.

  3. Effects of multiple modes interaction on the resistive wall mode instability

    International Nuclear Information System (INIS)

    Chen, Longxi; Lei, Wenqing; Ma, Zhiwei; Wu, Bin

    2013-01-01

    The effects of multiple modes interaction on the resistive wall mode (RWM) are studied in a slab geometry with and without plasma flow. The modes interaction can have a large effect on both the linear growth rate and the nonlinear saturation level of the RWM. We found that modes interaction can suppress the linear growth rate for the most unstable mode. The plasma flow can also help to control the growth of the RWM. The RWM can be stabilized completely by a plasma flow when considering the modes interaction. The effect of modes interaction on the RWM is stronger for the mode rational surface in the vacuum than that in the plasma. The modes interaction results in a substantially lowered saturation level for the most unstable RWM. (paper)

  4. Complexes of neutralizing and non-neutralizing affinity matured Fabs with a mimetic of the internal trimeric coiled-coil of HIV-1 gp41.

    Directory of Open Access Journals (Sweden)

    Elena Gustchina

    Full Text Available A series of mini-antibodies (monovalent and bivalent Fabs targeting the conserved internal trimeric coiled-coil of the N-heptad repeat (N-HR of HIV-1 gp41 has been previously constructed and reported. Crystal structures of two closely related monovalent Fabs, one (Fab 8066 broadly neutralizing across a wide panel of HIV-1 subtype B and C viruses, and the other (Fab 8062 non-neutralizing, representing the extremes of this series, were previously solved as complexes with 5-Helix, a gp41 pre-hairpin intermediate mimetic. Binding of these Fabs to covalently stabilized chimeric trimers of N-peptides of HIV-1 gp41 (named (CCIZN363 or 3-H has now been investigated using X-ray crystallography, cryo-electron microscopy, and a variety of biophysical methods. Crystal structures of the complexes between 3-H and Fab 8066 and Fab 8062 were determined at 2.8 and 3.0 Å resolution, respectively. Although the structures of the complexes with the neutralizing Fab 8066 and its non-neutralizing counterpart Fab 8062 were generally similar, small differences between them could be correlated with the biological properties of these antibodies. The conformations of the corresponding CDRs of each antibody in the complexes with 3-H and 5-Helix are very similar. The adaptation to a different target upon complex formation is predominantly achieved by changes in the structure of the trimer of N-HR helices, as well as by adjustment of the orientation of the Fab molecule relative to the N-HR in the complex, via rigid-body movement. The structural data presented here indicate that binding of three Fabs 8062 with high affinity requires more significant changes in the structure of the N-HR trimer compared to binding of Fab 8066. A comparative analysis of the structures of Fabs complexed to different gp41 intermediate mimetics allows further evaluation of biological relevance for generation of neutralizing antibodies, as well as provides novel structural insights into immunogen

  5. Molecular genetic and functional characterization implicate muscle-restricted coiled-coil gene (MURC) as a causal gene for familial dilated cardiomyopathy.

    Science.gov (United States)

    Rodriguez, Gabriela; Ueyama, Tomomi; Ogata, Takehiro; Czernuszewicz, Grazyna; Tan, Yanli; Dorn, Gerald W; Bogaev, Roberta; Amano, Katsuya; Oh, Hidemasa; Matsubara, Hiroaki; Willerson, James T; Marian, Ali J

    2011-08-01

    Dilated cardiomyopathy (DCM) and hypertrophic cardiomyopathy (HCM) are classic forms of systolic and diastolic heart failure, respectively. Mutations in genes encoding sarcomere and cytoskeletal proteins are major causes of HCM and DCM. MURC, encoding muscle-restricted coiled-coil, a Z-line protein, regulates cardiac function in mice. We investigated potential causal role of MURC in human cardiomyopathies. We sequenced MURC in 1199 individuals, including 383 probands with DCM, 307 with HCM, and 509 healthy control subjects. We found 6 heterozygous DCM-specific missense variants (p.N128K, p.R140W, p.L153P, p.S307T, p.P324L, and p.S364L) in 8 unrelated probands. Variants p.N128K and p.S307T segregated with inheritance of DCM in small families (χ(2)=8.5, P=0.003). Variants p.N128K, p.R140W, p.L153P, and p.S364L were considered probably or possibly damaging. Variant p.P324L recurred in 3 independent probands, including 1 proband with a TPM1 mutation (p.M245T). A deletion variant (p.L232-R238del) was present in 3 unrelated HCM probands, but it did not segregate with HCM in a family who also had a MYH7 mutation (p.L907V). The phenotype in mutation carriers was notable for progressive heart failure leading to heart transplantation in 4 patients, conduction defects, and atrial arrhythmias. Expression of mutant MURC proteins in neonatal rat cardiac myocytes transduced with recombinant adenoviruses was associated with reduced RhoA activity, lower mRNA levels of hypertrophic markers and smaller myocyte size as compared with wild-type MURC. MURC mutations impart loss-of-function effects on MURC functions and probably are causal variants in human DCM. The causal role of a deletion mutation in HCM is uncertain.

  6. Interacting collective modes in a laser cavity

    International Nuclear Information System (INIS)

    Graca, E.L.; Brito, A.L. de; Baseia, B.

    1985-01-01

    Collective operators are defined for the quantized radiation field in a one-dimensional laser cavity coupled to a semi-infinite outside region and the overlaps of neighbouring collective modes are considered to show how they modify, in the linear appoximation, the time evolution of the radiation field below threshold. The model and procedure work directly within a continuous spectrum of modes and allow us to get an improved insight on the prescription for the laser field in single-mode operation. (Author) [pt

  7. Multi-mode interactions in an FEL oscillator

    CERN Document Server

    Dong Zhi Wei; Masuda, K; Yamazaki, T; Yoshikawa, K

    2000-01-01

    A 3D time-dependent FEL oscillator simulation code has been developed by using the transverse mode spectral method to analyze interaction among transverse modes. The competition among them in an FEL oscillator was investigated based on the parameters of LANL FEL experiments. It is found that under typical FEL oscillator operation conditions, the TEM sub 0 sub 0 mode is dominant, and the effects of other transverse modes can be negligible.

  8. De novo design of peptide immunogens that mimic the coiled coil region of human T-cell leukemia virus type-1 glycoprotein 21 transmembrane subunit for induction of native protein reactive neutralizing antibodies.

    Science.gov (United States)

    Sundaram, Roshni; Lynch, Marcus P; Rawale, Sharad V; Sun, Yiping; Kazanji, Mirdad; Kaumaya, Pravin T P

    2004-06-04

    Peptide vaccines able to induce high affinity and protective neutralizing antibodies must rely in part on the design of antigenic epitopes that mimic the three-dimensional structure of the corresponding region in the native protein. We describe the design, structural characterization, immunogenicity, and neutralizing potential of antibodies elicited by conformational peptides derived from the human T-cell leukemia virus type 1 (HTLV-1) gp21 envelope glycoprotein spanning residues 347-374. We used a novel template design and a unique synthetic approach to construct two peptides (WCCR2T and CCR2T) that would each assemble into a triple helical coiled coil conformation mimicking the gp21 crystal structure. The peptide B-cell epitopes were grafted onto the epsilon side chains of three lysyl residues on a template backbone construct consisting of the sequence acetyl-XGKGKGKGCONH2 (where X represents the tetanus toxoid promiscuous T cell epitope (TT) sequence 580-599). Leucine substitutions were introduced at the a and d positions of the CCR2T sequence to maximize helical character and stability as shown by circular dichroism and guanidinium hydrochloride studies. Serum from an HTLV-1-infected patient was able to recognize the selected epitopes by enzyme-linked immunosorbent assay (ELISA). Mice immunized with the wild-type sequence (WCCR2T) and the mutant sequence (CCR2T) elicited high antibody titers that were capable of recognizing the native protein as shown by flow cytometry and whole virus ELISA. Sera and purified antibodies from immunized mice were able to reduce the formation of syncytia induced by the envelope glycoprotein of HTLV-1, suggesting that antibodies directed against the coiled coil region of gp21 are capable of disrupting cell-cell fusion. Our results indicate that these peptides represent potential candidates for use in a peptide vaccine against HTLV-1.

  9. Nonlinear PCA: characterizing interactions between modes of brain activity.

    OpenAIRE

    Friston, K; Phillips, J; Chawla, D; Büchel, C

    2000-01-01

    This paper presents a nonlinear principal component analysis (PCA) that identifies underlying sources causing the expression of spatial modes or patterns of activity in neuroimaging time-series. The critical aspect of this technique is that, in relation to conventional PCA, the sources can interact to produce (second-order) spatial modes that represent the modulation of one (first-order) spatial mode by another. This nonlinear PCA uses a simple neural network architecture that embodies a spec...

  10. Fuel-coolant interactions in a jet contact mode

    International Nuclear Information System (INIS)

    Konishi, K.; Isozaki, M.; Imahori, S.; Kondo, S.; Furutani, A.; Brear, D.J.

    1994-01-01

    Molten fuel-coolant interactions in a jet contact mode was studied with respect to the safety of liquid-metal-cooled fast reactors (LMFRs). From a series of molten Wood's metal (melting point: 79 deg. C, density: -8400 kg/m 3 ) jet-water interaction experiments, several distinct modes of interaction behaviors were observed for various combinations of initial temperature conditions of the two fluids. A semi-empirical model for a minimum film boiling temperature criterion was developed and used to reasonably explain the different interaction modes. It was concluded that energetic jet-water interactions are only possible under relatively narrow initial thermal conditions. Preliminary extrapolation of the present results in an oxide fuel-sodium system suggests that mild interactions with short breakup length and coolable debris formation should be most likely in LMFRs. (author)

  11. A typology of coastal researchers’ modes of interactions with stakeholders

    Directory of Open Access Journals (Sweden)

    Milligan Jessica

    2004-09-01

    Full Text Available A feature of the management of natural resources in the coastal zone is that it involves multiple stakeholders. It has been suggested that the effectiveness of coastal management relies on the cooperation of this multitude of stakeholders in decision-making. This study reports on the findings of an investigation into the modes of interaction used by coastal researchers to communicate with stakeholders. A qualitative research methodology was used through both telephone and in-depth face-toface interviews to elucidate the mechanisms of interaction and, in turn, produce a typology of interaction modes. It was found that there were five main modes of interaction: Limited; Mediator Achieved; Key Stakeholder; Full Interaction and Mixed and that the discipline area in which the researcher worked did not dictate their preferred mode of interaction. It was concluded that although there are a number of limitations to effective participation, these interactions have significant implications for meaningful participation in the management of coastal resources.

  12. Directional interacting whispering-gallery modes in coupled dielectric microdisks

    International Nuclear Information System (INIS)

    Ryu, Jung-Wan; Lee, Soo-Young; Kim, Chil-Min; Park, Young-Jai

    2006-01-01

    We study the optical interaction in a coupled dielectric microdisks by investigating the splitting of resonance positions of interacting whispering-gallery modes (WGM's) and their pattern change, depending on the distance between the microdisks. It is shown that the interaction between the WGM's with odd parity about the y axis becomes appreciable at a distance less than a wavelength and causes directional emissions of the resulting interacting WGM's. The directionality of the interacting WGM's can be understood in terms of an effective boundary deformation in ray dynamical analysis. We also discuss the oscillation of the splitting when the distance is greater than a wavelength

  13. Quark-interaction in the 1-mode QCD

    International Nuclear Information System (INIS)

    Wendel, M.H.

    1989-01-01

    We explain first the field operators in the N-mode representation. We choose the Hamiltonian formulation in temporal gauge. We come then across an intrinsic instability of the canonical formulation of the N-mode idea. The following chapter deals with the overvoming of the instability. It is shown that the generator of the instability carries simultaneously already the dynamical element of its cancelling. This transformation, which performs this, is of the BCS type and contains as quasi particles just the mesonic hybrid states already mentioned for instance by Pottinger and Warner. We come thereby across a second instability, which occurs in the limit of vanishing chromomagnetic contribution B 2 . The chapter concludes with a variational analysis of the transformed Hamiltonian operator. The following chapter deals first with the phenomenological results on the existence of hybride mesons and other oxotic quark-gluon states, as they occur in canonical way in the N-mode model with BCS transformations. We show for this reason, how the transformation can be extended to the spin degrees of freedom and calculate the resulting pairing interaction energies of quarks and antiquarks. In the last chapter we finally enter possible many-mode formulations and sketch thereby methods, which allow in a relatively simple way to conclude from the hitherto 1-mode results to certain N-mode analoga. (orig./HSI) [de

  14. Stochastic modeling of mode interactions via linear parabolized stability equations

    Science.gov (United States)

    Ran, Wei; Zare, Armin; Hack, M. J. Philipp; Jovanovic, Mihailo

    2017-11-01

    Low-complexity approximations of the Navier-Stokes equations have been widely used in the analysis of wall-bounded shear flows. In particular, the parabolized stability equations (PSE) and Floquet theory have been employed to capture the evolution of primary and secondary instabilities in spatially-evolving flows. We augment linear PSE with Floquet analysis to formally treat modal interactions and the evolution of secondary instabilities in the transitional boundary layer via a linear progression. To this end, we leverage Floquet theory by incorporating the primary instability into the base flow and accounting for different harmonics in the flow state. A stochastic forcing is introduced into the resulting linear dynamics to model the effect of nonlinear interactions on the evolution of modes. We examine the H-type transition scenario to demonstrate how our approach can be used to model nonlinear effects and capture the growth of the fundamental and subharmonic modes observed in direct numerical simulations and experiments.

  15. DIPA-family coiled-coils bind conserved isoform-specific head domain of p120-catenin family: potential roles in hydrocephalus and heterotopia.

    Science.gov (United States)

    Markham, Nicholas O; Doll, Caleb A; Dohn, Michael R; Miller, Rachel K; Yu, Huapeng; Coffey, Robert J; McCrea, Pierre D; Gamse, Joshua T; Reynolds, Albert B

    2014-09-01

    p120-catenin (p120) modulates adherens junction (AJ) dynamics by controlling the stability of classical cadherins. Among all p120 isoforms, p120-3A and p120-1A are the most prevalent. Both stabilize cadherins, but p120-3A is preferred in epithelia, whereas p120-1A takes precedence in neurons, fibroblasts, and macrophages. During epithelial-to-mesenchymal transition, E- to N-cadherin switching coincides with p120-3A to -1A alternative splicing. These isoforms differ by a 101-amino acid "head domain" comprising the p120-1A N-terminus. Although its exact role is unknown, the head domain likely mediates developmental and cancer-associated events linked to p120-1A expression (e.g., motility, invasion, metastasis). Here we identified delta-interacting protein A (DIPA) as the first head domain-specific binding partner and candidate mediator of isoform 1A activity. DIPA colocalizes with AJs in a p120-1A- but not 3A-dependent manner. Moreover, all DIPA family members (Ccdc85a, Ccdc85b/DIPA, and Ccdc85c) interact reciprocally with p120 family members (p120, δ-catenin, p0071, and ARVCF), suggesting significant functional overlap. During zebrafish neural tube development, both knockdown and overexpression of DIPA phenocopy N-cadherin mutations, an effect bearing functional ties to a reported mouse hydrocephalus phenotype associated with Ccdc85c. These studies identify a novel, highly conserved interaction between two protein families that may participate either individually or collectively in N-cadherin-mediated development. © 2014 Markham et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  16. Shock/vortex interaction and vortex-breakdown modes

    Science.gov (United States)

    Kandil, Osama A.; Kandil, H. A.; Liu, C. H.

    1992-01-01

    Computational simulation and study of shock/vortex interaction and vortex-breakdown modes are considered for bound (internal) and unbound (external) flow domains. The problem is formulated using the unsteady, compressible, full Navier-Stokes (NS) equations which are solved using an implicit, flux-difference splitting, finite-volume scheme. For the bound flow domain, a supersonic swirling flow is considered in a configured circular duct and the problem is solved for quasi-axisymmetric and three-dimensional flows. For the unbound domain, a supersonic swirling flow issued from a nozzle into a uniform supersonic flow of lower Mach number is considered for quasi-axisymmetric and three-dimensional flows. The results show several modes of breakdown; e.g., no-breakdown, transient single-bubble breakdown, transient multi-bubble breakdown, periodic multi-bubble multi-frequency breakdown and helical breakdown.

  17. Structural mode significance using INCA. [Interactive Controls Analysis computer program

    Science.gov (United States)

    Bauer, Frank H.; Downing, John P.; Thorpe, Christopher J.

    1990-01-01

    Structural finite element models are often too large to be used in the design and analysis of control systems. Model reduction techniques must be applied to reduce the structural model to manageable size. In the past, engineers either performed the model order reduction by hand or used distinct computer programs to retrieve the data, to perform the significance analysis and to reduce the order of the model. To expedite this process, the latest version of INCA has been expanded to include an interactive graphical structural mode significance and model order reduction capability.

  18. Analysis of event-mode data with Interactive Data Language

    International Nuclear Information System (INIS)

    De Young, P.A.; Hilldore, B.B.; Kiessel, L.M.; Peaslee, G.F.

    2003-01-01

    We have developed an analysis package for event-mode data based on Interactive Data Language (IDL) from Research Systems Inc. This high-level language is high speed, array oriented, object oriented, and has extensive visual (multi-dimensional plotting) and mathematical functions. We have developed a general framework, written in IDL, for the analysis of a variety of experimental data that does not require significant customization for each analysis. Unlike many traditional analysis package, spectra and gates are applied after data are read and are easily changed as analysis proceeds without rereading the data. The events are not sequentially processed into predetermined arrays subject to predetermined gates

  19. Destabilization of contained interacting modes by fusion products

    International Nuclear Information System (INIS)

    Penn, G.; Riconda, C.; Coppi, B.

    1996-01-01

    The instability related to the interaction between high-frequency open-quotes contained modesclose quotes and the fusion products population in a toroidal configuration is studied. Emphasis is placed on the dependence of the growth rate on finite Larmor radius effects of the fusion products, the characteristics of the particle distribution function, and factors, such as the magnetic drift velocity and bounce-averaging, related to the inhomogeneity of the magnetic field in a toroidal configuration. In particular, a sufficient degree of anisotropy in the energetic particle distribution is required in order to have a positive growth rate for realistic parameters. Only a small region of phase space is involved in the resonant interactions associated with the considered modes. We consider first the limit where the growth rate is larger than the bounce frequency (local approximation), that is the simplest case by which it is possible to identify the regions of phase space that are involved in the instability. Another evaluation of the growth rate is given in the case, that we consider realistic, where γ is comparable to the average bounce frequency of the interacting particles. We solve for γ by integrating the linearized Vlasov equation over the unperturbed particle orbits, and by reducing the integrals through saddle-point approximations

  20. Interaction of discrete and continuous boundary layer modes to cause transition

    International Nuclear Information System (INIS)

    Durbin, Paul A.; Zaki, Tamer A.; Liu Yang

    2009-01-01

    The interaction of discrete and continuous Orr-Sommerfeld modes in a boundary layer is studied by computer simulation. The discrete mode is an unstable Tollmien-Schlichting wave. The continuous modes generate jet-like disturbances inside the boundary layer. Either mode alone does not cause transition to turbulence; however, the interaction between them does. The continuous mode jets distort the discrete modes, producing Λ shaped vortices. Breakdown to turbulence is subsequent. The lateral spacing of the Λ's is sometimes the same as the wavelength of the continuous mode, sometimes it differs, depending on the ratio of wavelength to boundary layer thickness.

  1. Delivery of AAV2/9-microdystrophin genes incorporating helix 1 of the coiled-coil motif in the C-terminal domain of dystrophin improves muscle pathology and restores the level of α1-syntrophin and α-dystrobrevin in skeletal muscles of mdx mice.

    Science.gov (United States)

    Koo, Taeyoung; Malerba, Alberto; Athanasopoulos, Takis; Trollet, Capucine; Boldrin, Luisa; Ferry, Arnaud; Popplewell, Linda; Foster, Helen; Foster, Keith; Dickson, George

    2011-11-01

    Duchenne muscular dystrophy is a severe X-linked inherited muscle wasting disorder caused by mutations in the dystrophin gene. Adeno-associated virus (AAV) vectors have been extensively used to deliver genes efficiently for dystrophin expression in skeletal muscles. To overcome limited packaging capacity of AAV vectors (pathology of dystrophic mdx mice. However, the CT domain of dystrophin is thought to recruit part of the dystrophin-associated protein complex, which acts as a mediator of signaling between extracellular matrix and cytoskeleton in muscle fibers. In this study, we extended the ΔR4-23/ΔCT microdystrophin by incorporating helix 1 of the coiled-coil motif in the CT domain of dystrophin (MD2), which contains the α1-syntrophin and α-dystrobrevin binding sites. Intramuscular injection of AAV2/9 expressing CT domain-extended microdystrophin showed efficient dystrophin expression in tibialis anterior muscles of mdx mice. The presence of the CT domain of dystrophin in MD2 increased the recruitment of α1-syntrophin and α-dystrobrevin at the sarcolemma and significantly improved the muscle resistance to lengthening contraction-induced muscle damage in the mdx mice compared with MD1. These results suggest that the incorporation of helix 1 of the coiled-coil motif in the CT domain of dystrophin to the microdystrophins will substantially improve their efficiency in restoring muscle function in patients with Duchenne muscular dystrophy.

  2. Choice of Human-Computer Interaction Mode in Stroke Rehabilitation.

    Science.gov (United States)

    Mousavi Hondori, Hossein; Khademi, Maryam; Dodakian, Lucy; McKenzie, Alison; Lopes, Cristina V; Cramer, Steven C

    2016-03-01

    Advances in technology are providing new forms of human-computer interaction. The current study examined one form of human-computer interaction, augmented reality (AR), whereby subjects train in the real-world workspace with virtual objects projected by the computer. Motor performances were compared with those obtained while subjects used a traditional human-computer interaction, that is, a personal computer (PC) with a mouse. Patients used goal-directed arm movements to play AR and PC versions of the Fruit Ninja video game. The 2 versions required the same arm movements to control the game but had different cognitive demands. With AR, the game was projected onto the desktop, where subjects viewed the game plus their arm movements simultaneously, in the same visual coordinate space. In the PC version, subjects used the same arm movements but viewed the game by looking up at a computer monitor. Among 18 patients with chronic hemiparesis after stroke, the AR game was associated with 21% higher game scores (P = .0001), 19% faster reaching times (P = .0001), and 15% less movement variability (P = .0068), as compared to the PC game. Correlations between game score and arm motor status were stronger with the AR version. Motor performances during the AR game were superior to those during the PC game. This result is due in part to the greater cognitive demands imposed by the PC game, a feature problematic for some patients but clinically useful for others. Mode of human-computer interface influences rehabilitation therapy demands and can be individualized for patients. © The Author(s) 2015.

  3. Southern annular mode: tropical-extratropical interactions and impacts

    CSIR Research Space (South Africa)

    Fauchereau, N

    2009-09-01

    Full Text Available In this study the authors investigate in particular its links with the Madden Julian Oscillation and ENSO, the dominant modes of tropical atmospheric variability at the intraseasonal and interannual timescales, respectively. It is showed here that...

  4. Geometric phase due to orbit-orbit interaction: rotating LP11 modes in a two-mode fiber

    Science.gov (United States)

    Pradeep Chakravarthy, T.; Naik, Dinesh N.; Viswanathan, Nirmal K.

    2017-10-01

    Accumulation of geometric phase due to non-coplanar propagation of higher-order modes in an optical fiber is experimentally demonstrated. Vertically-polarized LP11 fiber mode, excited in a horizontally-held, torsion-free, step-index, two-mode optical fiber, rotates due to asymmetry in the propagating k-vectors, arising due to off-centered beam location at the fiber input. Perceiving the process as due to rotation of the fiber about the off-axis launch position, the orbital Berry phase accumulation upon scanning the launch position in a closed-loop around the fiber axis manifests as rotational Doppler effect, a consequence of orbit-orbit interaction. The anticipated phase accumulation as a function of the input launch position, observed through interferometry is connected to the mode rotation angle, quantified using the autocorrelation method.

  5. Cluster observations of trapped ions interacting with magnetosheath mirror modes

    Czech Academy of Sciences Publication Activity Database

    Souček, Jan; Escoubet, C. P.

    2011-01-01

    Roč. 29, - (2011), s. 1049-1060 ISSN 0992-7689 Institutional research plan: CEZ:AV0Z30420517 Keywords : mirror mode waves * trapped particles * magnetosheath ions Subject RIV: BL - Plasma and Gas Discharge Physics Impact factor: 1.842, year: 2011 http://www.ann-geophys.net/29/1049/2011/angeo-29-1049-2011.pdf

  6. Experimental evidence and theory for the interaction of superthermal electrons with the MHD modes during ECRH

    International Nuclear Information System (INIS)

    Lazaros, Avrilios

    2000-01-01

    The interaction of ECRH with the m/n=2/1 tearing mode, which was observed in toroidal plasmas, is attributed to the superthermal electrons which are produced on the EC resonance by the ECRH. Superthermal electrons diffusing across the q=2 surface, exchange power with the m/n=2/1 MHD mode which is either suppressed or enhanced. When the EC resonance is outside the rational surface, the mode is always suppressed. When the EC resonance is inside the rational surface, modes with large amplitude are enhanced while modes with small amplitude are suppressed. (author)

  7. Interaction of the ATA beam with the TM030 mode of the accelerating cells

    International Nuclear Information System (INIS)

    Neil, V.K.

    1985-01-01

    The interaction of the electron beam in the Advanced Test Accelerator with an azimuthally symmetric mode of the accelerating cells is investigated theoretically. The interaction possibly could cause modulation of the beam current at the resonant frequency of the mode. Values of the shunt impedance and Q value of the mode were obtained from previous measurement and analysis. Lagranian hydrodynamics is employed and a WKB solution to the equation of motion is obtained. Results indicate that the interaction will not be a problem in the accelerator

  8. Microwave-plasma interactions studied via mode diagnostics in ALPHA

    Energy Technology Data Exchange (ETDEWEB)

    Friesen, T., E-mail: tim.friesen@cern.ch [University of Calgary, Department of Physics and Astronomy (Canada); Andresen, G. B. [Aarhus University, Department of Physics and Astronomy (Denmark); Ashkezari, M. D. [Simon Fraser University, Department of Physics (Canada); Baquero-Ruiz, M. [University of California, Department of Physics (United States); Bertsche, W. [Swansea University, Department of Physics (United Kingdom); Bowe, P. D. [Aarhus University, Department of Physics and Astronomy (Denmark); Butler, E. [CERN, Physics Department (Switzerland); Cesar, C. L. [Universidade Federal do Rio de Janeiro, Instituto de Fisica (Brazil); Chapman, S. [University of California, Department of Physics (United States); Charlton, M.; Eriksson, S. [Swansea University, Department of Physics (United Kingdom); Fajans, J. [University of California, Department of Physics (United States); Fujiwara, M. C. [University of Calgary, Department of Physics and Astronomy (Canada); Gill, D. R. [TRIUMF (Canada); Gutierrez, A. [University of British Columbia, Department of Physics and Astronomy (Canada); Hangst, J. S. [Aarhus University, Department of Physics and Astronomy (Denmark); Hardy, W. N. [University of British Columbia, Department of Physics and Astronomy (Canada); Hayano, R. S. [University of Tokyo, Department of Physics (Japan); Hayden, M. E. [Simon Fraser University, Department of Physics (Canada); Humphries, A. J. [Swansea University, Department of Physics (United Kingdom); Collaboration: ALPHA Collaboration; and others

    2012-12-15

    The goal of the ALPHA experiment is the production, trapping and spectroscopy of antihydrogen. A direct comparison of the ground state hyperfine spectra in hydrogen and antihydrogen has the potential to be a high-precision test of CPT symmetry. We present a novel method for measuring the strength of a microwave field for hyperfine spectroscopy in a Penning trap. This method incorporates a non-destructive plasma diagnostic system based on electrostatic modes within an electron plasma. We also show how this technique can be used to measure the cyclotron resonance of the electron plasma, which can potentially serve as a non-destructive measurement of plasma temperature.

  9. Cluster observations of trapped ions interacting with magnetosheath mirror modes

    Directory of Open Access Journals (Sweden)

    J. Soucek

    2011-06-01

    Full Text Available Mirror modes are among the most intense low frequency plasma wave phenomena observed in the magnetosheaths of magnetized planets. They appear as large amplitude non-propagating fluctuations in the magnetic field magnitude and plasma density. These structures are widely accepted to represent a non-linear stage of the mirror instability, dominant in plasmas with large ion beta and a significant ion temperature anisotropy T⊥/T∥>1. It has long been recognized that the mirror instability both in the linear and non-linear stage is a kinetic process and that the behavior of resonant particles at small parallel velocities is crucial for its development and saturation. While the dynamics of the instability and the effect of trapped particles have been studied extensively in theoretical models and numerical simulations, only spurious observations of the trapped ions were published to date. In this work we used data from the Cluster spacecraft to perform the first detailed experimental study of ion velocity distribution associated with mirror mode oscillations. We show a conclusive evidence for the predicted cooling of resonant ions at small parallel velocities and heating of trapped ions at intermediate pitch angles.

  10. Reduction of Flight Control System/Structural Mode Interaction, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — A novel approach is proposed for reducing the degree of interaction of a high gain flight control system with the airframe structural vibration modes, representing a...

  11. Interaction mode between methylene blue-Sm(III) complex and ...

    African Journals Online (AJOL)

    Spectroscopic and viscosity methods were applied to investigate the interaction between methylene blue (MB)-Sm(III) complex and herring sperm DNA by using acridine orange as a spectral probe in Tris-HCl buffer (pH 7.40). By means of molar ratio method, the binding ratios between MB-Sm(III)and DNA were determined ...

  12. Protein prenylation: a new mode of host-pathogen interaction.

    Science.gov (United States)

    Amaya, Moushimi; Baranova, Ancha; van Hoek, Monique L

    2011-12-09

    Post translational modifications are required for proteins to be fully functional. The three step process, prenylation, leads to farnesylation or geranylgeranylation, which increase the hydrophobicity of the prenylated protein for efficient anchoring into plasma membranes and/or organellar membranes. Prenylated proteins function in a number of signaling and regulatory pathways that are responsible for basic cell operations. Well characterized prenylated proteins include Ras, Rac and Rho. Recently, pathogenic prokaryotic proteins, such as SifA and AnkB, have been shown to be prenylated by eukaryotic host cell machinery, but their functions remain elusive. The identification of other bacterial proteins undergoing this type of host-directed post-translational modification shows promise in elucidating host-pathogen interactions to develop new therapeutics. This review incorporates new advances in the study of protein prenylation into a broader aspect of biology with a focus on host-pathogen interaction. Copyright © 2011 Elsevier Inc. All rights reserved.

  13. G-mode magnetic force microscopy: Separating magnetic and electrostatic interactions using big data analytics

    Energy Technology Data Exchange (ETDEWEB)

    Collins, Liam; Belianinov, Alex; Kalinin, Sergei V.; Jesse, Stephen [Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 (United States); Institute for Functional Imaging of Materials, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 (United States); Proksch, Roger [Asylum Research, An Oxford Instruments Company, Santa Barbara, California 93117 (United States); Zuo, Tingting [State Key Laboratory for Advanced Metals and Materials, University of Science and Technology Beijing, Beijing 100083 (China); Deptarment of Materials Science and Engineering, The University of Tennessee, Knoxville, Tennessee 37996-2200 (United States); Zhang, Yong [State Key Laboratory for Advanced Metals and Materials, University of Science and Technology Beijing, Beijing 100083 (China); Liaw, Peter K. [Deptarment of Materials Science and Engineering, The University of Tennessee, Knoxville, Tennessee 37996-2200 (United States)

    2016-05-09

    In this work, we develop a full information capture approach for Magnetic Force Microscopy (MFM), referred to as generalized mode (G-Mode) MFM. G-Mode MFM acquires and stores the full data stream from the photodetector, captured at sampling rates approaching the intrinsic photodiode limit. The data can be subsequently compressed, denoised, and analyzed, without information loss. Here, G-Mode MFM is implemented and compared to the traditional heterodyne-based MFM on model systems, including domain structures in ferromagnetic Yttrium Iron Garnet and the electronically and magnetically inhomogeneous high entropy alloy, CoFeMnNiSn. We investigate the use of information theory to mine the G-Mode MFM data and demonstrate its usefulness for extracting information which may be hidden in traditional MFM modes, including signatures of nonlinearities and mode-coupling phenomena. Finally, we demonstrate detection and separation of magnetic and electrostatic tip-sample interactions from a single G-Mode image, by analyzing the entire frequency response of the cantilever. G-Mode MFM is immediately implementable on any atomic force microscopy platform and as such is expected to be a useful technique for probing spatiotemporal cantilever dynamics and mapping material properties, as well as their mutual interactions.

  14. Interaction of a putative BH3 domain of clusterin with anti-apoptotic Bcl-2 family proteins as revealed by NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Dong-Hwa; Ha, Ji-Hyang [Medical Proteomics Research Center, KRIBB, Daejeon 305-806 (Korea, Republic of); Kim, Yul [Department of Bio and Brain Engineering, KAIST, Daejeon 305-701 (Korea, Republic of); Bae, Kwang-Hee [Medical Proteomics Research Center, KRIBB, Daejeon 305-806 (Korea, Republic of); Park, Jae-Yong [Department of Physiology, Institute of Health Science, School of Medicine, Gyeongsang National University, Jinju, Gyeongnam 660-751 (Korea, Republic of); Choi, Wan Sung [Department of Anatomy and Neurobiology, Institute of Health Science, School of Medicine, Gyeongsang National University, Jinju, Gyeongnam 660-751 (Korea, Republic of); Yoon, Ho Sup [Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637511 (Singapore); Park, Sung Goo; Park, Byoung Chul [Medical Proteomics Research Center, KRIBB, Daejeon 305-806 (Korea, Republic of); Yi, Gwan-Su, E-mail: gsyi@kaist.ac.kr [Department of Bio and Brain Engineering, KAIST, Daejeon 305-701 (Korea, Republic of); Chi, Seung-Wook, E-mail: swchi@kribb.re.kr [Medical Proteomics Research Center, KRIBB, Daejeon 305-806 (Korea, Republic of)

    2011-05-20

    Highlights: {yields} Identification of a conserved BH3 motif in C-terminal coiled coil region of nCLU. {yields} The nCLU BH3 domain binds to BH3 peptide-binding grooves in both Bcl-X{sub L} and Bcl-2. {yields} A conserved binding mechanism of nCLU BH3 and the other pro-apoptotic BH3 peptides with Bcl-X{sub L}. {yields} The absolutely conserved Leu323 and Asp328 of nCLU BH3 domain are critical for binding to Bcl-X{sub L.} {yields} Molecular understanding of the pro-apoptotic function of nCLU as a novel BH3-only protein. -- Abstract: Clusterin (CLU) is a multifunctional glycoprotein that is overexpressed in prostate and breast cancers. Although CLU is known to be involved in the regulation of apoptosis and cell survival, the precise molecular mechanism underlying the pro-apoptotic function of nuclear CLU (nCLU) remains unclear. In this study, we identified a conserved BH3 motif in C-terminal coiled coil (CC2) region of nCLU by sequence analysis and characterized the molecular interaction of the putative nCLU BH3 domain with anti-apoptotic Bcl-2 family proteins by nuclear magnetic resonance (NMR) spectroscopy. The chemical shift perturbation data demonstrated that the nCLU BH3 domain binds to pro-apoptotic BH3 peptide-binding grooves in both Bcl-X{sub L} and Bcl-2. A structural model of the Bcl-X{sub L}/nCLU BH3 peptide complex reveals that the binding mode is remarkably similar to those of other Bcl-X{sub L}/BH3 peptide complexes. In addition, mutational analysis confirmed that Leu323 and Asp328 of nCLU BH3 domain, absolutely conserved in the BH3 motifs of BH3-only protein family, are critical for binding to Bcl-X{sub L}. Taken altogether, our results suggest a molecular basis for the pro-apoptotic function of nCLU by elucidating the residue specific interactions of the BH3 motif in nCLU with anti-apoptotic Bcl-2 family proteins.

  15. Study on the Implementation of Interaction Teaching Mode in Distance Education

    Science.gov (United States)

    Zhou, Chunyu; Xu, Zhenhui

    2015-01-01

    By analyzing the learning characteristics of learners and the features of interactive teaching in distance education, this paper proposes the curriculum implementation subject of network education, namely objects multi-directional interaction teaching mode, so as to improve teaching effectiveness and achieve teaching objectives to ensure the…

  16. Mode of Antifungal Drugs Interaction with Cytochrome P- 450

    Directory of Open Access Journals (Sweden)

    M- Mahmodian

    1991-07-01

    Full Text Available Computer was used to identify the interactions of substrates and antifungal drugs with the enzyme, Cytochrome P-450; and then Molplot.bas computer program was applied to get three dimensional figures of 5-hydroxy camphor.oxidation products of camphor analogues, and antifungal drugs.Cartesian characteristics of atoms building molecules, are taken from Buildz. for program, which can calculate X,Y,Z coordinates of atoms by Zmatrix data. The other program which can calculate X,Y,Z coordinates, using fractional characteristics, is the Coord, for program that, gives our cartesian characteristics of the atoms of molecule, then by using these data, we obtain three dimensional figures and distance between active atoms in compounds under consideration. Results show that distance between two oxygen atoms in 5-exo-hydroxy- camphor and the other compounds obtained from oxidation of camphor analogues, with the distance of two oxygen atoms in antifungal compounds under discussion are equal. Therefore, we can conclude that, the antifungal molecule also interacts with enzyme's active site, by its own sites, in a similar manner to the 5-hydroxy camphor molecule, which is:"n1. Nitrogen atom (N of Imidazole and Triazole ring in antifungal molecule with Iron atom in heam molecule belonging to Cytochrome P-450 enzyme, are coordinated."n2. The other atoms such as : 0,S or N in structure of the antifungal drug are coordinated with hydrogen atom of hydroxyl group belong ing to Tyr-96 in the structure of enzyme, forming hydrogen bonding.

  17. The nonlinear interaction of convection modes in a box of a saturated porous medium

    Science.gov (United States)

    Florio, Brendan J.; Bassom, Andrew P.; Fowkes, Neville; Judd, Kevin; Stemler, Thomas

    2015-05-01

    A plethora of convection modes may occur within a confined box of porous medium when the associated dimensionless Rayleigh number R is above some critical value dependent on the geometry. In many cases the crucial Rayleigh number Rc for onset is different for each mode, and in practice the mode with the lowest associated Rc is likely to be the dominant one. For particular sizes of box, however, it is possible for multiple modes (typically three) to share a common Rc. For box shapes close to these special geometries the modes interact and compete nonlinearly near the onset of convection. Here this mechanism is explored and it is shown that generically the dynamics of the competition takes on one of two possible structures. A specific example of each is described, while the general properties of the system enables us to compare our results with some previous calculations for particular box dimensions.

  18. Construction and Implementation of Teaching Mode for Digital Mapping based on Interactive Micro-course Technology

    Directory of Open Access Journals (Sweden)

    Ning Gao

    2018-02-01

    Full Text Available The era of “Internet + education” has caused reforms in teaching ideas, teaching modes, and learning styles. The emergence of micro-course technology provides new strategies for integrating learning styles. Task-driven digital mapping teaching, known as traditional classroom organization, has poor teaching effect due to single learning style and strategy. A new teaching mode for digital mapping was constructed in this study based on micro-course technology by combining interactive micro-course technology and digital mapping teaching to adapt to the demands of modern teaching. This teaching mode mainly included four modules, namely, micro-courseware, micro-video, micro-exercise, and micro-examination. It realized the hierarchical teaching of knowledge points in digital mapping course, simplification of basic principles, simulation of engineering cases, and self-evaluation of learning outcomes. The teaching mode was applied to 114 students from the Mapping Engineering Department of Henan University of Urban Construction. Results indicate that the proposed teaching mode based on interactive micro-course technology promoting the independent after-class learning of the students, stimulating their learning enthusiasm, enhancing their practical abilities of the students, and improving the effect of teaching. This mode of teaching provides a new concept for the teaching mode reform of other courses in mapping engineering.

  19. A testis-specific and testis developmentally regulated tumor protein D52 (TPD52)-like protein TPD52L3/hD55 interacts with TPD52 family proteins

    International Nuclear Information System (INIS)

    Cao Qinhong; Chen Jie; Zhu Li; Liu Yun; Zhou Zuomin; Sha Jiahao; Wang Shui; Li Jianmin

    2006-01-01

    Tumor protein D52-like proteins (TPD52) are small coiled-coil motif bearing proteins that were first identified in breast cancer. TPD52 and related proteins have been implicated in cell proliferation, apoptosis, and vesicle trafficking. To date, three human TPD52 members had been identified, named hD52 (TPD52), hD53 (TPD52L1), and hD54 (TPD52L2). The most important characteristic of the protein family is a highly conserved coiled-coil motif that is required for homo- and heteromeric interaction with other TPD52-like proteins. Herein, we identified a novel TPD52-like sequence (TPD52L3, or hD55) in human testis using cDNA microarray. Sequence analysis of the deduced protein suggests that hD55 contains a coiled-coil motif and is highly conserved compared with other TPD52-like sequences. Yeast two-hybrid and GST pull-down assays revealed that hD55 interacts with hD52, hD53, hD54, and itself. cDNA microarray detection found that hD55 was expressed at 5.6-fold higher levels in adult testis than in fetal testis. Additionally, the expression profile shows that hD55 is testis-specific, indicating a potential role for hD55 in testis development and spermatogenesis

  20. A high-order mode extended interaction klystron at 0.34 THz

    Science.gov (United States)

    Wang, Dongyang; Wang, Guangqiang; Wang, Jianguo; Li, Shuang; Zeng, Peng; Teng, Yan

    2017-02-01

    We propose the concept of high-order mode extended interaction klystron (EIK) at the terahertz band. Compared to the conventional fundamental mode EIK, it operates at the TM31-2π mode, and its remarkable advantage is to obtain a large structure and good performance. The proposed EIK consists of five identical cavities with five gaps in each cavity. The method is discussed to suppress the mode competition and self-oscillation in the high-order mode cavity. Particle-in-cell simulation demonstrates that the EIK indeed operates at TM31-2π mode without self-oscillation while other modes are well suppressed. Driven by the electron beam with a voltage of 15 kV and a current of 0.3 A, the saturation gain of 43 dB and the output power of 60 W are achieved at the center frequency of 342.4 GHz. The EIK operating at high-order mode seems a promising approach to generate high power terahertz waves.

  1. Scaling and interaction of self-similar modes in models of high Reynolds number wall turbulence.

    Science.gov (United States)

    Sharma, A S; Moarref, R; McKeon, B J

    2017-03-13

    Previous work has established the usefulness of the resolvent operator that maps the terms nonlinear in the turbulent fluctuations to the fluctuations themselves. Further work has described the self-similarity of the resolvent arising from that of the mean velocity profile. The orthogonal modes provided by the resolvent analysis describe the wall-normal coherence of the motions and inherit that self-similarity. In this contribution, we present the implications of this similarity for the nonlinear interaction between modes with different scales and wall-normal locations. By considering the nonlinear interactions between modes, it is shown that much of the turbulence scaling behaviour in the logarithmic region can be determined from a single arbitrarily chosen reference plane. Thus, the geometric scaling of the modes is impressed upon the nonlinear interaction between modes. Implications of these observations on the self-sustaining mechanisms of wall turbulence, modelling and simulation are outlined.This article is part of the themed issue 'Toward the development of high-fidelity models of wall turbulence at large Reynolds number'. © 2017 The Author(s).

  2. On the magnon interaction in haematite. I - Magnon energy of optical mode.

    Science.gov (United States)

    Nagai, O.; Tanaka, T.; Bonavito, N. L.

    1972-01-01

    The effect of magnon interaction on the magnon energies of haematite was studied by the use of a recently developed random phase approximation. In this study, the spin Hamiltonian and the magnon energy were written in a power series of (1/S), where S denotes the magnitude of spin. It is known that the expression of magnon energy is rigorous up to the second term of this series. It is found that the optic mode energy is small if the free optic mode energy is small, which is contrary to Herbert's (1969) conclusion. This direct proportionality between the optic mode energy and the free optic mode energy was not confirmed in the higher order terms of 1/S.

  3. Particle-Hole Character of the Higgs and Goldstone Modes in Strongly Interacting Lattice Bosons

    Science.gov (United States)

    Di Liberto, M.; Recati, A.; Trivedi, N.; Carusotto, I.; Menotti, C.

    2018-02-01

    We study the low-energy excitations of the Bose-Hubbard model in the strongly interacting superfluid phase using a Gutzwiller approach. We extract the single-particle and single-hole excitation amplitudes for each mode and report emergent mode-dependent particle-hole symmetry on specific arc-shaped lines in the phase diagram connecting the well-known Lorentz-invariant limits of the Bose-Hubbard model. By tracking the in-phase particle-hole symmetric oscillations of the order parameter, we provide an answer to the long-standing question about the fate of the pure amplitude Higgs mode away from the integer-density critical point. Furthermore, we point out that out-of-phase symmetric oscillations in the gapless Goldstone mode are responsible for a full suppression of the condensate density oscillations. Possible detection protocols are also discussed.

  4. Selection of peptides interfering with protein-protein interaction.

    Science.gov (United States)

    Gaida, Annette; Hagemann, Urs B; Mattay, Dinah; Räuber, Christina; Müller, Kristian M; Arndt, Katja M

    2009-01-01

    Cell physiology depends on a fine-tuned network of protein-protein interactions, and misguided interactions are often associated with various diseases. Consequently, peptides, which are able to specifically interfere with such adventitious interactions, are of high interest for analytical as well as medical purposes. One of the most abundant protein interaction domains is the coiled-coil motif, and thus provides a premier target. Coiled coils, which consist of two or more alpha-helices wrapped around each other, have one of the simplest interaction interfaces, yet they are able to confer highly specific homo- and heterotypic interactions involved in virtually any cellular process. While there are several ways to generate interfering peptides, the combination of library design with a powerful selection system seems to be one of the most effective and promising approaches. This chapter guides through all steps of such a process, starting with library options and cloning, detailing suitable selection techniques and ending with purification for further down-stream characterization. Such generated peptides will function as versatile tools to interfere with the natural function of their targets thereby illuminating their down-stream signaling and, in general, promoting understanding of factors leading to specificity and stability in protein-protein interactions. Furthermore, peptides interfering with medically relevant proteins might become important diagnostics and therapeutics.

  5. SU(2) and SU(1,1) squeezing of interacting radiation modes

    International Nuclear Information System (INIS)

    Abdalla Sebawe, M.; Faisal El-Orany, A.A.; Perina, J.

    2000-01-01

    In this communication we discuss SU(1,1) and SU(2) squeezing of an interacting system of radiation modes in a quadratic medium in the framework of Lie algebra. We show that regardless of which state being initially considered, squeezing can be periodically generated. (authors)

  6. Explaining Student Interaction and Satisfaction: An Empirical Investigation of Delivery Mode Influence

    Science.gov (United States)

    Johnson, Zachary S.; Cascio, Robert; Massiah, Carolyn A.

    2014-01-01

    How interpersonal interactions within a course affect student satisfaction differently between face-to-face and online modes is an important research question to answer with confidence. Using students from a marketing course delivered face-to-face and online concurrently, our first study demonstrates that student-to-professor and…

  7. The mode coupling theory in the FDR-preserving field theory of interacting Brownian particles

    International Nuclear Information System (INIS)

    Kim, Bongsoo; Kawasaki, Kyozi

    2007-01-01

    We develop a renormalized perturbation theory for the dynamics of interacting Brownian particles, which preserves the fluctuation-dissipation relation order by order. We then show that the resulting one-loop theory gives a closed equation for the density correlation function, which is identical with that in the standard mode coupling theory. (fast track communication)

  8. Experimental investigation of the dynamics in a strongly interacting Fermi gas : collective modes and rotational properties

    International Nuclear Information System (INIS)

    Riedl, S.

    2009-01-01

    This thesis explores the dynamics in an ultracold strongly interacting Fermi gas. Therefore we perform measurements on collective excitation modes and rotational properties of the gas. The strongly interacting gas is realized using an optically trapped Fermi gas of 6 Li atoms, where the interactions can be tuned using a broad Feshbach resonance. Our measurements allow to test the equation of state of the gas, study the transition from hydrodynamic to collisionless behavior, reveal almost ideal hydrodynamic behavior in the nonsuperfluid phase, investigate the lifetime of angular momentum, and show superfluidity through the quenching of the moment of inertia. (author)

  9. ELM phenomenon as an interaction between bootstrap-current driven peeling modes and pressure-driven ballooning modes

    International Nuclear Information System (INIS)

    Saarelma, S.; Kurki-Suonio, T.; Guenter, S.; Zehrfeld, H.-P.

    2000-01-01

    An ELMy ASDEX Upgrade plasma equilibrium is reconstructed taking into account the bootstrap current. The peeling mode stability of the equilibrium is numerically analysed using the GATO [1] code, and it is found that the bootstrap current can drive the plasma peeling mode unstable. A high-n ballooning mode stability analysis of the equilibria revealed that, while destabilizing the peeling modes, the bootstrap current has a stabilizing effect on the ballooning modes. A combination of these two instabilities is a possible explanation for the type I ELM phenomenon. A triangularity scan showed that increasing triangularity stabilizes the peeling modes and can produce ELM-free periods observed in the experiments. (author)

  10. Multi-scale-nonlinear interactions among macro-MHD mode, micro-turbulence, and zonal flow

    International Nuclear Information System (INIS)

    Ishizawa, Akihiro; Nakajima, Noriyoshi

    2007-01-01

    This is the first numerical simulation demonstrating that macro-magnetohydrodynamic (macro-MHD) mode is exited as a result of multi-scale interaction in a quasi-steady equilibrium formed by a balance between zonal flow and micro-turbulence via reduced-two-fluid simulation. Only after obtaining the equilibrium which includes zonal flow and the turbulence caused by kinetic ballooning mode is this simulation of macro-MHD mode, double tearing mode, accomplished. In the quasi-steady equilibrium a macro-fluctuation which has the same helicity as that of double tearing mode is a part of the turbulence until it grows as a macro-MHD mode finally. When the macro-MHD grows it effectively utilize free energy of equilibrium current density gradient because of positive feedback loop between suppression of zonal flow and growth of the macro-fluctuation causing magnetic reconnection. Thus once the macro-MHD grows from the quasi-equilibrium, it does not go back. This simulation is more comparable with experimental observation of growing macro-fluctuation than traditional MHD simulation of linear instabilities in a static equilibrium. (author)

  11. XTACC3-XMAP215 association reveals an asymmetric interaction promoting microtubule elongation

    DEFF Research Database (Denmark)

    Mortuza, Gulnahar B; Cavazza, Tommaso; Garcia-Mayoral, Maria Flor

    2014-01-01

    215 (chTOG), dissecting the mechanism by which their interaction promotes microtubule elongation during spindle assembly. Using SAXS, we show that the TACC domain (TD) is an elongated structure that mediates the interaction with the C terminus of XMAP215. Our data suggest that one TD and two XMAP215...... molecules associate to form a four-helix coiled-coil complex. A hybrid methods approach was used to define the precise regions of the TACC heptad repeat and the XMAP215 C terminus required for assembly and functioning of the complex. We show that XTACC3 can induce the recruitment of larger amounts of XMAP...

  12. Black phosphorus saturable absorber for ultrafast mode-locked pulse laser via evanescent field interaction

    Energy Technology Data Exchange (ETDEWEB)

    Park, Kichul; Lee, Young Tack; Choi, Won-Kook; Song, Yong-Won [Center for Opto-electronic Materials and Devices, Korea Institute of Science and Technology, Seoul (Korea, Republic of); Lee, Junsu; Lee, Ju Han [School of Electrical and Computer Engineering, University of Seoul (Korea, Republic of)

    2015-12-15

    Black phosphorus, or BP, has found a lot of applications in recent years including photonics. The most recent studies have shown that the material has an excellent optical nonlinearity useful in many areas, one of which is in saturable absorption for passive mode-locking. A direct interaction scheme for mode-locking, however, has a potential to optically cause permanent damage to the already delicate material. Evanescent field interaction scheme has already been proven to be a useful method to prevent such danger for other 2-dimensional nanomaterials. In this report, we have utilized the evanescent field interaction to demonstrate that the optical nonlinear characteristics of BP is sufficiently strong to use in such an indirect interaction method. The successful demonstration of the passive mode-locking operation has generated pulses with the pulse duration, repetition rate, and time bandwidth product of 2.18 ps, 15.59 MHz, and 0.336, respectively. (copyright 2015 by WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  13. Information Entropy Squeezing of a Two-Level Atom Interacting with Two-Mode Coherent Fields

    Institute of Scientific and Technical Information of China (English)

    LIU Xiao-Juan; FANG Mao-Fa

    2004-01-01

    From a quantum information point of view we investigate the entropy squeezing properties for a two-level atom interacting with the two-mode coherent fields via the two-photon transition. We discuss the influences of the initial state of the system on the atomic information entropy squeezing. Our results show that the squeezed component number,squeezed direction, and time of the information entropy squeezing can be controlled by choosing atomic distribution angle,the relative phase between the atom and the two-mode field, and the difference of the average photon number of the two field modes, respectively. Quantum information entropy is a remarkable precision measure for the atomic squeezing.

  14. Engineering non-linear resonator mode interactions in circuit QED by continuous driving: Introduction

    Science.gov (United States)

    Pfaff, Wolfgang; Reagor, Matthew; Heeres, Reinier; Ofek, Nissim; Chou, Kevin; Blumoff, Jacob; Leghtas, Zaki; Touzard, Steven; Sliwa, Katrina; Holland, Eric; Krastanov, Stefan; Frunzio, Luigi; Devoret, Michel; Jiang, Liang; Schoelkopf, Robert

    2015-03-01

    High-Q microwave resonators show great promise for storing and manipulating quantum states in circuit QED. Using resonator modes as such a resource in quantum information processing applications requires the ability to manipulate the state of a resonator efficiently. Further, one must engineer appropriate coupling channels without spoiling the coherence properties of the resonator. We present an architecture that combines millisecond lifetimes for photonic quantum states stored in a linear resonator with fast measurement provided by a low-Q readout resonator. We demonstrate experimentally how a continuous drive on a transmon can be utilized to generate highly non-classical photonic states inside the high-Q resonator via effective nonlinear resonator mode interactions. Our approach opens new avenues for using modes of long-lived linear resonators in the circuit QED platform for quantum information processing tasks.

  15. Tablet-Based Functional MRI of the Trail Making Test: Effect of Tablet Interaction Mode

    Directory of Open Access Journals (Sweden)

    Mahta Karimpoor

    2017-10-01

    Full Text Available The Trail Making Test (TMT is widely used for assessing executive function, frontal lobe abilities, and visual motor skills. Part A of this pen-and-paper test (TMT-A involves linking numbers randomly distributed in space, in ascending order. Part B (TMT-B alternates between linking numbers and letters. TMT-B is more demanding than TMT-A, but the mental processing that supports the performance of this test remains incompletely understood. Functional MRI (fMRI may help to clarify the relationship between TMT performance and brain activity, but providing an environment that supports real-world pen-and-paper interactions during fMRI is challenging. Previously, an fMRI-compatible tablet system was developed for writing and drawing with two modes of interaction: the original cursor-based, proprioceptive approach, and a new mode involving augmented reality to provide visual feedback of hand position (VFHP for enhanced user interaction. This study characterizes the use of the tablet during fMRI of young healthy adults (n = 22, with half of the subjects performing TMT with VFHP and the other half performing TMT without VFHP. Activation maps for both TMT-A and TMT-B performance showed considerable overlap between the two tablet modes, and no statistically differences in brain activity were detected when contrasting TMT-B vs. TMT-A for the two tablet modes. Behavioral results also showed no statistically different interaction effects for TMT-B vs. TMT-A for the two tablet modes. Tablet-based TMT scores showed reasonable convergent validity with those obtained by administering the standard pen-and-paper TMT to the same subjects. Overall, the results suggest that despite the slightly different mechanisms involved for the two modes of tablet interaction, both are suitable for use in fMRI studies involving TMT performance. This study provides information for using tablet-based TMT methods appropriately in future fMRI studies involving patients and healthy

  16. Nonlinear mode interaction in equal-leg angle struts susceptible to cellular buckling.

    Science.gov (United States)

    Bai, L; Wang, F; Wadee, M A; Yang, J

    2017-11-01

    A variational model that describes the interactive buckling of a thin-walled equal-leg angle strut under pure axial compression is presented. A formulation combining the Rayleigh-Ritz method and continuous displacement functions is used to derive a system of differential and integral equilibrium equations for the structural component. Solving the equations using numerical continuation reveals progressive cellular buckling (or snaking) arising from the nonlinear interaction between the weak-axis flexural buckling mode and the strong-axis flexural-torsional buckling mode for the first time-the resulting behaviour being highly unstable. Physical experiments conducted on 10 cold-formed steel specimens are presented and the results show good agreement with the variational model.

  17. Modes of Interaction of Pleckstrin Homology Domains with Membranes: Toward a Computational Biochemistry of Membrane Recognition.

    Science.gov (United States)

    Naughton, Fiona B; Kalli, Antreas C; Sansom, Mark S P

    2018-02-02

    Pleckstrin homology (PH) domains mediate protein-membrane interactions by binding to phosphatidylinositol phosphate (PIP) molecules. The structural and energetic basis of selective PH-PIP interactions is central to understanding many cellular processes, yet the molecular complexities of the PH-PIP interactions are largely unknown. Molecular dynamics simulations using a coarse-grained model enables estimation of free-energy landscapes for the interactions of 12 different PH domains with membranes containing PIP 2 or PIP 3 , allowing us to obtain a detailed molecular energetic understanding of the complexities of the interactions of the PH domains with PIP molecules in membranes. Distinct binding modes, corresponding to different distributions of cationic residues on the PH domain, were observed, involving PIP interactions at either the "canonical" (C) and/or "alternate" (A) sites. PH domains can be grouped by the relative strength of their C- and A-site interactions, revealing that a higher affinity correlates with increased C-site interactions. These simulations demonstrate that simultaneous binding of multiple PIP molecules by PH domains contributes to high-affinity membrane interactions, informing our understanding of membrane recognition by PH domains in vivo. Copyright © 2017. Published by Elsevier Ltd.

  18. Modeling mode interactions in boundary layer flows via the Parabolized Floquet Equations

    OpenAIRE

    Ran, Wei; Zare, Armin; Hack, M. J. Philipp; Jovanović, Mihailo R.

    2017-01-01

    In this paper, we develop a linear model to study interactions between different modes in slowly-growing boundary layer flows. Our method consists of two steps. First, we augment the Blasius boundary layer profile with a disturbance field resulting from the linear Parabolized Stability Equations (PSE) to obtain the modified base flow; and, second, we combine Floquet analysis with the linear PSE to capture the spatial evolution of flow fluctuations. This procedure yields the Parabolized Floque...

  19. HOM [higher order mode] losses at the IR [interaction region] of the B-factory

    International Nuclear Information System (INIS)

    Heifets, S.

    1990-08-01

    Masking at the interaction region (IR) will presumably reduce the synchrotron radiation background in the detector. One possible layout of the IR for B-factory shows a rather complicated system of masks. A bunch passing each mask will generate RF waves. These waves (called usually higher order modes, HOM-s) will be absorbed in the beam pipe wall producing additional heating and, interacting with the beam, kicking particles in the radial and azimuthal directions. This may change the bunch motion and its emittance. These effects are estimated in the present note

  20. Coalescence and movement of nanobubbles studied with tapping mode AFM and tip-bubble interaction analysis

    International Nuclear Information System (INIS)

    Bhushan, Bharat; Wang Yuliang; Maali, Abdelhamid

    2008-01-01

    Imaging of a polystyrene (PS) coated silicon wafer immersed in deionized (DI) water was conducted using atomic force microscopy (AFM) in the tapping mode (TMAFM). As reported earlier, spherical cap-like domains, referred to as nanobubbles, were observed to be distributed on the PS surface. Experiments reveal that, in addition to the well-known parameter of scan load, scan speed is also an important parameter which affects nanobubble coalescence. The process of nanobubble coalescence was studied. It was found that during coalescence, small nanobubbles were easily moved and merged into bigger ones. Based on the interaction between the AFM cantilever tip and a bubble in the so-called force modulation mode of TMAFM, bubble height and adhesive force information for a given bubble was extracted. A viscoelastic model is used to obtain the interaction stiffness and damping coefficient, which provides a method to obtain the mechanical properties of nanobubbles. The model was further used to study the effect of surface tension force on attractive interaction force and contact angle hysteresis on the changes of the interaction damping coefficient during tip-bubble interaction.

  1. How to separate ionic liquids: Use of Hydrophilic Interaction Liquid Chromatography and mixed mode phases

    International Nuclear Information System (INIS)

    Lamouroux, C.

    2011-01-01

    This chromatographic study deals with the development of a convenient and versatile method to separate Room Temperature Ionic Liquids. Different modes of chromatography were studied. The study attempts to answer the following question: 'what were the most important interactions for the separation of ionic liquids?'. The results show that the essential interactions to assure a good retention of RTILs are the ionic ones and that hydrophobic interactions play a role in the selectivity of the separation. The separation of five imidazolium salt with a traditional dial columns in Hydrophilic Interaction Chromatography (HILIC) was demonstrated. It shows that neutral diol grafted column allows an important retention that we assume is due to the capability of diol to develop a thick layer of water. Furthermore, stationary phase based on mixed interaction associating ion exchange and hydrophobic properties were studied. Firstly, it will be argued that it is possible to separate RTILs with a convenient retention and resolution according to a reverse phase elution with the Primesep columns made of a brush type long alkyl chain with an embedded negatively charged functional group. Secondly, a successful separation of RTILs in HILIC mode with a mixed phase column containing a cationic exchanger and a hydrophobic octyl chain length will be demonstrated. (author)

  2. Estrogen Receptor Folding Modulates cSrc Kinase SH2 Interaction via a Helical Binding Mode.

    Science.gov (United States)

    Nieto, Lidia; Tharun, Inga M; Balk, Mark; Wienk, Hans; Boelens, Rolf; Ottmann, Christian; Milroy, Lech-Gustav; Brunsveld, Luc

    2015-11-20

    The estrogen receptors (ERs) feature, next to their transcriptional role, important nongenomic signaling actions, with emerging clinical relevance. The Src Homology 2 (SH2) domain mediated interaction between cSrc kinase and ER plays a key role in this; however the molecular determinants of this interaction have not been elucidated. Here, we used phosphorylated ER peptide and semisynthetic protein constructs in a combined biochemical and structural study to, for the first time, provide a quantitative and structural characterization of the cSrc SH2-ER interaction. Fluorescence polarization experiments delineated the SH2 binding motif in the ER sequence. Chemical shift perturbation analysis by nuclear magnetic resonance (NMR) together with molecular dynamics (MD) simulations allowed us to put forward a 3D model of the ER-SH2 interaction. The structural basis of this protein-protein interaction has been compared with that of the high affinity SH2 binding sequence GpYEEI. The ER features a different binding mode from that of the "two-pronged plug two-hole socket" model in the so-called specificity determining region. This alternative binding mode is modulated via the folding of ER helix 12, a structural element directly C-terminal of the key phosphorylated tyrosine. The present findings provide novel molecular entries for understanding nongenomic ER signaling and targeting the corresponding disease states.

  3. Interaction of a single mode field cavity with the 1D XY model: Energy spectrum

    International Nuclear Information System (INIS)

    Tonchev, H; Donkov, A A; Chamati, H

    2016-01-01

    In this work we use the fundamental in quantum optics Jaynes-Cummings model to study the response of spin 1/2chain to a single mode of a laser light falling on one of the spins, a focused interaction model between the light and the spin chain. For the spin-spin interaction along the chain we use the XY model. We report here the exact analytical results, obtained with the help of a computer algebra system, for the energy spectrum in this model for chains of up to 4 spins with nearest neighbors interactions, either for open or cyclic chain configurations. Varying the sign and magnitude of the spin exchange coupling relative to the light-spin interaction we have investigated both cases of ferromagnetic or antiferromagnetic spin chains. (paper)

  4. Interaction of Fast Ions with Global Plasma Modes in the C-2 Field Reversed Configuration Experiment

    Science.gov (United States)

    Smirnov, Artem; Dettrick, Sean; Clary, Ryan; Korepanov, Sergey; Thompson, Matthew; Trask, Erik; Tuszewski, Michel

    2012-10-01

    A high-confinement operating regime [1] with plasma lifetimes significantly exceeding past empirical scaling laws was recently obtained by combining plasma gun edge biasing and tangential Neutral Beam Injection (NBI) in the C-2 field-reversed configuration (FRC) experiment [2, 3]. We present experimental and computational results on the interaction of fast ions with the n=2 rotational and n=1 wobble modes in the C-2 FRC. It is found that the n=2 mode is similar to quadrupole magnetic fields in its detrimental effect on the fast ion transport due to symmetry breaking. The plasma gun generates an inward radial electric field, thus stabilizing the n=2 rotational instability without applying the quadrupole magnetic fields. The resultant FRCs are nearly axisymmetric, which enables fast ion confinement. The NBI further suppresses the n=2 mode, improves the plasma confinement characteristics, and increases the plasma configuration lifetime [4]. The n=1 wobble mode has relatively little effect on the fast ion transport, likely due to the approximate axisymmetry about the displaced plasma column. [4pt] [1] M. Tuszewski et al., Phys. Rev. Lett. 108, 255008 (2012).[0pt] [2] M. Binderbauer et al., Phys. Rev. Lett. 105, 045003 (2010).[0pt] [3] H.Y. Guo et al., Phys. Plasmas 18, 056110 (2011).[0pt] [4] M. Tuszewski et al., Phys. Plasmas 19, 056108 (2012)

  5. Mode-coupling of interaction quenched ultracold bosons in periodically driven lattices

    Science.gov (United States)

    Mistakidis, Simeon; Schmelcher, Peter

    2016-05-01

    The out-of-equilibrium dynamics of interaction quenched finite ultracold bosonic ensembles in periodically driven one-dimensional optical lattices is investigated. As a first attempt a brief analysis of the dynamics caused exclusively by the periodically driven lattice is presented and the induced low-lying modes are introduced. It is shown that the periodic driving enforces the bosons in the outer wells to exhibit out-of-phase dipole-like modes, while in the central well the cloud experiences a local-breathing mode. The dynamical behavior of the system is investigated with respect to the driving frequency, revealing a resonant-like behavior of the intra-well dynamics. Subsequently, we drive the system to a highly non-equilibrium state by performing an interaction quench upon the periodically driven lattice. This protocol gives rise to admixtures of excitations in the outer wells, an enhanced breathing in the center and an amplification of the tunneling dynamics. As a result (of the quench) the system experiences multiple resonances between the inter- and intra-well dynamics at different quench amplitudes. Finally, our study reveals that the position of the resonances can be adjusted e.g. via the driving frequency or the atom number manifesting their many-body nature. Deutsche Forschungsgemeinschaft (DFG) in the framework of the SFB 925 ``Light induced dynamics and control of correlated quantum systems''.

  6. Effects of plasma current on nonlinear interactions of ITG turbulence, zonal flows and geodesic acoustic modes

    International Nuclear Information System (INIS)

    Angelino, P; Bottino, A; Hatzky, R; Jolliet, S; Sauter, O; Tran, T M; Villard, L

    2006-01-01

    The mutual interactions of ion temperature gradient (ITG) driven modes, zonal flows and geodesic acoustic modes (GAM) in tokamak plasmas are investigated using a global nonlinear gyrokinetic formulation with totally unconstrained evolution of temperature gradient and profile. A series of numerical simulations with the same initial temperature and density profile specifications is performed using a sequence of ideal MHD equilibria differing only in the value of the total plasma current, in particular with identical magnetic shear profiles and shapes of magnetic surfaces. On top of a bursty or quasi-steady state behaviour the zonal flows oscillate at the GAM frequency. The amplitude of these oscillations increases with the value of the safety factor q, resulting in a less effective suppression of ITG turbulence by zonal flows at a lower plasma current. The turbulence-driven volume-averaged radial heat transport is found to scale inversely with the total plasma current

  7. Interaction mode and nanoparticle formation of bovine serum albumin and anthocyanin in three buffer solutions

    International Nuclear Information System (INIS)

    Zhou, Rui; Dong, Xueyan; Song, Lanlan; Jing, Hao

    2014-01-01

    Investigation of interaction mode of bovine serum albumin (BSA) and anthocyanin (ACN) in different solutions will help us understand the interaction mechanism and functional change of bioactive small molecule and biomacromolecule. This study investigated the binding mode, including binding constant, number of binding sites, binding force of BSA and ACN interaction in three buffer solutions of phosphate (PBS), sodium chloride (NaCl), and PBS-NaCl, using fluorescence spectroscopy and synchronous fluorescence spectroscopy. Formation and characteristics of BSA–ACN complex were also investigated using dynamic light scattering (DLS) and transmission electron microscopy (TEM). The results showed that ACN could interact with BSA at both tyrosine (Tyr) and tryptophan (Trp) residues through both hydrogen bonds and van der Waals force, and the same binding mode was seen in dH 2 O and three buffer solutions. The value of binding constant K was decreased as the temperature increased from 298 K to 308 K, and the decreasing degree was in the order of dH 2 O (9.0×10 4 )>NaCl (2.64×10 4 )/PBS (2.37×10 4 )>PBS-NaCl (0.88×10 4 ), which was inversely correlated with the ionic strength of the buffer solutions of PBS-NaCl>NaCl>PBS. It indicated that stability of BSA–ACN complex was affected most in dH 2 O than in three buffer solutions. The BSA and ACN interaction led to formation of BSA–ACN nanoparticles. The sizes of BSA–ACN nanoparticles in dH 2 O were smaller than that in three buffer solutions, which correlated with stronger binding force between BSA and ACN in dH 2 O than in three buffer solutions at room temperature (25 °C, 298 K). - Highlights: • We report the influences of four solutions on the BSA–ACN interaction. • We report the relationship between BSA–ACN interaction and particle size of complex. • The stability of BSA–ACN complex was affected most in dH 2 O than in buffer solutions

  8. Effect of dipole interaction on collective modes in 3He-A

    International Nuclear Information System (INIS)

    Tewordt, L.; Schopohl, N.; Vollhardt, D.

    1977-01-01

    A general theory for the correlation functions of superfluid 3 He which takes into account rigorously the magnetic dipole interaction is developed. The resulting equations are solved for the Anderson--Brinkman--Morel (ABM) state and for wave vectors q oriented parallel to the energy gap axis. Then the dispersion relations of low-frequency modes, including Fermi liquid corrections and damping due to pair breaking, are calculated in the zero-temperature and zero-field limit. There are two real frequency modes arising from each of the longitudinal and transverse spin density correlation functions: a spin wave and an orbit wave, both exhibiting a frequency gap where that of the spin wave is somewhat modified in comparison to the unperturbed longitudinal nuclear magnetic resonance frequency Ω/sup ABM//sub L/. The orbit wave is damped much more strongly than the spin wave. Further, there are two real frequency modes arising from the density correlation function: the sound wave, having a frequency gap of the order Ω/sup ABM//sub L/, and an orbit wave, exhibiting a gap in wave number of order Ω/sup ABM//sub L//v/sub F/.: The NMR frequency undergoes a small splitting, which is the result of the splitting of the energy gap due to the dipole interaction. One of the two gaps still has nodes.: In addition to these low-frequency modes our equations yield resonances at frequencies of the order of the gap frequency Δ 0 /h, i.e., at ω=1.22Δ 0 /h and at ω=1.58 Δ 0 /h. The damping and the oscillator strengths of these resonances are calculated

  9. Mode selectivity in cluster-molecule interactions: Ni13 + D2

    International Nuclear Information System (INIS)

    Jellinek, J.; Guevenc, Z.B.

    1991-01-01

    Results of a detailed quasiclassical simulation study of the Ni 13 + D 2 collision system are presented. The dissociative adsorption of the molecule as well as its scattering from the cluster are analyzed as functions of the initial rovibrational molecular state, collision energy and structure of the cluster. Mode-specific features of the reactive and nonreactive channels of the cluster-molecule interaction are displayed and discussed. Evidence for resonances and for a strong cluster structure-reactivity correlation is presented. 13 refs., 6 figs

  10. New "Field" of Vocal Music Teaching and Research: Research on the Construction of a Novel Interaction Mode

    Science.gov (United States)

    Li, Donglan

    2015-01-01

    This paper, as an attempt to find a solution to the problem of "Identity Crisis" brought about by the traditional spoon-feeding Education Mode, explores to construct a new mode of vocal music teaching characterized by an interaction on an equal and democratic footing between learners and the teacher in light of Habermas' Communicative…

  11. Intersegment interactions and helix-coil transition within the generalized model of polypeptide chains approach

    Science.gov (United States)

    Badasyan, A. V.; Hayrapetyan, G. N.; Tonoyan, Sh. A.; Mamasakhlisov, Y. Sh.; Benight, A. S.; Morozov, V. F.

    2009-09-01

    The generalized model of polypeptide chains is extended to describe the helix-coil transition in a system comprised of two chains interacting side-by-side. The Hamiltonian of the model takes into account four possible types of interactions between repeated units of the two chains, i.e., helix-helix, helix-coil, coil-helix, and coil-coil. Analysis reveals when the energy Ihh+Icc of (h-h, c-c) interactions overwhelms the energy Ihc+Ich of mixed (h-c, c-h) interactions, the correlation length rises substantially, resulting in narrowing of the transition interval. In the opposite case, when Ihh+Iccinteractions from the same theoretical perspective.

  12. Pigeon interaction mode switch-based UAV distributed flocking control under obstacle environments.

    Science.gov (United States)

    Qiu, Huaxin; Duan, Haibin

    2017-11-01

    Unmanned aerial vehicle (UAV) flocking control is a serious and challenging problem due to local interactions and changing environments. In this paper, a pigeon flocking model and a pigeon coordinated obstacle-avoiding model are proposed based on a behavior that pigeon flocks will switch between hierarchical and egalitarian interaction mode at different flight phases. Owning to the similarity between bird flocks and UAV swarms in essence, a distributed flocking control algorithm based on the proposed pigeon flocking and coordinated obstacle-avoiding models is designed to coordinate a heterogeneous UAV swarm to fly though obstacle environments with few informed individuals. The comparative simulation results are elaborated to show the feasibility, validity and superiority of our proposed algorithm. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

  13. Effect of dynamical phase on the resonant interaction among tsunami edge wave modes

    Science.gov (United States)

    Geist, Eric L.

    2018-01-01

    Different modes of tsunami edge waves can interact through nonlinear resonance. During this process, edge waves that have very small initial amplitude can grow to be as large or larger than the initially dominant edge wave modes. In this study, the effects of dynamical phase are established for a single triad of edge waves that participate in resonant interactions. In previous studies, Jacobi elliptic functions were used to describe the slow variation in amplitude associated with the interaction. This analytical approach assumes that one of the edge waves in the triad has zero initial amplitude and that the combined phase of the three waves φ = θ1 + θ2 − θ3 is constant at the value for maximum energy exchange (φ = 0). To obtain a more general solution, dynamical phase effects and non-zero initial amplitudes for all three waves are incorporated using numerical methods for the governing differential equations. Results were obtained using initial conditions calculated from a subduction zone, inter-plate thrust fault geometry and a stochastic earthquake slip model. The effect of dynamical phase is most apparent when the initial amplitudes and frequencies of the three waves are within an order of magnitude. In this case, non-zero initial phase results in a marked decrease in energy exchange and a slight decrease in the period of the interaction. When there are large differences in frequency and/or initial amplitude, dynamical phase has less of an effect and typically one wave of the triad has very little energy exchange with the other two waves. Results from this study help elucidate under what conditions edge waves might be implicated in late, large-amplitude arrivals.

  14. Interactive Mode of Teaching Students in the Context of the Competence Paradigm

    Directory of Open Access Journals (Sweden)

    G. P. Sikorskaya

    2012-01-01

    Full Text Available The paper explores the theoretical and practical aspects of interactive mode of teaching students by using active educational methods improving the quality of educational process and increasing students’ motivation for comprehensive and in-depth learning. The list of interactive teaching techniques is given providing the development of necessary professional abilities and skills, and fostering students’ responsibility for training results, critical thinking, reflexive skills, self-dependency in solving educational problems, training mobility, etc. The detailed descriptions of effective, yet comparatively new in subject-based teaching, methods of case studies and cross-cultural communication are provided, the opportunities for their implementation indicated. The paper emphasizes such aspects of educational process as self-assessment and peer-assessment of students’ achievements. The authors suggest the original approach to educational results evaluation in interactive educational environment, shifting the emphasis from students’ lack of knowledge and skills onto their abilities and achievements. The exact criteria of current control help optimize students’ extracurricular self-dependent work, providing teaches with the feasible leverages for controlling this important activity significantly enlarged in proportion in modern education. As the final control, the authors have chosen defending the thematic portfolio in electronic form, which allows integrating qualitative and behavioral assessment of the assimilated training course. The present research was carried out in the context of the competence paradigm of education. The paper contains the research findings in the field of comparative pedagogy and demonstrates the experience of implementing the interactive teaching mode exemplified by «Sustainability and the Environment» virtual course for bachelors and master’s degree holders training in the humanities and natural sciences

  15. Effect of Dynamical Phase on the Resonant Interaction Among Tsunami Edge Wave Modes

    Science.gov (United States)

    Geist, Eric L.

    2018-04-01

    Different modes of tsunami edge waves can interact through nonlinear resonance. During this process, edge waves that have very small initial amplitude can grow to be as large or larger than the initially dominant edge wave modes. In this study, the effects of dynamical phase are established for a single triad of edge waves that participate in resonant interactions. In previous studies, Jacobi elliptic functions were used to describe the slow variation in amplitude associated with the interaction. This analytical approach assumes that one of the edge waves in the triad has zero initial amplitude and that the combined phase of the three waves φ = θ 1 + θ 2 - θ 3 is constant at the value for maximum energy exchange ( φ = 0). To obtain a more general solution, dynamical phase effects and non-zero initial amplitudes for all three waves are incorporated using numerical methods for the governing differential equations. Results were obtained using initial conditions calculated from a subduction zone, inter-plate thrust fault geometry and a stochastic earthquake slip model. The effect of dynamical phase is most apparent when the initial amplitudes and frequencies of the three waves are within an order of magnitude. In this case, non-zero initial phase results in a marked decrease in energy exchange and a slight decrease in the period of the interaction. When there are large differences in frequency and/or initial amplitude, dynamical phase has less of an effect and typically one wave of the triad has very little energy exchange with the other two waves. Results from this study help elucidate under what conditions edge waves might be implicated in late, large-amplitude arrivals.

  16. Effect of Dynamical Phase on the Resonant Interaction Among Tsunami Edge Wave Modes

    Science.gov (United States)

    Geist, Eric L.

    2018-02-01

    Different modes of tsunami edge waves can interact through nonlinear resonance. During this process, edge waves that have very small initial amplitude can grow to be as large or larger than the initially dominant edge wave modes. In this study, the effects of dynamical phase are established for a single triad of edge waves that participate in resonant interactions. In previous studies, Jacobi elliptic functions were used to describe the slow variation in amplitude associated with the interaction. This analytical approach assumes that one of the edge waves in the triad has zero initial amplitude and that the combined phase of the three waves φ = θ 1 + θ 2 - θ 3 is constant at the value for maximum energy exchange (φ = 0). To obtain a more general solution, dynamical phase effects and non-zero initial amplitudes for all three waves are incorporated using numerical methods for the governing differential equations. Results were obtained using initial conditions calculated from a subduction zone, inter-plate thrust fault geometry and a stochastic earthquake slip model. The effect of dynamical phase is most apparent when the initial amplitudes and frequencies of the three waves are within an order of magnitude. In this case, non-zero initial phase results in a marked decrease in energy exchange and a slight decrease in the period of the interaction. When there are large differences in frequency and/or initial amplitude, dynamical phase has less of an effect and typically one wave of the triad has very little energy exchange with the other two waves. Results from this study help elucidate under what conditions edge waves might be implicated in late, large-amplitude arrivals.

  17. Effects of three-mode field interactions in laser instabilities and in beat-frequency spectroscopy

    International Nuclear Information System (INIS)

    Herdow, S.T.

    1982-01-01

    Population pulsations are fluctuations in the population difference (of a two level system) due to the presence of two or more coherent waves interfering in the medium. In this work, the author shows that population pulsations generated by three waves, a central wave and two mode-locked sidebands, are responsible for both the multiwavelength and the single-wavelength instabilities of single-mode lasers containing homgeneously-broadened media. The role of the population pulsations in establishing these instabilities, however, diminish as the central mode is detuned away from the atomic resonance frequency. For homogeneously-broadened lasers, the author finds two regions of single-wavelength instability. The first is at line center, for which population pulsations are solely responsible, and the second is off line center where the unsaturated medium provides the required gain and anomalous dispersion. For the case of inhomogeneously-broadened lasers, the author shows that population pulsations significantly increase the instability range over that predicted by Casperson for single-mode bad-cavity lasers. Both the unidirectional ring and the standing-wave cavities are treated. The Fourier expansion technique, used in this work, for treating three-frequency operation in saturation spectroscopy is shown to be equivalent (in appropriate limits) to the linear stability analysis in laser theory and optical bistability. The author also shows, in single-sideband saturation spectroscopy, that for long interaction lengths propagation effects can significantly influence the absorption and dispersion coefficients of the medium. Finally, the author shows that under certain conditions the pronounced splitting effects of the population pulsations develop into regions of intense absorption

  18. A quantum mechanical model of Rabi oscillations between two interacting harmonic oscillator modes and the interconversion of modes in a Penning trap

    International Nuclear Information System (INIS)

    Kretzschmar, Martin

    1999-01-01

    When a Penning trap is operated with an additional quadrupole driving field with a frequency that equals a suitable combination (sum or difference) of the frequencies of the fundamental modes of motion (modified cyclotron, magnetron and axial frequency), then a periodic conversion of the participating modes into each other is observed, strongly resembling the Rabi oscillations in a 2-level atom driven by a laser field tuned to the transition frequency. This investigation attempts to understand on a fundamental level how and why the motion of a classical particle in a macroscopic apparatus can be truely analogous to the oscillations of states of quantum mechanical 2-level systems (2-level atom or magnetic resonance). Ion motion in a Penning trap with an additional quadrupole driving field is described in a quantum mechanical frame work. The Heisenberg equations of motion for the creation and annihilation operators of the interacting oscillators have been explicitly solved, the time development operator of the Schroedinger picture has been determined. The driving field provides for two types of intermode interaction: Type I preserves the total number of excitation quanta present in the two interacting modes, the system oscillates between the modes with a frequency corresponding to the Rabi frequency in two-level systems. Type II preserves the difference of the numbers of excitation quanta present in the two interacting modes, it causes the ion motion to become unbounded. The two types of interaction are associated in a natural way with a SU(2) and a SU(1,1) Lie algebra. The three generators of these algebras form a vector operator that we denote as the Bloch vector operator. The Hilbert space decomposes in a natural way into invariant subspaces, finite dimensional in the case of type I interaction (SU(2)-algebra) and infinite dimensional in the case of type II interaction (SU(1,1)-algebra). The physics of the 2-level atom in the laser field can be described in the 2

  19. Interactions of Mineral Dust with Clouds, Sea Surface Temperature, and Climate Modes of Variability

    Science.gov (United States)

    DeFlorio, Michael J.

    Global climate models (GCMs) are a vital tool for ensuring the prosperity and security of modern society. They allow scientists to understand complex interactions between the air, ocean, and land, and are used by policymakers to project future changes in climate on regional and global scales. The previous generation of GCMs, represented by CMIP3 models, are shown to be deficient in their representation of precipitation over the western United States, a region that depends critically on wintertime orographically enhanced precipitation for drinking water. In addition, aerosol-cloud interactions were prescribed in CMIP3 models, which decreased the value of their representation of global aerosol, cloud, and precipitation features. This has potentially large impacts on global radiation budgets, since aerosol-cloud interactions affect the spatial extent and magnitude of clouds and precipitation. The newest suite of GCMs, the Coupled Model Intercomparison Project Phase 5 (CMIP5) models, includes state-of-the-art parameterizations of small-scale features such as aerosols, clouds, and precipitation, and is widely used by the scientific community to learn more about the climate system. The Community Earth System Model (CESM), in conjunction with observations, provides several simulations to investigate the role of aerosols, clouds, and precipitation in the climate system and how they interact with larger modes of climate variability. We show that CESM produces a realistic spatial distribution of precipitation extremes over the western U.S., and that teleconnected signals of ENSO and the Pacific Decadal Oscillation to large-scale circulation patterns and precipitation over the western U.S. are improved when compared to CCSM3. We also discover a new semi-direct effect between dust and stratocumulus clouds over the subtropical North Atlantic, whereby boundary layer inversion strength increases during the most dusty summers due to shortwave absorption of dust above the planetary

  20. Simulation of mode converted ion Bernstein wave - beam deuteron interactions on TFTR

    Science.gov (United States)

    Herrmann, Mark; Fisch, Nathaniel

    1998-11-01

    Experiments on TFTR have documented strong interactions between mode converted ion Bernstein waves (MCIBW) and beam deuterons(D. S. Darrow et al.), Nucl. Fusion 36, 509 (1996).^,(N. J. Fisch et al.), IAEA, Vol. 1, p. 271 (1996). This is of particular interest in the study of α channelling, since the most promising scenarios(M. C. Herrmann and N. J. Fisch, Phys. Rev. Lett. 79), 1495 (1997). rely on a suitable combination of MCIBW and Alfvén eigenmodes to achieve the cooling of the α particles. Collisional effects, realistic wave fields, and a detailed model of the wave-particle interaction have been added to the Monte Carlo simulations which are used to simulate α channelling in order to model TFTR experiments(M. C. Herrmann, Ph.D. thesis, Princeton University, 1998.). The results are found to be in qualitative agreement with the data. In addition, the simulation is used, in conjunction with the data, to demonstrate the existence of the k_\\|-flip of the MCIBW, and to infer a diffusion coefficient for the beam deuterons interacting with the wave. This diffusion coefficient significantly exceeds what would be expected on the basis of quasilinear theory with the fields specified by 1 D ray tracing of the MCIBW.

  1. Privacy effects on self-reported drug use: interactions with survey mode and respondent characteristics.

    Science.gov (United States)

    Aquilino, W S

    1997-01-01

    This chapter examines the impact of interview privacy on self-reported illicit drug use. In 1991, interviews were completed with an urban-suburban sample of 2,417 adults aged 18 to 45. Results show that the presence of third parties during the interview significantly influences respondents' willingness to reveal illicit drug use. Among married respondents, presence of a spouse resulted in higher reporting of illicit drug use, while the presence of adults other than the spouse had a consistent negative effect on drug use reports. A parent's presence during the interview significantly reduced respondents' willingness to report illicit drug use. The pattern of findings suggests that the direction of effects due to third party presence is linked to two factors: the extent of the third party's knowledge of the information requested, and the degree of personal stake the third party may have in the respondent's answers. The differential impact of privacy by interview mode was also examined. Tests of interactions between privacy and interview mode failed to support the hypothesis that the use of self-administered answer sheets reduces privacy effects compared with interviewer-administered interviews.

  2. On-orbit evaluation of the control system/structural mode interactions on OSO-8

    Science.gov (United States)

    Slafer, L. I.

    1980-01-01

    The Orbiting Solar Observatory-8 experienced severe structural mode/control loop interaction problems during the spacecraft development. Extensive analytical studies, using the hybrid coordinate modeling approach, and comprehensive ground testing were carried out in order to achieve the system's precision pointing performance requirements. A recent series of flight tests were conducted with the spacecraft in which a wide bandwidth, high resolution telemetry system was utilized to evaluate the on-orbit flexible dynamics characteristics of the vehicle along with the control system performance. This paper describes the results of these tests, reviewing the basic design problem, analytical approach taken, ground test philosophy, and on-orbit testing. Data from the tests was used to determine the primary mode frequency, damping, and servo coupling dynamics for the on-orbit condition. Additionally, the test results have verified analytically predicted differences between the on-orbit and ground test environments. The test results have led to a validation of both the analytical modeling and servo design techniques used during the development of the control system, and also verified the approach taken to vehicle and servo ground testing.

  3. Interaction mode between catalytic and regulatory subunits in glucosidase II involved in ER glycoprotein quality control.

    Science.gov (United States)

    Satoh, Tadashi; Toshimori, Takayasu; Noda, Masanori; Uchiyama, Susumu; Kato, Koichi

    2016-11-01

    The glycoside hydrolase family 31 (GH31) α-glucosidases play vital roles in catabolic and regulated degradation, including the α-subunit of glucosidase II (GIIα), which catalyzes trimming of the terminal glucose residues of N-glycan in glycoprotein processing coupled with quality control in the endoplasmic reticulum (ER). Among the known GH31 enzymes, only GIIα functions with its binding partner, regulatory β-subunit (GIIβ), which harbors a lectin domain for substrate recognition. Although the structural data have been reported for GIIα and the GIIβ lectin domain, the interaction mode between GIIα and GIIβ remains unknown. Here, we determined the structure of a complex formed between GIIα and the GIIα-binding domain of GIIβ, thereby providing a structural basis underlying the functional extension of this unique GH31 enzyme. © 2016 The Protein Society.

  4. Controlling the Host-Guest Interaction Mode through a Redox Stimulus.

    Science.gov (United States)

    Szalóki, György; Croué, Vincent; Carré, Vincent; Aubriet, Frédéric; Alévêque, Olivier; Levillain, Eric; Allain, Magali; Aragó, Juan; Ortí, Enrique; Goeb, Sébastien; Sallé, Marc

    2017-12-18

    A proof-of-concept related to the redox-control of the binding/releasing process in a host-guest system is achieved by designing a neutral and robust Pt-based redox-active metallacage involving two extended-tetrathiafulvalene (exTTF) ligands. When neutral, the cage is able to bind a planar polyaromatic guest (coronene). Remarkably, the chemical or electrochemical oxidation of the host-guest complex leads to the reversible expulsion of the guest outside the cavity, which is assigned to a drastic change of the host-guest interaction mode, illustrating the key role of counteranions along the exchange process. The reversible process is supported by various experimental data ( 1 H NMR spectroscopy, ESI-FTICR, and spectroelectrochemistry) as well as by in-depth theoretical calculations performed at the density functional theory (DFT) level. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. The interaction between fishbone modes and shear Alfvén waves in tokamak plasmas

    Science.gov (United States)

    He, Hongda; Liu, Yueqiang; Dong, J. Q.; Hao, G. Z.; Wu, Tingting; He, Zhixiong; Zhao, K.

    2016-05-01

    The resonant interaction between the energetic particle triggered fishbone mode and the shear Alfvén waves is computationally investigated and firmly demonstrated based on a tokamak plasma equilibrium, using the self-consistent MHD-kinetic hybrid code MARS-K (Liu et al 2008 Phys. Plasmas 15 112503). This type of continuum resonance, occurring critically due to the mode’s toroidal rotation in the plasma frame, significantly modifies the eigenmode structure of the fishbone instability, by introducing two large peaks of the perturbed parallel current density near but offside the q  =  1 rational surface (q is the safety factor). The self-consistently computed radial plasma displacement substantially differs from that being assumed in the conventional fishbone theory.

  6. A key centriole assembly interaction interface between human PLK4 and STIL appears to not be conserved in flies

    Directory of Open Access Journals (Sweden)

    Matthew A. Cottee

    2017-03-01

    Full Text Available A small number of proteins form a conserved pathway of centriole duplication. In humans and flies, the binding of PLK4/Sak to STIL/Ana2 initiates daughter centriole assembly. In humans, this interaction is mediated by an interaction between the Polo-Box-3 (PB3 domain of PLK4 and the coiled-coil domain of STIL (HsCCD. We showed previously that the Drosophila Ana2 coiled-coil domain (DmCCD is essential for centriole assembly, but it forms a tight parallel tetramer in vitro that likely precludes an interaction with PB3. Here, we show that the isolated HsCCD and HsPB3 domains form a mixture of homo-multimers in vitro, but these readily dissociate when mixed to form the previously described 1:1 HsCCD:HsPB3 complex. In contrast, although Drosophila PB3 (DmPB3 adopts a canonical polo-box fold, it does not detectably interact with DmCCD in vitro. Thus, surprisingly, a key centriole assembly interaction interface appears to differ between humans and flies.

  7. Interactions between large-scale modes of climate and their relationship with Australian climate and hydrology

    Science.gov (United States)

    Whan, K. R.; Lindesay, J. A.; Timbal, B.; Raupach, M. R.; Williams, E.

    2010-12-01

    Australia’s natural environment is adapted to low rainfall availability and high variability but human systems are less able to adapt to variability in the hydrological cycle. Understanding the mechanisms underlying drought persistence and severity is vital to contextualising future climate change. Multiple external forcings mean the mechanisms of drought occurrence in south-eastern Australian are complex. The key influences on SEA climate are El Niño-Southern Oscillation (ENSO), the Indian Ocean Dipole (IOD), the Southern Annular Mode (SAM) and the sub-tropical ridge (STR); each of these large-scale climate modes (LSCM) has been studied widely. The need for research into the interactions among the modes has been noted [1], although to date this has received limited attention. Relationships between LSCM and hydrometeorological variability are nonlinear, making linearity assumptions underlying usual statistical techniques (e.g. correlation, principle components analysis) questionable. In the current research a statistical technique that can deal with nonlinear interactions is applied to a new dataset enabling a full examination of the Australian water balance. The Australian Water Availability Project (AWAP) dataset models the Australian water balance on a fine grid [2]. Hydrological parameters (e.g. soil moisture, evaporation, runoff) are modelled from meteorological data, allowing the complete Australian water balance (climate and hydrology) to be examined and the mechanisms of drought to be studied holistically. Classification and regression trees (CART) are a powerful regression-based technique that is capable of accounting for nonlinear effects. Although it has limited previous application in climate research [3] this methodology is particularly informative in cases with multiple predictors and nonlinear relationships such as climate variability. Statistical relationships between variables are the basis for the decision rules in CART that are used to split

  8. A direct proofreader-clamp interaction stabilizes the Pol III replicase in the polymerization mode

    KAUST Repository

    Jergic, Slobodan; Horan, Nicholas P.; Elshenawy, Mohamed; Mason, Claire E.; Urathamakul, Thitima; Ozawa, Kiyoshi; Robinson, Andrew J.; Goudsmits, Joris M H; Wang, Yao; Pan, Xuefeng; Beck, Jennifer L.; Van Oijen, Antoine M.; Huber, Thomas L.; Hamdan, Samir; Dixon, Nicholas E.

    2013-01-01

    Processive DNA synthesis by the αÉ"θ core of the Escherichia coli Pol III replicase requires it to be bound to the β 2 clamp via a site in the α polymerase subunit. How the É" proofreading exonuclease subunit influences DNA synthesis by α was not previously understood. In this work, bulk assays of DNA replication were used to uncover a non-proofreading activity of É". Combination of mutagenesis with biophysical studies and single-molecule leading-strand replication assays traced this activity to a novel β-binding site in É" that, in conjunction with the site in α, maintains a closed state of the αÉ"θ-β 2 replicase in the polymerization mode of DNA synthesis. The É"-β interaction, selected during evolution to be weak and thus suited for transient disruption to enable access of alternate polymerases and other clamp binding proteins, therefore makes an important contribution to the network of protein-protein interactions that finely tune stability of the replicase on the DNA template in its various conformational states. © 2013 European Molecular Biology Organization.

  9. A direct proofreader-clamp interaction stabilizes the Pol III replicase in the polymerization mode

    KAUST Repository

    Jergic, Slobodan

    2013-02-22

    Processive DNA synthesis by the αÉ"θ core of the Escherichia coli Pol III replicase requires it to be bound to the β 2 clamp via a site in the α polymerase subunit. How the É" proofreading exonuclease subunit influences DNA synthesis by α was not previously understood. In this work, bulk assays of DNA replication were used to uncover a non-proofreading activity of É". Combination of mutagenesis with biophysical studies and single-molecule leading-strand replication assays traced this activity to a novel β-binding site in É" that, in conjunction with the site in α, maintains a closed state of the αÉ"θ-β 2 replicase in the polymerization mode of DNA synthesis. The É"-β interaction, selected during evolution to be weak and thus suited for transient disruption to enable access of alternate polymerases and other clamp binding proteins, therefore makes an important contribution to the network of protein-protein interactions that finely tune stability of the replicase on the DNA template in its various conformational states. © 2013 European Molecular Biology Organization.

  10. Synergistic interaction and mode of action of Citrus hystrix essential oil against bacteria causing periodontal diseases.

    Science.gov (United States)

    Wongsariya, Karn; Phanthong, Phanida; Bunyapraphatsara, Nuntavan; Srisukh, Vimol; Chomnawang, Mullika Traidej

    2014-03-01

    Citrus hystrix de Candolle (Rutaceae), an edible plant regularly used as a food ingredient, possesses antibacterial activity, but there is no current data on the activity against bacteria causing periodontal diseases. C. hystrix essential oil from leaves and peel were investigated for antibiofilm formation and mode of action against bacteria causing periodontal diseases. In vitro antibacterial and antibiofilm formation activities were determined by broth microdilution and time kill assay. Mode of action of essential oil was observed by SEM and the active component was identified by bioautography and GC/MS. C. hystrix leaves oil exhibited antibacterial activity at the MICs of 1.06 mg/mL for P. gingivalis and S. mutans and 2.12 mg/mL for S. sanguinis. Leaf oil at 4.25 mg/mL showed antibiofilm formation activity with 99% inhibition. The lethal effects on P. gingivalis were observed within 2 and 4 h after treated with 4 × MIC and 2 × MIC, respectively. S. sanguinis and S. mutans were completely killed within 4 and 8 h after exposed to 4 × MIC and 2 × MIC of oil. MICs of tested strains showed 4 times reduction suggesting synergistic interaction of oil and chlorhexidine. Bacterial outer membrane was disrupted after treatment with leaves oil. Additionally, citronellal was identified as the major active compound of C. hystrix oil. C. hystrix leaf oil could be used as a natural active compound or in combination with chlorhexidine in mouthwash preparations to prevent the growth of bacteria associated with periodontal diseases and biofilm formation.

  11. The interaction between gambling activities and modes of access: a comparison of Internet-only, land-based only, and mixed-mode gamblers.

    Science.gov (United States)

    Gainsbury, Sally M; Russell, Alex; Blaszczynski, Alex; Hing, Nerilee

    2015-02-01

    Research suggests that Internet-based gambling includes risk factors that may increase gambling problems. The current study aimed to investigate subgroups of gamblers to identify the potential harms associated with various forms and modes of gambling. An online survey was completed by 4,594 respondents identified as Internet-only (IG), land-based only (LBGs), or mixed-mode (MMG) gamblers based on self-reported gambling behaviour in the last 12months. Results showed significant socio-demographic differences between groups, with the LBGs being the oldest and MMGs the youngest. MMGs engaged in the greatest variety of gambling forms, had the highest average problem gambling severity scores, and were more likely to attribute problems to sports betting than the other groups. IGs were involved in the lowest number of divergent gambling activities, most likely to gamble frequently on sports and races, and attribute problems to these forms. Compared to the other groups, LBs had a higher proportion of problem gamblers than IGs and were most likely to play electronic gaming machines weekly, with this form of gambling contributing to problems at a substantially greater rate. This study confirms the importance of considering gambling involvement across subgroups of Internet or land-based gamblers. There is a need to consider the interaction between forms and modes of gambling to advance our understanding of the potential risk of mode of gambling to contribute to problems. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. Tailoring light-sound interactions in a single mode fiber for the high-power transmission or sensing applications

    Science.gov (United States)

    Gulistan, Aamir; Rahman, M. M.; Ghosh, Souvik; Rahman, B. M. A.

    2018-03-01

    A full-vectorial numerically efficient Finite Element Method (FEM) based computer code is developed to study complex light-sound interactions in a single mode fiber (SMF). The SBS gain or SBS threshold in a fiber is highly related to the overlap between the optical and acoustic modes. For a typical SMF the acoustic-optic overlap strongly depends on the optical and acoustic mode profiles and it is observed that the acoustic mode is more confined in the core than the optical mode and reported overlap is around 94 % between these fundamental optical and acoustic modes. However, it is shown here that selective co-doping of Aluminum and Germanium in core reduces the acoustic index while keeping the optical index of the same value and thus results in increased acoustic- optic overlap of 99.7%. On the other hand, a design of acoustic anti-guide fiber for high-power transmission systems is also proposed, where the overlap between acoustic and optical modes is reduced. Here, we show that by keeping the optical properties same as a standard SMF and introducing a Boron doped 2nd layer in the cladding, a very low value of 2.7% overlap is achieved. Boron doping in cladding 2nd layer results in a high acoustic index and acoustic modes shifts in the cladding from the core, allowing much high power delivery through this SMF.

  13. Interaction of acupuncture treatment and manipulation laterality modulated by the default mode network.

    Science.gov (United States)

    Niu, Xuan; Zhang, Ming; Liu, Zhenyu; Bai, Lijun; Sun, Chuanzhu; Wang, Shan; Wang, Xiaocui; Chen, Zhen; Chen, Hongyan; Tian, Jie

    2017-01-01

    Appropriate selection of ipsilateral or contralateral electroacupuncture (corresponding to the pain site) plays an important role in reaching its better curative effect; however, the involving brain mechanism still remains unclear. Compared with the heat pain model generally established in previous study, capsaicin pain model induces reversible cutaneous allodynia and is proved to be better simulating aspects of clinical nociceptive and neuropathic pain. In the current study, 24 subjects were randomly divided into two groups with a 2 × 2 factorial design: laterality (ipsi- or contralateral side, inter-subject) × treatment with counter-balanced at an interval of one week (verum and placebo electroacupuncture, within-subject). We observed subjective pain intensity and brain activations changes induced by capsaicin allodynia pain stimuli before and after electroacupuncture treatment at acupoint LI4 for 30 min. Analysis of variance results indicated that ipsilateral electroacupuncture treatment produced significant pain relief and wide brain signal suppressions in pain-related brain areas compared with contralateral electroacupuncture. We also found that verum electroacupuncture at either ipsi- or contralateral side to the pain site exhibited comparable significant magnitudes of analgesic effect. By contrast, placebo electroacupuncture elicited significant pain reductions only on the ipsilateral rather than contralateral side. It was inferred that placebo analgesia maybe attenuated on the region of the body (opposite to pain site) where attention was less focused, suggesting that analgesic effect of placebo electroacupuncture mainly rely on the motivation of its spatial-specific placebo responses via attention mechanism. This inference can be further supported by the evidence that the significant interaction effect of manipulation laterality and treatment was exclusively located within the default mode network, including the bilateral superior parietal

  14. Modes of Escherichia coli Dps Interaction with DNA as Revealed by Atomic Force Microscopy.

    Directory of Open Access Journals (Sweden)

    Vladislav V Melekhov

    Full Text Available Multifunctional protein Dps plays an important role in iron assimilation and a crucial role in bacterial genome packaging. Its monomers form dodecameric spherical particles accumulating ~400 molecules of oxidized iron ions within the protein cavity and applying a flexible N-terminal ends of each subunit for interaction with DNA. Deposition of iron is a well-studied process by which cells remove toxic Fe2+ ions from the genetic material and store them in an easily accessible form. However, the mode of interaction with linear DNA remained mysterious and binary complexes with Dps have not been characterized so far. It is widely believed that Dps binds DNA without any sequence or structural preferences but several lines of evidence have demonstrated its ability to differentiate gene expression, which assumes certain specificity. Here we show that Dps has a different affinity for the two DNA fragments taken from the dps gene regulatory region. We found by atomic force microscopy that Dps predominantly occupies thermodynamically unstable ends of linear double-stranded DNA fragments and has high affinity to the central part of the branched DNA molecule self-assembled from three single-stranded oligonucleotides. It was proposed that Dps prefers binding to those regions in DNA that provide more contact pads for the triad of its DNA-binding bundle associated with one vertex of the protein globule. To our knowledge, this is the first study revealed the nucleoid protein with an affinity to branched DNA typical for genomic regions with direct and inverted repeats. As a ubiquitous feature of bacterial and eukaryotic genomes, such structural elements should be of particular care, but the protein system evolutionarily adapted for this function is not yet known, and we suggest Dps as a putative component of this system.

  15. Entanglement Criteria of Two Two-Level Atoms Interacting with Two Coupled Modes

    Science.gov (United States)

    Baghshahi, Hamid Reza; Tavassoly, Mohammad Kazem; Faghihi, Mohammad Javad

    2015-08-01

    In this paper, we study the interaction between two two-level atoms and two coupled modes of a quantized radiation field in the form of parametric frequency converter injecting within an optical cavity enclosed by a medium with Kerr nonlinearity. It is demonstrated that, by applying the Bogoliubov-Valatin canonical transformation, the introduced model is reduced to a well-known form of the generalized Jaynes-Cummings model. Then, under particular initial conditions for the atoms (in a coherent superposition of its ground and upper states) and the fields (in a standard coherent state) which may be prepared, the time evolution of state vector of the entire system is analytically evaluated. In order to understand the degree of entanglement between subsystems (atom-field and atom-atom), the dynamics of entanglement through different measures, namely, von Neumann reduced entropy, concurrence and negativity is evaluated. In each case, the effects of Kerr nonlinearity and detuning parameter on the above measures are numerically analyzed, in detail. It is illustrated that the amount of entanglement can be tuned by choosing the evolved parameters, appropriately.

  16. Self-processing and the default mode network: Interactions with the mirror neuron system

    Directory of Open Access Journals (Sweden)

    Istvan eMolnar-Szakacs

    2013-09-01

    Full Text Available Recent evidence for the fractionation of the default mode network (DMN into functionally distinguishable subdivisions with unique patterns of connectivity calls for a reconceptualization of the relationship between this network and self-referential processing. Advances in resting-state functional connectivity analyses are beginning to reveal increasingly complex patterns of organization within the key nodes of the DMN - medial prefrontal cortex (MPFC and posterior cingulate cortex (PCC – as well as between these nodes and other brain systems. Here we review recent examinations of the relationships between the DMN and various aspects of self-relevant and social-cognitive processing in light of emerging evidence for heterogeneity within this network. Drawing from a rapidly evolving social cognitive neuroscience literature, we propose that embodied simulation and mentalizing are processes which allow us to gain insight into another's physical and mental state by providing privileged access to our own physical and mental states. Embodiment implies that the same neural systems are engaged for self- and other-understanding through a simulation mechanism, while mentalizing refers to the use of high-level conceptual information to make inferences about the mental states of self and others. These mechanisms work together to provide a coherent representation of the self and by extension, of others. Nodes of the DMN selectively interact with brain systems for embodiment and mentalizing, including the mirror neuron system, to produce appropriate mappings in the service of social cognitive demands.

  17. Different modes of interaction by TIAR and HuR with target RNA and DNA.

    Science.gov (United States)

    Kim, Henry S; Wilce, Matthew C J; Yoga, Yano M K; Pendini, Nicole R; Gunzburg, Menachem J; Cowieson, Nathan P; Wilson, Gerald M; Williams, Bryan R G; Gorospe, Myriam; Wilce, Jacqueline A

    2011-02-01

    TIAR and HuR are mRNA-binding proteins that play important roles in the regulation of translation. They both possess three RNA recognition motifs (RRMs) and bind to AU-rich elements (AREs), with seemingly overlapping specificity. Here we show using SPR that TIAR and HuR bind to both U-rich and AU-rich RNA in the nanomolar range, with higher overall affinity for U-rich RNA. However, the higher affinity for U-rich sequences is mainly due to faster association with U-rich RNA, which we propose is a reflection of the higher probability of association. Differences between TIAR and HuR are observed in their modes of binding to RNA. TIAR is able to bind deoxy-oligonucleotides with nanomolar affinity, whereas HuR affinity is reduced to a micromolar level. Studies with U-rich DNA reveal that TIAR binding depends less on the 2'-hydroxyl group of RNA than HuR binding. Finally we show that SAXS data, recorded for the first two domains of TIAR in complex with RNA, are more consistent with a flexible, elongated shape and not the compact shape that the first two domains of Hu proteins adopt upon binding to RNA. We thus propose that these triple-RRM proteins, which compete for the same binding sites in cells, interact with their targets in fundamentally different ways.

  18. Plasma interaction with tungsten samples in the COMPASS tokamak in ohmic ELMy H-modes

    International Nuclear Information System (INIS)

    Dimitrova, M; Weinzettl, V; Matejicek, J; Dejarnac, R; Stöckel, J; Havlicek, J; Panek, R; Popov, Tsv; Marinov, S; Costea, S

    2016-01-01

    This paper reports experimental results on plasma interaction with tungsten samples with or without pre-grown He fuzz. Under the experimental conditions, arcing was observed on the fuzzy tungsten samples, resulting in localized melting of the fuzz structure that did not extend into the bulk. The parallel power flux densities were obtained from the data measured by Langmuir probes embedded in the divertor tiles on the COMPASS tokamak. Measurements of the current-voltage probe characteristics were performed during ohmic ELMy H-modes reached in deuterium plasmas at a toroidal magnetic field B T = 1.15 T, plasma current I p = 300 kA and line-averaged electron density n e = 5×10 19 m -3 . The data obtained between the ELMs were processed by the recently published first-derivative probe technique for precise determination of the plasma potential and the electron energy distribution function (EEDF). The spatial profile of the EEDF shows that at the high-field side it is Maxwellian with a temperature of 5 -- 10 eV. The electron temperatures and the ion-saturation current density obtained were used to evaluate the radial distribution of the parallel power flux density as being in the order of 0.05 -- 7 MW/m 2 . (paper)

  19. Performance goals in conflictual social interactions: towards the distinction between two modes of relational conflict regulation.

    Science.gov (United States)

    Sommet, Nicolas; Darnon, Céline; Mugny, Gabriel; Quiamzade, Alain; Pulfrey, Caroline; Dompnier, Benoît; Butera, Fabrizio

    2014-03-01

    Socio-cognitive conflict has been defined as a situation of confrontation with a disagreeing other. Previous research suggests that individuals can regulate conflict in a relational way, namely by focusing on social comparison between relative levels of competences. Relational conflict regulation has been described as yielding particularly negative effects on social interactions and learning, but has been understudied. The present research addresses the question of the origin of relational conflict regulation by introducing a fundamental distinction between two types of regulation, one based on the affirmation of one's own point of view and the invalidation of the other's (i.e., 'competitive' regulation), the other corresponding to the protection of self-competence via compliance (i.e., 'protective' regulation). Three studies show that these modes of relational conflict regulation result from the endorsement of distinct performance goals, respectively, performance-approach goals (trying to outperform others) and performance-avoidance goals (avoiding performing more poorly than others). Theoretical implications for the literature on both conflict regulation and achievement goals are discussed. © 2012 The British Psychological Society.

  20. Open quantum systems and the two-level atom interacting with a single mode of the electromagnetic field

    International Nuclear Information System (INIS)

    Sandulescu, A.; Stefanescu, E.

    1987-07-01

    On the basis of Lindblad theory of open quantum systems we obtain new optical equations for the system of two-level atom interacting with a single mode of the electromagnetic field. The conventional Block equations in a generalized form with field phases are obtained in the hypothesis that all the terms are slowly varying in the rotating frame.(authors)

  1. Factors controlling the mode of rift interaction in brittle-ductile coupled systems: A 3D numerical study

    NARCIS (Netherlands)

    Allken, V.; Huismans, R.S.; Thieulot, C.

    2012-01-01

    The way individual faults and rift segments link up is a fundamental aspect of lithosphere extension and continental break-up. Little is known however about the factors that control the selection of the different modes of rift interaction observed in nature. Here we use state-of-the-art large

  2. Uncoupling PIP2-calmodulin regulation of Kv7.2 channels by an assembly destabilizing epileptogenic mutation.

    Science.gov (United States)

    Alberdi, Araitz; Gomis-Perez, Carolina; Bernardo-Seisdedos, Ganeko; Alaimo, Alessandro; Malo, Covadonga; Aldaregia, Juncal; Lopez-Robles, Carlos; Areso, Pilar; Butz, Elisabeth; Wahl-Schott, Christian; Villarroel, Alvaro

    2015-11-01

    We show that the combination of an intracellular bi-partite calmodulin (CaM)-binding site and a distant assembly region affect how an ion channel is regulated by a membrane lipid. Our data reveal that regulation by phosphatidylinositol(4,5)bisphosphate (PIP2) and stabilization of assembled Kv7.2 subunits by intracellular coiled-coil regions far from the membrane are coupled molecular processes. Live-cell fluorescence energy transfer measurements and direct binding studies indicate that remote coiled-coil formation creates conditions for different CaM interaction modes, each conferring different PIP2 dependency to Kv7.2 channels. Disruption of coiled-coil formation by epilepsy-causing mutation decreases apparent CaM-binding affinity and interrupts CaM influence on PIP2 sensitivity. © 2015. Published by The Company of Biologists Ltd.

  3. Fluid dynamics, cavitation, and tip-to-tissue interaction of longitudinal and torsional ultrasound modes during phacoemulsification.

    Science.gov (United States)

    Zacharias, Jaime; Ohl, Claus-Dieter

    2013-04-01

    To describe the fluidic events that occur in a test chamber during phacoemulsification with longitudinal and torsional ultrasound (US) modalities. Pasteur Ophthalmic Clinic Phacodynamics Laboratory, Santiago, Chile, and Nanyang Technological University, Singapore. Experimental study. Ultra-high-speed videos of a phacoemulsifying tip were recorded while the tip operated in longitudinal and torsional US modalities using variable US power. Two high-speed video cameras were used to record videos up to 625,000 frames per second. A high-intensity spotlight source was used for illumination to engage shadowgraphy techniques. Particle image velocimetry was used to evaluate fluidic patterns while a hyperbaric environmental system allowed the evaluation of cavitation effects. Tip-to-tissue interaction at high speed was evaluated using human cataract fragments. Particle imaging velocimetry showed the following flow patterns for longitudinal and torsional modes at high US powers: forward-directed streaming with longitudinal mode and backward-directed streaming with torsional mode. The ultrasound power threshold for the appearance of cavitation was 60% for longitudinal mode and 80% for torsional mode. Cavitation was suppressed with pressure of 1.0 bar for longitudinal mode and 0.3 bar for torsional mode. Generation of previously unseen stable gaseous microbubbles was noted. Tip-to-tissue interaction analysis showed the presence of cavitation bubbles close to the site of fragmentation with no apparent effect on cutting. High-speed imaging and particle image velocimetry yielded a better understanding and differentiated the fluidic pattern behavior between longitudinal and torsional US during phacoemulsification. These recordings also showed more detailed aspects of cavitation that clarified its role in lens material cutting for both modalities. Copyright © 2013 ASCRS and ESCRS. Published by Elsevier Inc. All rights reserved.

  4. Long-term evolution of electron distribution function due to nonlinear resonant interaction with whistler mode waves

    Science.gov (United States)

    Artemyev, Anton V.; Neishtadt, Anatoly I.; Vasiliev, Alexei A.

    2018-04-01

    Accurately modelling and forecasting of the dynamics of the Earth's radiation belts with the available computer resources represents an important challenge that still requires significant advances in the theoretical plasma physics field of wave-particle resonant interaction. Energetic electron acceleration or scattering into the Earth's atmosphere are essentially controlled by their resonances with electromagnetic whistler mode waves. The quasi-linear diffusion equation describes well this resonant interaction for low intensity waves. During the last decade, however, spacecraft observations in the radiation belts have revealed a large number of whistler mode waves with sufficiently high intensity to interact with electrons in the nonlinear regime. A kinetic equation including such nonlinear wave-particle interactions and describing the long-term evolution of the electron distribution is the focus of the present paper. Using the Hamiltonian theory of resonant phenomena, we describe individual electron resonance with an intense coherent whistler mode wave. The derived characteristics of such a resonance are incorporated into a generalized kinetic equation which includes non-local transport in energy space. This transport is produced by resonant electron trapping and nonlinear acceleration. We describe the methods allowing the construction of nonlinear resonant terms in the kinetic equation and discuss possible applications of this equation.

  5. Comprehensive analysis of pharmaceutical products using simultaneous mixed-mode (ion-exchange/reversed-phase) and hydrophilic interaction liquid chromatography.

    Science.gov (United States)

    Kazarian, Artaches A; Nesterenko, Pavel N; Soisungnoen, Phimpha; Burakham, Rodjana; Srijaranai, Supalax; Paull, Brett

    2014-08-01

    Liquid chromatographic assays were developed using a mixed-mode column coupled in sequence with a hydrophilic interaction liquid chromatography column to allow the simultaneous comprehensive analysis of inorganic/organic anions and cations, active pharmaceutical ingredients, and excipients (carbohydrates). The approach utilized dual sample injection and valve-mediated column switching and was based upon a single high-performance liquid chromatography gradient pump. The separation consisted of three distinct sequential separation mechanisms, namely, (i) ion-exchange, (ii) mixed-mode interactions under an applied dual gradient (reversed-phase/ion-exchange), and (iii) hydrophilic interaction chromatography. Upon first injection, the Scherzo SS C18 column (Imtakt) provided resolution of inorganic anions and cations under isocratic conditions, followed by a dual organic/salt gradient to elute active pharmaceutical ingredients and their respective organic counterions and potential degradants. At the top of the mixed-mode gradient (high acetonitrile content), the mobile phase flow was switched to a preconditioned hydrophilic interaction liquid chromatography column, and the standard/sample was reinjected for the separation of hydrophilic carbohydrates, some of which are commonly known excipients in drug formulations. The approach afforded reproducible separation and resolution of up to 23 chemically diverse solutes in a single run. The method was applied to investigate the composition of commercial cough syrups (Robitussin®), allowing resolution and determination of inorganic ions, active pharmaceutical ingredients, excipients, and numerous well-resolved unknown peaks. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Confinement of acoustical modes due to the electron-phonon interaction within 2D-electron gas

    International Nuclear Information System (INIS)

    Kochelap, V.A.; Gulseren, O.

    1992-09-01

    We study the confinement of acoustical modes within 2DEG due only to the electron-phonon interaction. The confined modes split out from the bulk phonons even at uniform lattice parameters, when the 2DEG is created by means of modulation doping. The effect is more pronounced when the wave vector q of the modes increases and is maximum at q = 2 k F (k F is the Fermi wave vector). In the case of several electron sheets the additional features of the confinement effect appear. In the limit of the strong electron-phonon coupling and high surface concentration of the electrons the considered system can suffer Peierls-type phase transition. In this case periodical deformation of the lattice and charge density wave are confined within the electron sheet. (author). 18 refs, 2 figs

  7. On Interactions of Oscillation Modes for a Weakly Non-Linear Undamped Elastic Beam with AN External Force

    Science.gov (United States)

    BOERTJENS, G. J.; VAN HORSSEN, W. T.

    2000-08-01

    In this paper an initial-boundary value problem for the vertical displacement of a weakly non-linear elastic beam with an harmonic excitation in the horizontal direction at the ends of the beam is studied. The initial-boundary value problem can be regarded as a simple model describing oscillations of flexible structures like suspension bridges or iced overhead transmission lines. Using a two-time-scales perturbation method an approximation of the solution of the initial-boundary value problem is constructed. Interactions between different oscillation modes of the beam are studied. It is shown that for certain external excitations, depending on the phase of an oscillation mode, the amplitude of specific oscillation modes changes.

  8. Oliver E. Buckley Condensed Matter Prize: Emergent gravity from interacting Majorana modes

    Science.gov (United States)

    Kitaev, Alexei

    I will describe a concrete many-body Hamiltonian that exhibits some features of a quantum black hole. The Sachdev-Ye-Kitaev model is a system of N >> 1 Majorana modes that are all coupled by random 4-th order terms. The problem admits an approximate dynamic mean field solution. At low temperatures, there is a fluctuating collective mode that corresponds to reparametrization of time. The effective action for this mode is equivalent to dilaton gravity in two space-time dimensions. Some important questions are how to quantize the reparametrization mode in Lorentzian time, include dissipative effects, and understand this system from the quantum information perspective. Supported by the Simons Foundation, Award Number 376205.

  9. ARG1 (altered response to gravity) encodes a DnaJ-like protein that potentially interacts with the cytoskeleton

    Science.gov (United States)

    Sedbrook, J. C.; Chen, R.; Masson, P. H.

    1999-01-01

    Gravitropism allows plant organs to direct their growth at a specific angle from the gravity vector, promoting upward growth for shoots and downward growth for roots. Little is known about the mechanisms underlying gravitropic signal transduction. We found that mutations in the ARG1 locus of Arabidopsis thaliana alter root and hypocotyl gravitropism without affecting phototropism, root growth responses to phytohormones or inhibitors of auxin transport, or starch accumulation. The positional cloning of ARG1 revealed a DnaJ-like protein containing a coiled-coil region homologous to coiled coils found in cytoskeleton-interacting proteins. These data suggest that ARG1 participates in a gravity-signaling process involving the cytoskeleton. A combination of Northern blot studies and analysis of ARG1-GUS fusion-reporter expression in transgenic plants demonstrated that ARG1 is expressed in all organs. Ubiquitous ARG1 expression in Arabidopsis and the identification of an ortholog in Caenorhabditis elegans suggest that ARG1 is involved in other essential processes.

  10. Theory of Collective Spin-Wave Modes of Interacting Ferromagnetic Spheres

    Science.gov (United States)

    2004-09-29

    Office (Durham) through Contract No. CS0001028. R. A. thanks also Proyecto Fondecyt Grant No. 7030063. *Present address: Universidad de Chile...Departamento de Fisica FCFM, Santiago, Chile. 1 For examples of experimental studies of the collective spin wave modes of superlattices and multilayers, see M...character to those shown above. In this case, there is no simple symmetry de - composition one canmake for the collective modes, so all branches appear

  11. Research on the Operation Mode of Intelligent-town Energy Internet Based on Source-Load Interaction

    Science.gov (United States)

    Li, Hao; Li, Wen; Miao, Bo; Li, Bin; Liu, Chang; Lv, Zhipeng

    2018-01-01

    On the background of the rise of intelligence and the increasing deepening of “Internet +”application, the energy internet has become the focus of the energy research field. This paper, based on the fundamental understanding on the energy internet of the intelligent town, discusses the mode of energy supply in the source-load interactive region, and gives an in-depth study on the output characteristics of the energy supply side and the load characteristics of the demand side, so as to derive the law of energy-load interaction of the intelligent-town energy internet.

  12. Interaction Mode between Inclusion Complex of Vitamin K3 with γ- Cyclodextrin and Herring-Sperm DNA.

    Science.gov (United States)

    Tang, Yan; Cai, Li; Xue, Kang; Wang, Chunling; Xiong, Xiaoli

    2016-05-03

    Methods including spectroscopy, electronic chemistry and thermodynamics were used to study the inclusion effect between γ-cyclodextrin (CD) and vitamin K3(K3), as well as the interaction mode between herring-sperm DNA (hsDNA) and γ-CD-K3 inclusion complex. The results from ultraviolet spectroscopic method indicated that VK3 and γ-CD formed 1:1 inclusion complex, with the inclusion constant Kf = 1.02 × 10(4) L/mol, which is based on Benesi-Hildebrand's viewpoint. The outcomes from the probe method and Scatchard methods suggested that the interaction mode between γ-CD-K3 and DNA was a mixture mode, which included intercalation and electrostatic binding effects. The binding constants were K (θ)25°C = 2.16 × 10(4) L/mol, and K(θ)37°C = 1.06 × 10(4) L/mol. The thermodynamic functions of the interaction between γ-CD-K3 and DNA were ΔrHm(θ) = -2.74 × 10(4) J/mol, ΔrSm(θ) = 174.74 J·mol(-1)K(-1), therefore, both ΔrHm(θ) (enthalpy) and ΔrSm(θ) (entropy) worked as driven forces in this action.

  13. Interactions between default mode and control networks as a function of increasing cognitive reasoning complexity.

    Science.gov (United States)

    Hearne, Luke; Cocchi, Luca; Zalesky, Andrew; Mattingley, Jason B

    2015-07-01

    Successful performance of challenging cognitive tasks depends on a consistent functional segregation of activity within the default-mode network, on the one hand, and control networks encompassing frontoparietal and cingulo-opercular areas on the other. Recent work, however, has suggested that in some cognitive control contexts nodes within the default-mode and control networks may actually cooperate to achieve optimal task performance. Here, we used functional magnetic resonance imaging to examine whether the ability to relate variables while solving a cognitive reasoning problem involves transient increases in connectivity between default-mode and control regions. Participants performed a modified version of the classic Wason selection task, in which the number of variables to be related is systematically varied across trials. As expected, areas within the default-mode network showed a parametric deactivation with increases in relational complexity, compared with neural activity in null trials. Critically, some of these areas also showed enhanced connectivity with task-positive control regions. Specifically, task-based connectivity between the striatum and the angular gyri, and between the thalamus and right temporal pole, increased as a function of relational complexity. These findings challenge the notion that functional segregation between regions within default-mode and control networks invariably support cognitive task performance, and reveal previously unknown roles for the striatum and thalamus in managing network dynamics during cognitive reasoning. © 2015 Wiley Periodicals, Inc.

  14. Simulation of operation modes of isochronous cyclotron by a new interactive method

    International Nuclear Information System (INIS)

    Taraszkiewicz, R.; Talach, M.; Sulikowski, J.; Doruch, H.; Norys, T.; Sroka, A.; Kiyan, I.N.; )

    2007-01-01

    Operation mode simulation methods are based on selection of trim coil currents in the isochronous cyclotron for formation of the required magnetic field at a certain level of the main coil current. The traditional current selection method is based on finding a solution for all trim coils simultaneously. After setting the calculated operation mode, it is usually necessary to perform a control measurement of the magnetic field map and to repeat the calculation for a more accurate solution. The new current selection method is based on successively finding solutions for each particular trim coil. The trim coils are taken one by one in reverse order from the edge to the center of the isochronous cyclotron. The new operation mode simulation method is based on the new current selection method. The new method, as against the traditional one, includes iterative calculation of the kinetic energy at the extraction radius. A series of experiments on proton beam formation within the range of working acceleration radii at extraction energies from 32 to 59 MeV, which were carried out at the AIC144 multipurpose isochronous cyclotron (designed mainly for the eye melanoma treatment and production of radioisotopes) at the INP PAS (Cracow), showed that the new method makes unnecessary any control measurements of magnetic fields for getting the desired operation mode, which indicates a high accuracy of the calculation. (authors)

  15. Different modes of APC/C activation control growth and neuron-glia interaction in the developing Drosophila eye.

    Science.gov (United States)

    Neuert, Helen; Yuva-Aydemir, Yeliz; Silies, Marion; Klämbt, Christian

    2017-12-15

    The development of the nervous system requires tight control of cell division, fate specification and migration. The anaphase-promoting complex/cyclosome (APC/C) is an E3 ubiquitin ligase that affects different steps of cell cycle progression, as well as having postmitotic functions in nervous system development. It can therefore link different developmental stages in one tissue. The two adaptor proteins, Fizzy/Cdc20 and Fizzy-related/Cdh1, confer APC/C substrate specificity. Here, we show that two distinct modes of APC/C function act during Drosophila eye development. Fizzy/Cdc20 controls the early growth of the eye disc anlage and the concomitant entry of glial cells onto the disc. In contrast, fzr/cdh1 acts during neuronal patterning and photoreceptor axon growth, and subsequently affects neuron-glia interaction. To further address the postmitotic role of Fzr/Cdh1 in controlling neuron-glia interaction, we identified a series of novel APC/C candidate substrates. Four of our candidate genes are required for fzr/cdh1 -dependent neuron-glia interaction, including the dynein light chain Dlc90F Taken together, our data show how different modes of APC/C activation can couple early growth and neuron-glia interaction during eye disc development. © 2017. Published by The Company of Biologists Ltd.

  16. Application of the H-Mode, a Design and Interaction Concept for Highly Automated Vehicles, to Aircraft

    Science.gov (United States)

    Goodrich, Kenneth H.; Flemisch, Frank O.; Schutte, Paul C.; Williams, Ralph A.

    2006-01-01

    Driven by increased safety, efficiency, and airspace capacity, automation is playing an increasing role in aircraft operations. As aircraft become increasingly able to autonomously respond to a range of situations with performance surpassing human operators, we are compelled to look for new methods that help us understand their use and guide their design using new forms of automation and interaction. We propose a novel design metaphor to aid the conceptualization, design, and operation of highly-automated aircraft. Design metaphors transfer meaning from common experiences to less familiar applications or functions. A notable example is the "Desktop metaphor" for manipulating files on a computer. This paper describes a metaphor for highly automated vehicles known as the H-metaphor and a specific embodiment of the metaphor known as the H-mode as applied to aircraft. The fundamentals of the H-metaphor are reviewed followed by an overview of an exploratory usability study investigating human-automation interaction issues for a simple H-mode implementation. The envisioned application of the H-mode concept to aircraft is then described as are two planned evaluations.

  17. Nonlinear interaction between a pair of oblique modes in a supersonic mixing layer: Long-wave limit

    Science.gov (United States)

    Balsa, Thomas F.; Gartside, James

    1995-01-01

    The nonlinear interaction between a pair of symmetric, oblique, and spatial instability modes is studied in the long-wave limit using asymptotic methods. The base flow is taken to be a supersonic mixing layer whose Mach number is such that the corresponding vortex sheet is marginally stable according to Miles' criterion. It is shown that the amplitude of the mode obeys a nonlinear integro-differential equation. Numerical solutions of this equation show that, when the obliqueness angle is less than pi/4, the effect of the nonlinearity is to enhance the growth rate of the instability. The solution terminates in a singularity at a finite streamwise location. This result is reminiscent of that obtained in the vicinity of the neutral point by other authors in several different types of flows. On the other hand, when the obliqueness angle is more than pi/4, the streamwise development of the amplitude is characterized by a series of modulations. This arises from the fact that the nonlinear term in the amplitude equation may be either stabilizing or destabilizing, depending on the value of the streamwise coordinate. However, even in this case the amplitude of the disturbance increases, though not as rapidly as in the case for which the angle is less than pi/4. Quite generally then, the nonlinear interaction between two oblique modes in a supersonic mixing layer enhances the growth of the disturbance.

  18. Expanding Interaction Potentials within Virtual Environments: Investigating the Usability of Speech and Manual Input Modes for Decoupled Interaction

    Directory of Open Access Journals (Sweden)

    Alex Stedmon

    2011-01-01

    Full Text Available Distributed technologies and ubiquitous computing now support users who may be detached or decoupled from traditional interactions. In order to investigate the potential usability of speech and manual input devices, an evaluation of speech input across different user groups and a usability assessment of independent-user and collaborative-user interactions was conducted. Whilst the primary focus was on a formative usability evaluation, the user group evaluation provided a formal basis to underpin the academic rigor of the exercise. The results illustrate that using a speech interface is important in understanding user acceptance of such technologies. From the usability assessment it was possible to translate interactions and make them compatible with innovative input devices. This approach to interaction is still at an early stage of development, and the potential or validity of this interfacing concept is still under evaluation; however, as a concept demonstrator, the results of these initial evaluations demonstrate the potential usability issues of both input devices as well as highlighting their suitability for advanced virtual applications.

  19. Structural Dynamics Investigation of Human Family 1 & 2 Cystatin-Cathepsin L1 Interaction: A Comparison of Binding Modes.

    Directory of Open Access Journals (Sweden)

    Suman Kumar Nandy

    Full Text Available Cystatin superfamily is a large group of evolutionarily related proteins involved in numerous physiological activities through their inhibitory activity towards cysteine proteases. Despite sharing the same cystatin fold, and inhibiting cysteine proteases through the same tripartite edge involving highly conserved N-terminal region, L1 and L2 loop; cystatins differ widely in their inhibitory affinity towards C1 family of cysteine proteases and molecular details of these interactions are still elusive. In this study, inhibitory interactions of human family 1 & 2 cystatins with cathepsin L1 are predicted and their stability and viability are verified through protein docking & comparative molecular dynamics. An overall stabilization effect is observed in all cystatins on complex formation. Complexes are mostly dominated by van der Waals interaction but the relative participation of the conserved regions varied extensively. While van der Waals contacts prevail in L1 and L2 loop, N-terminal segment chiefly acts as electrostatic interaction site. In fact the comparative dynamics study points towards the instrumental role of L1 loop in directing the total interaction profile of the complex either towards electrostatic or van der Waals contacts. The key amino acid residues surfaced via interaction energy, hydrogen bonding and solvent accessible surface area analysis for each cystatin-cathepsin L1 complex influence the mode of binding and thus control the diverse inhibitory affinity of cystatins towards cysteine proteases.

  20. Assessment of soil-structure interaction effects based on simple modes

    International Nuclear Information System (INIS)

    Philippacopoulos, A.J.; Miller, C.A.

    1983-01-01

    Soil-structure interaction effects are investigated using a simple mathematical model which employs three degrees-of-freedom. The foundation is approximated by a homogeneous, isotropic, elastic half-space. Harmonic functions and a recorded earthquake are used to represent the free-field input motion. Variations of the response characteristics due to structural and interaction parameters are demonstrated. Response spectra are presented that display the magnitude of the maximum structural response for a range of fixed-base structural frequencies, interaction frequencies and damping. Conclusions are obtained regarding the behavior of the response of the soil-structure system. The findings reported herein can be used for the interpretation of the results of soil-structure interaction analyses of nuclear plant structures that are performed with available computer codes

  1. An in silico analysis of the binding modes and binding affinities of small molecule modulators of PDZ-peptide interactions.

    Directory of Open Access Journals (Sweden)

    Garima Tiwari

    Full Text Available Inhibitors of PDZ-peptide interactions have important implications in a variety of biological processes including treatment of cancer and Parkinson's disease. Even though experimental studies have reported characterization of peptidomimetic inhibitors of PDZ-peptide interactions, the binding modes for most of them have not been characterized by structural studies. In this study we have attempted to understand the structural basis of the small molecule-PDZ interactions by in silico analysis of the binding modes and binding affinities of a set of 38 small molecules with known K(i or K(d values for PDZ2 and PDZ3 domains of PSD-95 protein. These two PDZ domains show differential selectivity for these compounds despite having a high degree of sequence similarity and almost identical peptide binding pockets. Optimum binding modes for these ligands for PDZ2 and PDZ3 domains were identified by using a novel combination of semi-flexible docking and explicit solvent molecular dynamics (MD simulations. Analysis of the binding modes revealed most of the peptidomimectic ligands which had high K(i or K(d moved away from the peptide binding pocket, while ligands with high binding affinities remained in the peptide binding pocket. The differential specificities of the PDZ2 and PDZ3 domains primarily arise from differences in the conformation of the loop connecting βB and βC strands, because this loop interacts with the N-terminal chemical moieties of the ligands. We have also computed the MM/PBSA binding free energy values for these 38 compounds with both the PDZ domains from multiple 5 ns MD trajectories on each complex i.e. a total of 228 MD trajectories of 5 ns length each. Interestingly, computational binding free energies show good agreement with experimental binding free energies with a correlation coefficient of approximately 0.6. Thus our study demonstrates that combined use of docking and MD simulations can help in identification of potent inhibitors

  2. Soft mode characteristics of up-up-down-down spin chains: The role of exchange interactions on lattice dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Y. J. [School of Physics and Electronic Engineering, Jiangsu Second Normal University, Nanjing 210013 (China); Laboratory of Solid State Microstructures, Nanjing University, Nanjing 210093 (China); Gao, Y. J.; Ge, C. N [School of Physics and Electronic Engineering, Jiangsu Second Normal University, Nanjing 210013 (China); Guo, Y. Y. [College of Electronic Science and Engineering, Nanjing University of Posts and Telecommunications, Nanjing 210003 (China); Yan, Z. B.; Liu, J.-M., E-mail: liujm@nju.edu.cn [Laboratory of Solid State Microstructures, Nanjing University, Nanjing 210093 (China)

    2015-05-07

    In this work, the dynamics of a diatomic chain is investigated with ↑↑↓↓ spin order in which the dispersion relation characterizes the effect of magnetic interactions on the lattice dynamics. The optical or acoustic mode softening in the center or boundary of the Brillouin zone can be observed, indicating the transitions of ferroelectric state, antiferromagnetic state, or ferroelastic state. The coexistence of the multiferroic orders related to the ↑↑↓↓ spin order represents a type of intrinsic multiferroic with strong ferroelectric order and different microscopic mechanisms.

  3. Dipolar interaction induced band gaps and flat modes in surface-modulated magnonic crystals

    Science.gov (United States)

    Gallardo, R. A.; Schneider, T.; Roldán-Molina, A.; Langer, M.; Fassbender, J.; Lenz, K.; Lindner, J.; Landeros, P.

    2018-04-01

    Theoretical results for the magnetization dynamics of a magnonic crystal formed by grooves on the surface of a ferromagnetic film, called a surface-modulated magnonic crystal, are presented. For such a system, the role of the periodic dipolar field induced by the geometrical modulation is addressed by using the plane-wave method. The results reveal that, under the increasing of the depth of the grooves, zones with magnetizing and demagnetizing fields act on the system in such a way that magnonic band gaps are observed in both Damon-Eshbach and backward volume geometries. Particularly, in the backward volume configuration, high-frequency band gaps and low-frequency flat modes are obtained. By taking into account the properties of the internal field induced by the grooves, the flattening of the modes and their shift towards low frequencies are discussed and explained. To test the validity of the model, the theoretical results of this work are confirmed by micromagnetic simulations, and good agreement between both methods is achieved. The theoretical model allows for a detailed understanding of the physics underlying these kinds of systems, thereby providing an outlook for potential applications on magnonic devices.

  4. Modes of interaction between nanostructured metal and a conducting mirror as a function of separation and incident polarization

    Science.gov (United States)

    Bonnie, F.; Arnold, M. D.; Smith, G. B.; Gentle, A. R.

    2013-09-01

    The optical resonances that occur in nanostructured metal layers are modulated in thin film stacks if the nanostructured layer is separated from a reflecting conducting layer by various thicknesses of thin dielectric. We have measured and modeled the optical response of interacting silver layers, with alumina spacer thickness ranging from a few nm to 50 nm, for s- and p-polarized incident light, and a range of incident angles. Standard thin film models, including standard effective medium models for the nanostructured layer, will break down for spacer thickness below a critical threshold. For example, with polarisation in the film plane and some nano-islands, it may occur at around 10 nm depending on spacer refractive index. Of particular interest here are novel effects observed with the onset of percolation in the nanolayer. Hot spot effects can be modified by nearby mirrors. Other modes to consider include (a) a two-particle mode involving a particle and its mirror image (b) A Fano resonance from hybridisation of localized and de-localised plasmon modes (c) a Babinet's core-(partial) shell particle with metal core-dielectric shell in metal (d) spacing dependent phase modulation (e) the impact of field gradients induced by the mirror at the nano-layer.

  5. Elevated temperature cyclic deformation of stainless-steel and interaction effects with other modes of deformation

    International Nuclear Information System (INIS)

    Turner, A.P.L.

    1976-01-01

    Since pertinent information concerning the deformation history of a material is stored in its current structure, an attempt has been made to determine the number of state variables necessary to uniquely describe the material's present condition. An experimental program has been carried out to determine the number of state variables which is required to describe the tensile test, cyclic, and creep behavior of 304 stainless steel at elevated temperature. Tests have been conducted at 300 0 C and 560 0 C which correspond to homologous temperatures of 1 / 3 and 1 / 2 , respectively. The experiments consisted of subjecting samples to deformation histories during which the mode of deformation was changed so that two material responses could be measured for the same state of the material. Results strongly suggest that at least two state variables are necessary

  6. Specific modes of vibratory technological machines: mathematical models, peculiarities of interaction of system elements

    Science.gov (United States)

    Eliseev, A. V.; Sitov, I. S.; Eliseev, S. V.

    2018-03-01

    The methodological basis of constructing mathematical models of vibratory technological machines is developed in the article. An approach is proposed that makes it possible to introduce a vibration table in a specific mode that provides conditions for the dynamic damping of oscillations for the zone of placement of a vibration exciter while providing specified vibration parameters in the working zone of the vibration table. The aim of the work is to develop methods of mathematical modeling, oriented to technological processes with long cycles. The technologies of structural mathematical modeling are used with structural schemes, transfer functions and amplitude-frequency characteristics. The concept of the work is to test the possibilities of combining the conditions for reducing loads with working components of a vibration exciter while simultaneously maintaining sufficiently wide limits in variating the parameters of the vibrational field.

  7. Shear flows at the tokamak edge and their interaction with edge-localized modes

    International Nuclear Information System (INIS)

    Aydemir, A. Y.

    2007-01-01

    Shear flows in the scrape-off layer (SOL) and the edge pedestal region of tokamaks are shown to arise naturally out of transport processes in a magnetohydrodynamic model. In quasi-steady-state conditions, collisional resistivity coupled with a simple bootstrap current model necessarily leads to poloidal and toroidal flows, mainly localized to the edge and SOL. The role of these flows in the grad-B drift direction dependence of the power threshold for the L (low) to H (high) transition, and their effect on core rotation, are discussed. Theoretical predictions based on symmetries of the underlying equations, coupled with computational results, are found to be in agreement with observations in Alcator C-Mod [Phys. Plasmas 12, 056111 (2005)]. The effects of these self-consistent flows on linear peeling/ballooning modes and their nonlinear consequences are also examined

  8. New ICT's and social interaction : modelling communication frequency and communication mode choice

    NARCIS (Netherlands)

    Berg, van den P.E.W.; Arentze, T.A.; Timmermans, H.J.P.

    2012-01-01

    New information and communication technologies (ICTs) have provided new ways of communicating and maintaining social networks. However, relatively little is known on the effect of ICT-use on social interaction. Therefore, this article aims to explore the factors influencing individuals’

  9. Pair Interactions and Mode of Communication: Comparing Face-to-Face and Computer Mediated Communication

    Science.gov (United States)

    Tan, Lan Liana; Wigglesworth, Gillian; Storch, Neomy

    2010-01-01

    In today's second language classrooms, students are often asked to work in pairs or small groups. Such collaboration can take place face-to-face, but now more often via computer mediated communication. This paper reports on a study which investigated the effect of the medium of communication on the nature of pair interaction. The study involved…

  10. Estrogen Receptor Folding Modulates cSrc Kinase SH2 Interaction via a Helical Binding Mode

    NARCIS (Netherlands)

    Nieto, Lidia; Tharun, Inga M; Balk, Mark; Wienk, Hans; Boelens, Rolf; Ottmann, Christian; Milroy, Lech-Gustav; Brunsveld, Luc

    2015-01-01

    The estrogen receptors (ERs) feature, next to their transcriptional role, important nongenomic signaling actions, with emerging clinical relevance. The Src Homology 2 (SH2) domain mediated interaction between cSrc kinase and ER plays a key role in this; however the molecular determinants of this

  11. Estrogen receptor folding modulates cSrc kinase SH2 interaction via a helical binding mode

    NARCIS (Netherlands)

    Nieto, L.; Tharun, I.M.; Balk, M.; Wienk, H.; Boelens, R.; Ottmann, C.; Milroy, L.-G.; Brunsveld, L.

    2015-01-01

    The estrogen receptors (ERs) feature, next to their transcriptional role, important nongenomic signaling actions, with emerging clinical relevance. The Src Homology 2 (SH2) domain mediated interaction between cSrc kinase and ER plays a key role in this; however the molecular determinants of this

  12. Dynamics of entanglement of a three-level atom in motion interacting with two coupled modes including parametric down conversion

    Science.gov (United States)

    Faghihi, M. J.; Tavassoly, M. K.; Hatami, M.

    In this paper, a model by which we study the interaction between a motional three-level atom and two-mode field injected simultaneously in a bichromatic cavity is considered; the three-level atom is assumed to be in a Λ-type configuration. As a result, the atom-field and the field-field interaction (parametric down conversion) will be appeared. It is shown that, by applying a canonical transformation, the introduced model can be reduced to a well-known form of the generalized Jaynes-Cummings model. Under particular initial conditions, which may be prepared for the atom and the field, the time evolution of state vector of the entire system is analytically evaluated. Then, the dynamics of atom by considering ‘atomic population inversion’ and two different measures of entanglement, i.e., ‘von Neumann entropy’ and ‘idempotency defect’ is discussed, in detail. It is deduced from the numerical results that, the duration and the maximum amount of the considered physical quantities can be suitably tuned by selecting the proper field-mode structure parameter p and the detuning parameters.

  13. Anticancer drug mithramycin interacts with core histones: An additional mode of action of the DNA groove binder

    Directory of Open Access Journals (Sweden)

    Amrita Banerjee

    2014-01-01

    Full Text Available Mithramycin (MTR is a clinically approved DNA-binding antitumor antibiotic currently in Phase 2 clinical trials at National Institutes of Health for treatment of osteosarcoma. In view of the resurgence in the studies of this generic antibiotic as a human medicine, we have examined the binding properties of MTR with the integral component of chromatin – histone proteins – as a part of our broad objective to classify DNA-binding molecules in terms of their ability to bind chromosomal DNA alone (single binding mode or both histones and chromosomal DNA (dual binding mode. The present report shows that besides DNA, MTR also binds to core histones present in chromatin and thus possesses the property of dual binding in the chromatin context. In contrast to the MTR–DNA interaction, association of MTR with histones does not require obligatory presence of bivalent metal ion like Mg2+. As a consequence of its ability to interact with core histones, MTR inhibits histone H3 acetylation at lysine 18, an important signature of active chromatin, in vitro and ex vivo. Reanalysis of microarray data of Ewing sarcoma cell lines shows that upon MTR treatment there is a significant down regulation of genes, possibly implicating a repression of H3K18Ac-enriched genes apart from DNA-binding transcription factors. Association of MTR with core histones and its ability to alter post-translational modification of histone H3 clearly indicates an additional mode of action of this anticancer drug that could be implicated in novel therapeutic strategies.

  14. Interaction effects on the unstable discharge-energy characteristic of pump-turbine in pump mode

    Science.gov (United States)

    Tao, R.; Xiao, R. F.; Yang, W.; Liu, W. C.

    2013-12-01

    For a pump-turbine, unstable discharge-energy characteristic is an important factor for operating stability. In this study, the rotor-stator interaction effects on the pump-turbine which has the unstable discharge-energy characteristic has been studied. A series of transient CFD simulations under different discharge conditions have been conducted. Through the contrast between the simulations and experiments, it is found out that the energy decline is strongly affected by the flow loss in the adjustable vane. More importantly, the magnitude and direction of fluid flowing into the adjustable vane are varying with the impeller rotating. Disordered flow structure occurs in the adjustable vane and causes the energy losses due to the interaction effects. Based on this study, improvements on the flow uniformity at impeller outlet will help us to solve the unstable discharge-energy problem.

  15. Quadrupole modes in linearized beam-beam interaction in e+e- colliding rings

    International Nuclear Information System (INIS)

    Matsumoto, Shuji; Hirata, Kohji.

    1992-01-01

    The dynamic-beta model is extended, incorporating the synchrotron radiation effects. The model yields dynamic-emittance effect. The steady-state envelope matrix is explicitly obtained. Both equal-beam and flip-flop solutions are found. The stability of the steady-state solutions are investigated by numerical calculations. The model illustrates some characteristic features of the beam-beam interaction at e + e - colliding rings in spite of containing some qualitatively unrealistic points. (author)

  16. Dynamics of impurity modes and electron–phonon interaction in Heavy Fermion (HF) systems

    International Nuclear Information System (INIS)

    Shadangi, N.; Sahoo, J.; Mohanty, S.; Nayak, P.

    2014-01-01

    A theoretical explanation is provided to understand the effect of small concentration of impurities characterized by change in mass and nearest neighbor force constants on the phonon spectrum as well as on the electron–phonon interaction in some Heavy Fermion (HF) systems in the normal state within theoretical framework of the Periodic Anderson Model (PAM). Three different mechanisms of the electron–phonon interactions, namely, the usual interaction between the phonons with the electrons in the f-bands, electrons arising from that of hybridization term of PAM and the local electron–phonon coupling at the impurity sites are considered. Coherent Potential Approximation (CPA) is used to evaluate the configuration averaged self–energy and the total Green function. For simplicity of calculation the CPA self–energy is evaluated in Average t -matrix Approximation (ATA). The analytical analysis is carried out for finite T in the long wavelength limit. The influence of impurity mass parameter λ and other system parameters such as d, the position of f-level, the effective coupling strength g on the calculated re-normalized phonon frequency and the excitation spectrum through the spectral function is studied. The numerical analysis of the results does show the influence of impurities as evident from different plots in this paper.

  17. Electron acceleration at Jupiter: input from cyclotron-resonant interaction with whistler-mode chorus waves

    Directory of Open Access Journals (Sweden)

    E. E. Woodfield

    2013-10-01

    Full Text Available Jupiter has the most intense radiation belts of all the outer planets. It is not yet known how electrons can be accelerated to energies of 10 MeV or more. It has been suggested that cyclotron-resonant wave-particle interactions by chorus waves could accelerate electrons to a few MeV near the orbit of Io. Here we use the chorus wave intensities observed by the Galileo spacecraft to calculate the changes in electron flux as a result of pitch angle and energy diffusion. We show that, when the bandwidth of the waves and its variation with L are taken into account, pitch angle and energy diffusion due to chorus waves is a factor of 8 larger at L-shells greater than 10 than previously shown. We have used the latitudinal wave intensity profile from Galileo data to model the time evolution of the electron flux using the British Antarctic Survey Radiation Belt (BAS model. This profile confines intense chorus waves near the magnetic equator with a peak intensity at ∼5° latitude. Electron fluxes in the BAS model increase by an order of magnitude for energies around 3 MeV. Extending our results to L = 14 shows that cyclotron-resonant interactions with chorus waves are equally important for electron acceleration beyond L = 10. These results suggest that there is significant electron acceleration by cyclotron-resonant interactions at Jupiter contributing to the creation of Jupiter's radiation belts and also increasing the range of L-shells over which this mechanism should be considered.

  18. Learning in Different Modes: The Interaction Between Incremental and Radical Change

    DEFF Research Database (Denmark)

    Petersen, Anders Hedegaard; Boer, Harry; Gertsen, Frank

    2004-01-01

    The objective of the study presented in this article is to contribute to the development of theory on continuous innovation, i.e. the combination of operationally effective exploitation and strategically flexible exploration. A longitudinal case study is presented of the interaction between...... incremental and radical change in Danish company, observed through the lens of organizational learning. The radical change process is described in five phases, each of which had its own effects on incremental change initiatives in the company. The research identified four factors explaining these effects, all...

  19. Observation of dynamic interactions between fundamental and second-harmonic modes in a high-power sub-terahertz gyrotron operating in regimes of soft and hard self-excitation.

    Science.gov (United States)

    Saito, Teruo; Tatematsu, Yoshinori; Yamaguchi, Yuusuke; Ikeuchi, Shinji; Ogasawara, Shinya; Yamada, Naoki; Ikeda, Ryosuke; Ogawa, Isamu; Idehara, Toshitaka

    2012-10-12

    Dynamic mode interaction between fundamental and second-harmonic modes has been observed in high-power sub-terahertz gyrotrons [T. Notake et al., Phys. Rev. Lett. 103, 225002 (2009); T. Saito et al. Phys. Plasmas 19, 063106 (2012)]. Interaction takes place between a parasitic fundamental or first-harmonic (FH) mode and an operating second-harmonic (SH) mode, as well as among SH modes. In particular, nonlinear excitation of the parasitic FH mode in the hard self-excitation regime with assistance of a SH mode in the soft self-excitation regime was clearly observed. Moreover, both cases of stable two-mode oscillation and oscillation of the FH mode only were observed. These observations and theoretical analyses of the dynamic behavior of the mode interaction verify the nonlinear hard self-excitation of the FH mode.

  20. Interaction of the Yersinia pestis type III regulatory proteins LcrG and LcrV occurs at a hydrophobic interface

    Directory of Open Access Journals (Sweden)

    Nilles Matthew L

    2002-06-01

    Full Text Available Abstract Background Secretion of anti-host proteins by Yersinia pestis via a type III mechanism is not constitutive. The process is tightly regulated and secretion occurs only after an appropriate signal is received. The interaction of LcrG and LcrV has been demonstrated to play a pivotal role in secretion control. Previous work has shown that when LcrG is incapable of interacting with LcrV, secretion of anti-host proteins is prevented. Therefore, an understanding of how LcrG interacts with LcrV is required to evaluate how this interaction regulates the type III secretion system of Y. pestis. Additionally, information about structure-function relationships within LcrG is necessary to fully understand the role of this key regulatory protein. Results In this study we demonstrate that the N-terminus of LcrG is required for interaction with LcrV. The interaction likely occurs within a predicted amphipathic coiled-coil domain within LcrG. Our results demonstrate that the hydrophobic face of the putative helix is required for LcrV interaction. Additionally, we demonstrate that the LcrG homolog, PcrG, is incapable of blocking type III secretion in Y. pestis. A genetic selection was utilized to obtain a PcrG variant capable of blocking secretion. This PcrG variant allowed us to locate a region of LcrG involved in secretion blocking. Conclusion Our results demonstrate that LcrG interacts with LcrV via hydrophobic interactions located in the N-terminus of LcrG within a predicted coiled-coil motif. We also obtained preliminary evidence that the secretion blocking activity of LcrG is located between amino acids 39 and 53.

  1. Staphylokinase has distinct modes of interaction with antimicrobial peptides, modulating its plasminogen-activation properties

    Science.gov (United States)

    Nguyen, Leonard T.; Vogel, Hans J.

    2016-01-01

    Staphylokinase (Sak) is a plasminogen activator protein that is secreted by many Staphylococcus aureus strains. Sak also offers protection by binding and inhibiting specific antimicrobial peptides (AMPs). Here, we evaluate Sak as a more general interaction partner for AMPs. Studies with melittin, mCRAMP, tritrpticin and bovine lactoferricin indicate that the truncation of the first ten residues of Sak (SakΔN10), which occurs in vivo and uncovers important residues in a bulge region, improves its affinity for AMPs. Melittin and mCRAMP have a lower affinity for SakΔN10, and in docking studies, they bind to the N-terminal segment and bulge region of SakΔN10. By comparison, lactoferricin and tritrpticin form moderately high affinity 1:1 complexes with SakΔN10 and their cationic residues form several electrostatic interactions with the protein’s α-helix. Overall, our work identifies two distinct AMP binding surfaces on SakΔN10 whose occupation would lead to either inhibition or promotion of its plasminogen activating properties. PMID:27554435

  2. Search for primarily non-interacting decay modes of the upsilon

    International Nuclear Information System (INIS)

    Leffler, J.S.

    1986-03-01

    The hadronic transition UPSILON(2S) → π 0 π 0 UPSILON(1S) is utilized to search for the reactions: UPSILON(1S) → non-interacting particles and UPSILON(1S) → γ + non-interacting particles. 44 pb -1 of UPSILON(2S) data were taken by the Crystal Ball detector at the DORIS II storage ring in order to perform this study. An upper limit of BR(UPSILON → Unseen) -1 of UPSILON(2S) data was available for this study. An upper limit on the branching ratio BR(UPSILON → γ + Unseen) is measured for photon energies in the range 500 MeV -3 (90% C.L.), is obtained. The compact size of the Crystal Ball detector enhances the observable branching ratio for noninteracting particles with short lifetimes such as massive axions. The identification of the recent Darmstadt events with a 1.6 MeV axion is excluded by the present result assuming the minimal Peccei-Quinn model. Limits on the spontaneous supersymmetry breaking mass scale are also derived as a function of gravitino mass

  3. Interactions between excitation and extraction modes in an organic-based plasmon-emitting diode

    Energy Technology Data Exchange (ETDEWEB)

    Chiu, Nan-Fu, E-mail: nfchiu@ntnu.edu.tw [Institute of Electro-Optical Science and Technology, National Taiwan Normal University, Taipei 11677, Taiwan (China); Le Ster, Maxime [Institute of Electro-Optical Science and Technology, National Taiwan Normal University, Taipei 11677, Taiwan (China); Material Sciences and Engineering, Institut National des Sciences Appliquées de Rennes, Rennes 35708 (France); Yang, Cheng-Du [Institute of Electro-Optical Science and Technology, National Taiwan Normal University, Taipei 11677, Taiwan (China); Tseng, Ming-Hung; Tsai, Feng-Yu [Department of Material Science and Engineering, National Taiwan University, Taipei 10617, Taiwan (China)

    2015-03-30

    Highlights: • Directional emission properties give rise to a spectral band-gap response enhancement. • The subsequent emission intensity can increase by up to 3.5 times. • FWHM of approximately 60 nm in a defined direction is achieved. • SP coupling rate is approximately 80% on the metal grating structure. - Abstract: This study demonstrates the feasibility of enhancing an organic-based plasmon-emitting diode on the directional light beaming efficiency by near-field surface plasmon polaritons (SPPs) in both metal grating and polymer grating nanostructures. The interaction between organic/metal and PR/metal interfaces to cause SPPs can facilitate specific directional emission. Directional emission properties give rise to a spectral band-gap response enhancement. Our results also verify that efficient surface plasmon grating coupled emissions (SPGCEs) can improve directionality under index-mediated tuning. Experimental results indicate SP decoupling emission in the visible light. The subsequent emission intensity can increase by up to 3.5 times. Moreover, a narrow FWHM of approximately 60 nm in a defined direction is achieved, and an SP coupling rate is approximately 80% on the metal grating structure. The proposed method is highly promising for use as an active plasmonic emitter and discoloration biosensors with enhanced SPPs resonance energy, owing to interactions with the organic/metal nanostructure.

  4. In-orbit evaluation of the control system/structural mode interactions of the OSO-8 spacecraft

    Science.gov (United States)

    Slafer, L. I.

    1979-01-01

    The Orbiting Solar Observatory-8 experienced severe structural mode/control loop interaction problems during the spacecraft development. Extensive analytical studies, using the hybrid coordinate modeling approach, and comprehensive ground testing were carried out in order to achieve the system's precision pointing performance requirements. A recent series of flight tests were conducted with the spacecraft in which a wide bandwidth, high resolution telemetry system was utilized to evaluate the on-orbit flexible dynamics characteristics of the vehicle along with the control system performance. The paper describes the results of these tests, reviewing the basic design problem, analytical approach taken, ground test philosophy, and on-orbit testing. Data from the tests was used to determine the primary mode frequency, damping, and servo coupling dynamics for the on-orbit condition. Additionally, the test results have verified analytically predicted differences between the on-orbit and ground test environments, and have led to a validation of both the analytical modeling and servo design techniques used during the development of the control system.

  5. Dynamic evolution of double Λ five-level atom interacting with one-mode electromagnetic cavity field

    Science.gov (United States)

    Abdel-Wahab, N. H.; Salah, Ahmed

    2017-12-01

    In this paper, the model describing a double Λ five-level atom interacting with a single mode electromagnetic cavity field in the (off) non-resonate case is studied. We obtained the constants of motion for the considered model. Also, the state vector of the wave function is given by using the Schrödinger equation when the atom is initially prepared in its excited state. The dynamical evolutions for the collapse revivals, the antibunching of photons and the field squeezing phenomena are investigated when the field is considered in a coherent state. The influence of detuning parameters on these phenomena is investigated. We noticed that the atom-field properties are influenced by changing the detuning parameters. The investigation of these aspects by numerical simulations is carried out using the Quantum Toolbox in Python (QuTip).

  6. Evaluation of different delivery modes of an interactive e-learning programme for teaching cultural diversity.

    Science.gov (United States)

    Hawthorne, Kamila; Prout, Hayley; Kinnersley, Paul; Houston, Helen

    2009-01-01

    UK medical schools find it challenging to provide standardised teaching to expanding year intakes. In addition, developing and implementing diversity training can cause difficulties. This paper describes the evaluation of an interactive e-learning programme to raise awareness and understanding of communication difficulties in diversity consultations. The programme was part of an undergraduate portfolio-based community module. Three hundred and two students were assigned to one of three delivery methods--a large group setting, small groups with a facilitator, and as part of distance learning while on community placement. The evaluation included analysis of their coursework marks, a self-completed evaluation questionnaire, and small group discussions. Two hundred and twenty-three students took part in the evaluation. They were able to apply the concepts they learnt to clinical examples from their own experiences. Type of delivery did not affect coursework marks, but students tended to prefer the e-learning as part of a distance learning package. They offered helpful suggestions to improve its complexity and range. The acceptability and utility of this e-learning module both in face to face teaching and remote placement has been demonstrated, and evaluation by the students has provided valuable information for its further development. All medical schools should include some diversity training, and further research should concentrate on the effects of this type of learning on longer term outcomes such as attitude and performance tests. Such tools could reduce demands on staff time in facilitation of small groupwork, and their cost effectiveness could be increased by making them available to other medical schools.

  7. Molecular identification of the mode of interaction of nitrous oxide with the opiate receptor system

    Energy Technology Data Exchange (ETDEWEB)

    Wallar, D D

    1985-01-01

    The discovery of the opioid receptors in 1973 has led to a great deal of in vivo and in vitro research in order to understand the mechanism of binding of endogenous and synthetic opiate ligands. The use of nitrous oxide (N/sub 2/O) in anaesthesia is well documented. However, at lower concentrations N/sub 2/O produces analgesia. In 1976, it was reported that N/sub 2/O analgesia in man could be modified by the opiate antagonist naloxone. This clearly linked nitrous oxide analgesia to the opioid receptor system. It is the purpose of this dissertation to examine the molecular mechanism of action of N/sub 2/O at the opioid receptor through the use of in vitro binding studies. In addition, a model of the opioid receptor will be proposed. The following radiolabelled ligands were used in classical competitive binding assays to determine K (sub D),B(sub max), and IC/sub 50/ values in the presence of nitrous oxide and other control gases: dihydromorphine, N-allyl-N-normetazocine (SKF 10,047), and ethylketocyclazocine, for putative ..mu.., sigma and kappa opioid binding sites, respectively. All assays were performed using rat forebrain homogenates suspended in buffer previously saturated with the gas. Results indicate that N/sub 2/O differentially affects the binding kinetics of dihydromorphine. The binding kinetics of SKF 10,047 or ethylketocyclazocine were not altered significantly by N/sub 2/O indicating that N/sub 2/O is specific in its effects for the putative ..mu..-binding site. It is suggested that N/sub 2/O exerts its analgesic effects by perturbation of protein/lipid interactions within a multiple binding site opioid receptor complex.

  8. The Impulse-Refractive Mode in the Neural Network with Ring Synaptic Interaction

    Directory of Open Access Journals (Sweden)

    Margarita M. Preobrazhenskaia

    2017-01-01

    Full Text Available In the paper, a mathematical model of a neural network with an even number of ring synaptic interaction elements is considered. The model is a system of scalar nonlinear differentialdifference equations, the right parts of which depend on large parameters. The unknown functions included in the system characterize the membrane potentials of the neurons. The search of special impulse-refraction cycles within the system of equations is of interest. The functions with odd numbers of the impulse-refraction cycle have an asymptotically high pulses and the functions with even numbers are asymptotically small. Two changes allow to study a two-dimension nonlinear differential-difference system with two delays instead of the system. Further, a limit object that represents a relay system with two delays is defined by a large parameter tending to infinity. There exists the only periodic solution of the relay system with the initial function from a suitable function class. This is structurally proved, by using the step method. Next, the existence of relaxation periodic solutions of the two-dimension singularly perturbed system is proved by using the Poincare operator and the Schauder principle. The asymptotics of this solution is constructed, and it is proved that the solution is close to the decision of the relay system. Because of the exponential estimate of the Frechet derivative of the Poincare operator it implies the uniqueness and stability of solutions of the two-dimension differential-difference equation with two delays. Furthermore, with the help of reverse replacement the proved result is transferred to the original system. 

  9. Study of Wave-Particle Interactions for Whistler Mode Waves at Oblique Angles by Utilizing the Gyroaveraging Method

    Science.gov (United States)

    Hsieh, Yi-Kai; Omura, Yoshiharu

    2017-10-01

    We investigate the properties of whistler mode wave-particle interactions at oblique wave normal angles to the background magnetic field. We find that electromagnetic energy of waves at frequencies below half the electron cyclotron frequency can flow nearly parallel to the ambient magnetic field. We thereby confirm that the gyroaveraging method, which averages the cyclotron motion to the gyrocenter and reduces the simulation from two-dimensional to one-dimensional, is valid for oblique wave-particle interaction. Multiple resonances appear for oblique propagation but not for parallel propagation. We calculate the possible range of resonances with the first-order resonance condition as a function of electron kinetic energy and equatorial pitch angle. To reveal the physical process and the efficiency of electron acceleration by multiple resonances, we assume a simple uniform wave model with constant amplitude and frequency in space and time. We perform test particle simulations with electrons starting at specific equatorial pitch angles and kinetic energies. The simulation results show that multiple resonances contribute to acceleration and pitch angle scattering of energetic electrons. Especially, we find that electrons with energies of a few hundred keV can be accelerated efficiently to a few MeV through the n = 0 Landau resonance.

  10. Influence of the nuclear matter equation of state on the r-mode instability using the finite-range simple effective interaction

    Science.gov (United States)

    Pattnaik, S. P.; Routray, T. R.; Viñas, X.; Basu, D. N.; Centelles, M.; Madhuri, K.; Behera, B.

    2018-05-01

    The characteristic physical properties of rotating neutron stars under the r-mode oscillation are evaluated using the finite-range simple effective interaction. Emphasis is given on examining the influence of the stiffness of both the symmetric and asymmetric parts of the nuclear equation of state on these properties. The amplitude of the r-mode at saturation is calculated using the data of particular neutron stars from the considerations of ‘spin equilibrium’ and ‘thermal equilibrium’. The upper limit of the r-mode saturation amplitude is found to lie in the range 10‑8–10‑6, in agreement with the predictions of earlier work.

  11. Plasma-wall interaction and locked modes in the toroidal pinch experiment TPE-RX reversed-field pinch

    International Nuclear Information System (INIS)

    Pasqualini, D.; Martin, P.; Koguchi, H.; Yagi, Y.; Hirano, Y.; Sakakita, H.; Spizzo, G.

    2006-01-01

    The MHD instabilities that sustain the reversed-field pinch (RFP) configuration tend to phase-lock together and also to wall-lock, forming a bulging of the plasma column, called 'locked mode'. This phenomenon is of particular interest, since the locked mode causes a larger plasma resistivity, plasma cooling, and, in some cases, anomalous discharge termination. Up to now, studies of the locked mode have been focused on m=1 modes (being m the poloidal mode number). In this Letter we show that m=0 modes also play a role, based on the cross-check between magnetic spectra and toroidally resolved D α array measurements. (author)

  12. Quantum dynamics of a BEC interacting with a single-mode quantized field in the presence of interatom collisions

    Energy Technology Data Exchange (ETDEWEB)

    Ghasemian, E. [Atomic and Molecular Group, Faculty of Physics, Yazd University, Yazd (Iran, Islamic Republic of); Tavassoly, M.K., E-mail: mktavassoly@yazd.ac.ir [Atomic and Molecular Group, Faculty of Physics, Yazd University, Yazd (Iran, Islamic Republic of); Photonics Research Group, Engineering Research Center, Yazd University, Yazd (Iran, Islamic Republic of); The Laboratory of Quantum Information Processing, Yazd University, Yazd (Iran, Islamic Republic of)

    2016-09-23

    In this paper, we consider a model in which N two-level atoms in a Bose–Einstein condensate (BEC) interact with a single-mode quantized laser field. Our goal is to investigate the quantum dynamics of atoms in the BEC in the presence of interatom interactions. To achieve the purpose, at first, using the collective angular momentum operators, we try to reduce the dynamical Hamiltonian of the system to a well-known Jaynes–Cummings like model (JCM). We also use the Dicke model to construct the state of atomic subsystem, by which the analytical solution of the system may be obtained. Then, we analyze the atomic population inversion, the degree of entanglement between the “atoms in BEC” and the “field” as well as the Mandel parameter. Numerical results show that, the atomic population inversion, atom-field entanglement and quantum statistics of photons are very sensitive to the evolved parameters in the model (and so can be well-adjusted), such as the number of atoms in BEC, the intensity of initial field, the interatom coupling constant and detuning. To investigate the entanglement properties, we pay attention to the entropy and linear entropy. It is shown that, oscillations in the two entropy criteria may be seen, with some maxima of entanglement at some moments of time. Finally, looking for the quantum statistics, we evaluate the Mandel parameter, by which we demonstrate the sub-Poissonian statistics and so the nonclassical characteristics of the field state of system. Collapse-revival phenomenon, which is a distinguishable nonclassical characteristic of the system, can be apparently observed in the atomic population inversion and the Mandel parameter. - Highlights: • N two-level atoms in a BEC interacting with a laser field in the presence of interatom interactions is considered. • The atomic population inversion, degree of entanglement between the “atoms in BEC” and the “field” and the Mandel parameter are investigated. • Collapse

  13. Mode stability analysis in the beam—wave interaction process for a three-gap Hughes-type coupled cavity chain

    International Nuclear Information System (INIS)

    Luo Ji-Run; Zhu Min; Guo Wei; Cui Jian

    2013-01-01

    Based on space-charge wave theory, the formulae of the beam—wave coupling coefficient and the beam-loaded conductance are given for the beam—wave interaction in an N-gap Hughes-type coupled cavity chain. The ratio of the non-beam-loaded quality factor of the coupled cavity chain to the beam quality factor is used to determine the stability of the beam—wave interaction. As an example, the stabilities of the beam—wave interaction in a three-gap Hughes-type coupled cavity chain are discussed with the formulae and the CST code for the operations of the 2π, π, and π/2 modes, respectively. The results show that stable operation of the 2π, π, and π/2 modes may all be realized in an extended-interaction klystron with the three-gap Hughes-type coupled cavity chain

  14. Multiwavelength mode-locked erbium-doped fiber laser based on the interaction of graphene and fiber-taper evanescent field

    International Nuclear Information System (INIS)

    Luo, Z Q; Wang, J Z; Zhou, M; Xu, H Y; Cai, Z P; Ye, C C

    2012-01-01

    We report on the generation of multiwavelength passively mode-locked pulses in an erbium-doped fiber laser (EDFL) based on the interaction of graphene and fiber-taper evanescent field. Graphene-polymer nanocomposites in aqueous suspension are trapped by the optical evanescent light and deposited on taper region. The graphene-deposited fiber-taper device not only acts as an excellent saturable absorber for mode-locking, but also induces a polarizing effect to form an artificial birefringent filter for multiwavelength selection. By simultaneously exploiting both functions of this device, four-wavelength continuous-wave mode-locking operation of an EDFL is stably initiated with a pulse width of 8.8 ps and a fundamental repetition rate of 8.034 MHz. This is the first time, to our knowledge, the mode-locked EDFL using such a new geometry of graphene-based tapered-fiber saturable absorber has been demonstrated

  15. Construction of an Interactive Mode between Teacher Education and Basic Education%教师教育与基础教育互动模式构建

    Institute of Scientific and Technical Information of China (English)

    冼秀丽

    2011-01-01

    系统学理论是教师教育与基础教育互动模式构建的理论基础。"伙伴合作+协议合作+中介合作"的教师教育与基础教育互动模式的构建,可促使两者深度互动,从全方位进行合作,真正实现共同发展的愿景。教师教育与基础教育互动模式的有效运行,需要建立双向互利的机制、融合互动的文化、完善互动的管理制度等作为保障。%System theory and basic education,teacher education is the interactive mode to build the theoretical basis.The construction of an interactive mode called "Partnership Cooperation + Agreement Cooperation + Intermediary Cooperation" between teacher education and basic education may bring about the profound interaction and the all-wave cooperation between these two,and it may indeed satisfy the mutual desire of collaborative development.In order to ensure the effective running of the interactive mode between teacher education and basic education,it needs to establish mechanisms for mutual benefit,the integration of cultural interaction,sound management systems to interact as a guarantee.

  16. National and transnational strategies of LGBT civil society organizations in different political environments : Modes of interaction in Western and Eastern Europe for equality

    NARCIS (Netherlands)

    Holzhacker, Ronald

    This article focuses on the national and transnational strategies of five European Lesbian, Gay, Bisexual and Transgender civil society organizations (CSOs) pressing for equality and non-discrimination. We present three modes of interaction between CSOs and their political environment. The first

  17. Game changing - tracing the positions, strategies and interaction modes of the German Länder towards the (ever expanding?) European Union

    DEFF Research Database (Denmark)

    Jensen, Mads Christian Dagnis

    2014-01-01

    This article investigates how the positions, strategies and modes of interaction of the German Länder have changed over time in response to the process of Europeanization. By applying the method of process tracing within a theoretical framework of rational choice institutionalism, the article...... resulted in a more sceptical attitude of the Länder towards (the perceived ever expanding) European Union....

  18. A theoretical interpretation of the antibody-antigen interactions between Salmonella and a thickness shear mode (TSM) quartz resonator

    Science.gov (United States)

    Bailey, Claude Albert

    This dissertation outlines the developmental procedure for a real-time food-borne pathogen detector that uses a thickness shear mode (TSM) quartz resonator. A theory is discussed which provides some understanding of the measured signals obtained from the TSM resonator-based Salmonella detector. The theory explains surface viscosity and mass effects, but has yet to be fully implemented for anomalous bacterial interactions. An equivalent circuit model for an immunochemical coating and its effect on the TSM resonator frequency is presented. The latter part of this dissertation describes immunological experiments with precoated piezoelectric quartz crystals. A highly purified immunological system was used to optimize the immobilization procedure. The use of biosensors is becoming a viable alternative to conventional analysis and promises to experience dramatic growth, especially after their true potential is realized and more cost-effective assays are developed. Concern about the safety of our food and water supplies will undoubtedly stimulate further research, and miniaturized biosensors will be developed for use by safety inspectors, and concerned personnel. A Salmonella detector has been demonstrated consisting of a TSM resonator with antibodies immobilized in a Langmuir Blodgett (LB) film on the surface [3]. Scanning Electron Microscopy (SEM) images of bound Salmonella bacteria to both polished and unpolished TSM resonators were taken to correlate the mass of the bound organism to the Sauerbrey equation. Antigen-antibody interactions change the acoustic resonant properties that are reflected in the sensor frequency response. The Salmonella detector operates in a liquid environment (Salmonella suspended in a phosphate buffered saline solution). The viscous properties of this liquid overlayer could influence the TSM resonator's response. Various liquid media (buffer solutions, chicken exudate, and varying fat contents of milk) were studied as a function of

  19. Two modes of interaction of the single-stranded DNA-binding protein of bacteriophage T7 with the DNA polymerase-thioredoxin complex

    KAUST Repository

    Ghosh, Sharmistha; Hamdan, Samir; Richardson, Charles C.

    2010-01-01

    The DNA polymerase encoded by bacteriophage T7 has low processivity. Escherichia coli thioredoxin binds to a segment of 76 residues in the thumb subdomain of the polymerase and increases the processivity. The binding of thioredoxin leads to the formation of two basic loops, loops A and B, located within the thioredoxin-binding domain (TBD). Both loops interact with the acidic C terminus of the T7 helicase. A relatively weak electrostatic mode involves the C-terminal tail of the helicase and the TBD, whereas a high affinity interaction that does not involve the C-terminal tail occurs when the polymerase is in a polymerization mode. T7 gene 2.5 single-stranded DNA-binding protein (gp2.5) also has an acidic C-terminal tail. gp2.5 also has two modes of interaction with the polymerase, but both involve the C-terminal tail of gp2.5. An electrostatic interaction requires the basic residues in loops A and B, and gp2.5 binds to both loops with similar affinity as measured by surface plasmon resonance. When the polymerase is in a polymerization mode, the C terminus of gene 2.5 protein interacts with the polymerase in regions outside the TBD.gp2.5 increases the processivity of the polymerase-helicase complex during leading strand synthesis. When loop B of the TBD is altered, abortive DNA products are observed during leading strand synthesis. Loop B appears to play an important role in communication with the helicase and gp2.5, whereas loop A plays a stabilizing role in these interactions. © 2010 by The American Society for Biochemistry and Molecular Biology, Inc.

  20. Two modes of interaction of the single-stranded DNA-binding protein of bacteriophage T7 with the DNA polymerase-thioredoxin complex

    KAUST Repository

    Ghosh, Sharmistha

    2010-04-06

    The DNA polymerase encoded by bacteriophage T7 has low processivity. Escherichia coli thioredoxin binds to a segment of 76 residues in the thumb subdomain of the polymerase and increases the processivity. The binding of thioredoxin leads to the formation of two basic loops, loops A and B, located within the thioredoxin-binding domain (TBD). Both loops interact with the acidic C terminus of the T7 helicase. A relatively weak electrostatic mode involves the C-terminal tail of the helicase and the TBD, whereas a high affinity interaction that does not involve the C-terminal tail occurs when the polymerase is in a polymerization mode. T7 gene 2.5 single-stranded DNA-binding protein (gp2.5) also has an acidic C-terminal tail. gp2.5 also has two modes of interaction with the polymerase, but both involve the C-terminal tail of gp2.5. An electrostatic interaction requires the basic residues in loops A and B, and gp2.5 binds to both loops with similar affinity as measured by surface plasmon resonance. When the polymerase is in a polymerization mode, the C terminus of gene 2.5 protein interacts with the polymerase in regions outside the TBD.gp2.5 increases the processivity of the polymerase-helicase complex during leading strand synthesis. When loop B of the TBD is altered, abortive DNA products are observed during leading strand synthesis. Loop B appears to play an important role in communication with the helicase and gp2.5, whereas loop A plays a stabilizing role in these interactions. © 2010 by The American Society for Biochemistry and Molecular Biology, Inc.

  1. Excitation of macromagnetohydrodynamic mode due to multiscale interaction in a quasi-steady equilibrium formed by a balance between microturbulence and zonal flow

    International Nuclear Information System (INIS)

    Ishizawa, A.; Nakajima, N.

    2007-01-01

    This is the first numerical simulation demonstrating that a macromagnetohydrodynamic (macro-MHD) mode is excited as a result of multi-scale interaction in a quasi-steady equilibrium formed by a balance between microturbulence and zonal flow based on a reduced two-fluid model. This simulation of a macro-MHD mode, a double tearing mode, is accomplished in a reversed shear equilibrium that includes zonal flow and turbulence due to kinetic ballooning modes. In the quasi-steady equilibrium, a macroscale fluctuation that has the same helicity as the double tearing mode is a part of the turbulence. After a certain period of time, the macro-MHD mode begins to grow. It effectively utilizes free energy of the equilibrium current density gradient and is destabilized by a positive feedback loop between zonal flow suppression and magnetic island growth. Thus, once the macro-MHD appears from the quasi-equilibrium, it continues to grow steadily. This simulation is more comparable with experimental observations of growing macro-MHD activity than earlier MHD simulations starting from linear macroinstabilities in a static equilibrium

  2. Interactions of the Salience Network and Its Subsystems with the Default-Mode and the Central-Executive Networks in Normal Aging and Mild Cognitive Impairment.

    Science.gov (United States)

    Chand, Ganesh B; Wu, Junjie; Hajjar, Ihab; Qiu, Deqiang

    2017-09-01

    Previous functional magnetic resonance imaging (fMRI) investigations suggest that the intrinsically organized large-scale networks and the interaction between them might be crucial for cognitive activities. A triple network model, which consists of the default-mode network, salience network, and central-executive network, has been recently used to understand the connectivity patterns of the cognitively normal brains versus the brains with disorders. This model suggests that the salience network dynamically controls the default-mode and central-executive networks in healthy young individuals. However, the patterns of interactions have remained largely unknown in healthy aging or those with cognitive decline. In this study, we assess the patterns of interactions between the three networks using dynamical causal modeling in resting state fMRI data and compare them between subjects with normal cognition and mild cognitive impairment (MCI). In healthy elderly subjects, our analysis showed that the salience network, especially its dorsal subnetwork, modulates the interaction between the default-mode network and the central-executive network (Mann-Whitney U test; p control correlated significantly with lower overall cognitive performance measured by Montreal Cognitive Assessment (r = 0.295; p control, especially the dorsal salience network, over other networks provides a neuronal basis for cognitive decline and may be a candidate neuroimaging biomarker of cognitive impairment.

  3. The kinetochore proteins CENP-E and CENP-F directly and specifically interact with distinct BUB mitotic checkpoint Ser/Thr kinases.

    Science.gov (United States)

    Ciossani, Giuseppe; Overlack, Katharina; Petrovic, Arsen; Huis In 't Veld, Pim J; Koerner, Carolin; Wohlgemuth, Sabine; Maffini, Stefano; Musacchio, Andrea

    2018-05-10

    The segregation of chromosomes during cell division relies on the function of the kinetochores, protein complexes that physically connect chromosomes with microtubules of the spindle. The metazoan proteins, centromere protein E (CENP-E) and CENP-F, are components of a fibrous layer of mitotic kinetochores named the corona. Several of their features suggest that CENP-E and CENP-F are paralogs: they are very large (comprising approximately 2700 and 3200 residues, respectively), contain abundant predicted coiled-coil structures, are C-terminally prenylated, and are endowed with microtubule-binding sites at their termini. Moreover, CENP-E contains an ATP-hydrolyzing motor domain that promotes microtubule plus end-directed motion. Here, we show that both CENP-E and CENP-F are recruited to mitotic kinetochores independently of the main corona constituent, the Rod-Zwilch-ZW10 (RZZ) complex. We identified specific interactions of CENP-F and CENP-E with budding uninhibited by benzimidazole 1 (BUB1) and BUB1-related (BUBR1) mitotic checkpoint Ser/Thr kinases, respectively, paralogous proteins involved in mitotic checkpoint control and chromosome alignment. Whereas BUBR1 was dispensable for kinetochore localization of CENP-E, BUB1 was stringently required for CENP-F localization. Through biochemical reconstitution, we demonstrated that the CENP-E-BUBR1 and CENP-F-BUB1 interactions are direct and require similar determinants, a dimeric coiled-coil in CENP-E or CENP-F and a kinase domain in BUBR1 or BUB1. Our findings are consistent with the existence of structurally similar BUB1-CENP-F and BUBR1-CENP-E complexes, supporting the notion that CENP-E and CENP-F are evolutionarily related. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

  4. Interaction of the N-(3-Methylpyridin-2-ylamide Derivatives of Flurbiprofen and Ibuprofen with FAAH: Enantiomeric Selectivity and Binding Mode.

    Directory of Open Access Journals (Sweden)

    Jessica Karlsson

    Full Text Available Combined fatty acid amide hydrolase (FAAH and cyclooxygenase (COX inhibition is a promising approach for pain-relief. The Flu-AM1 and Ibu-AM5 derivatives of flurbiprofen and ibuprofen retain similar COX-inhibitory properties and are more potent inhibitors of FAAH than the parent compounds. However, little is known as to the nature of their interaction with FAAH, or to the importance of their chirality. This has been explored here.FAAH inhibitory activity was measured in rat brain homogenates and in lysates expressing either wild-type or FAAH(T488A-mutated enzyme. Molecular modelling was undertaken using both docking and molecular dynamics. The (R- and (S-enantiomers of Flu-AM1 inhibited rat FAAH with similar potencies (IC50 values of 0.74 and 0.99 μM, respectively, whereas the (S-enantiomer of Ibu-AM5 (IC50 0.59 μM was more potent than the (R-enantiomer (IC50 5.7 μM. Multiple inhibition experiments indicated that both (R-Flu-AM1 and (S-Ibu-AM5 inhibited FAAH in a manner mutually exclusive to carprofen. Computational studies indicated that the binding site for the Flu-AM1 and Ibu-AM5 enantiomers was located between the acyl chain binding channel and the membrane access channel, in a site overlapping the carprofen binding site, and showed a binding mode in line with that proposed for carprofen and other non-covalent ligands. The potency of (R-Flu-AM1 was lower towards lysates expressing FAAH mutated at the proposed carprofen binding area than in lysates expressing wild-type FAAH.The study provides kinetic and structural evidence that the enantiomers of Flu-AM1 and Ibu-AM5 bind in the substrate channel of FAAH. This information will be useful in aiding the design of novel dual-action FAAH: COX inhibitors.

  5. The entanglement of two moving atoms interacting with a single-mode field via a three-photon process

    International Nuclear Information System (INIS)

    Chao, Wu; Mao-Fa, Fang

    2010-01-01

    In this paper, the entanglement of two moving atoms induced by a single-mode field via a three-photon process is investigated. It is shown that the entanglement is dependent on the category of the field, the average photon number N, the number p of half-wave lengths of the field mode and the atomic initial state. Also, the sudden death and the sudden birth of the entanglement are detected in this model and the results show that the existence of the sudden death and the sudden birth depends on the parameter and the category of the mode field. In addition, the three-photon process is a higher order nonlinear process. (general)

  6. Generation of three-mode continuous-variable entanglement by cascaded nonlinear interactions in a quasiperiodic superlattice

    International Nuclear Information System (INIS)

    Yu, Y. B.; Xie, Z. D.; Yu, X. Q.; Li, H. X.; Xu, P.; Yao, H. M.; Zhu, S. N.

    2006-01-01

    The generation of three-mode continuous-variable entanglement in a quasiperiodically optical superlattice is studied theoretically in this paper. This work is based on the previous experiment result in which three-color light generated from a quasiperiodically optical superlattice through a stimulated parametric down-conversion cascaded with a sum-frequency process. The degree of quadrature phase amplitude correlations, a nonclassical characteristic, among the three mode was discussed by a sufficient inseparability criterion for continuous-variable entanglement, which was proposed by van Loock and Furusawa

  7. Oligomeric coiled-coil adhesin YadA is a double-edged sword.

    Directory of Open Access Journals (Sweden)

    Salome Casutt-Meyer

    Full Text Available Yersinia adhesin A (YadA is an essential virulence factor for the food-borne pathogens Yersinia enterocolitica and Yersinia pseudotuberculosis. Surprisingly, it is a pseudogene in Yersinia pestis. Even more intriguing, the introduction of a functional yadA gene in Y. pestis EV76 was shown to correlate with a decrease in virulence in a mouse model. Here, we report that wild type (wt Y. enterocolitica E40, as well as YadA-deprived E40 induced the synthesis of neutrophil extracellular traps (NETs upon contact with neutrophils, but only YadA-expressing Y. enterocolitica adhered to NETs and were killed. As binding seemed to be a prerequisite for killing, we searched for YadA-binding substrates and detected the presence of collagen within NETs. E40 bacteria expressing V98D,N99A mutant YadA with a severely reduced ability to bind collagen were found to be more resistant to killing, suggesting that collagen binding contributes significantly to sensitivity to NETs. Wt Y. pestis EV76 were resistant to killing by NETs, while recombinant EV76 expressing YadA from either Y. pseudotuberculosis or Y. enterocolitica were sensitive to killing by NETs, outlining the importance of YadA for susceptibility to NET-dependent killing. Recombinant EV76 endowed with YadA from Y. enterocolitica were also less virulent for the mouse than wt EV76, as shown before. In addition, EV76 carrying wt YadA were less virulent for the mouse than EV76 expressing YadA(V₉₈D,N₉₉A. The observation that YadA makes Yersinia sensitive to NETs provides an explanation as for why evolution selected for the inactivation of yadA in the flea-borne Y. pestis and clarifies an old enigma. Since YadA imposes the same cost to the food-borne Yersinia but was nevertheless conserved by evolution, this observation also illustrates the duality of some virulence functions.

  8. Folding Topology of a Short Coiled-Coil Peptide Structure Templated by an Oligonucleotide Triplex

    DEFF Research Database (Denmark)

    Lou, Chenguang; Christensen, Niels Johan; Martos Maldonado, Manuel Cristo

    2017-01-01

    by oligonucleotide duplex and triplex formation. POC synthesis was achieved by copper-free alkyne-azide cycloaddition between three oligonucleotides and a 23-mer peptide, which by itself exhibited multiple oligomeric states in solution. The oligonucleotide domain was designed to furnish a stable parallel triplex......, small-angle X-ray scattering (SAXS), and molecular modeling. Stabilizing cooperativity was observed between the trimeric peptide and the oligonucleotide triplex domains, and the overall molecular size (ca. 12nm) in solution was revealed to be independent of concentration. The topological folding...

  9. Interaction vs. observation: distinctive modes of social cognition in human brain and behavior? A combined fMRI and eye-tracking study.

    Science.gov (United States)

    Tylén, Kristian; Allen, Micah; Hunter, Bjørk K; Roepstorff, Andreas

    2012-01-01

    Human cognition has usually been approached on the level of individual minds and brains, but social interaction is a challenging case. Is it best thought of as a self-contained individual cognitive process aiming at an "understanding of the other," or should it rather be approached as an collective, inter-personal process where individual cognitive components interact on a moment-to-moment basis to form coupled dynamics? In a combined fMRI and eye-tracking study we directly contrasted these models of social cognition. We found that the perception of situations affording social contingent responsiveness (e.g., someone offering or showing you an object) elicited activations in regions of the right posterior temporal sulcus and yielded greater pupil dilation corresponding to a model of coupled dynamics (joint action). In contrast, the social-cognitive perception of someone "privately" manipulating an object elicited activation in medial prefrontal cortex, the right inferior frontal gyrus and right inferior parietal lobus, regions normally associated with Theory of Mind and with the mirror neuron system. Our findings support a distinction in social cognition between social observation and social interaction, and demonstrate that simple ostensive cues may shift participants' experience, behavior, and brain activity between these modes. The identification of a distinct, interactive mode has implications for research on social cognition, both in everyday life and in clinical conditions.

  10. Interaction versus Observation: distinctive modes of social cognition in human brain and behavior? A combined fMRI and eye-tracking study.

    Directory of Open Access Journals (Sweden)

    Kristian eTylen

    2012-12-01

    Full Text Available Human cognition has usually been approached on the level of individual minds and brains, but social interaction is a challenging case. Is it best thought of as a self-contained individual cognitive process aiming at an ‘understanding of the other’, or should it rather be approached as an collective, inter-personal process where individual cognitive components interact on a moment-to-moment basis to form coupled dynamics? In a combined fMRI and eye tracking study we directly contrasted these models of social cognition. We found that the perception of situations affording social contingent responsiveness (e.g. someone offering or showing you an object elicited activations in regions of the right posterior temporal sulcus and yielded greater pupil dilation corresponding to a model of coupled dynamics (joint action. In contrast, the social-cognitive perception of someone ‘privately’ manipulating an object elicited activation in medial prefrontal cortex, the right inferior frontal gyrus and right inferior parietal lobus, regions normally associated with Theory of Mind and with the mirror neuron system. Our findings support a distinction in social cognition between social observation and social interaction, and demonstrate that simple ostensive cues may shift participants’ experience, behavior and brain activity between these modes. The identification of a distinct, interactive mode has implications for research on social cognition, both in everyday life and in clinical conditions.

  11. Effects of an applied low frequency field on the dynamics of a two-level atom interacting with a single-mode field

    International Nuclear Information System (INIS)

    Xun-Wei, Xu; Nian-Hua, Liu

    2010-01-01

    The effects of an applied low frequency field on the dynamics of a two-level atom interacting with a single-mode field are investigated. It is shown that the time evolution of the atomic population is mainly controlled by the coupling constants and the frequency of the low frequency field, which leads to a low frequency modulation function for the time evolution of the upper state population. The amplitude of the modulation function becomes larger as the coupling constants increase. The frequency of the modulation function is proportional to the frequency of the low frequency field, and decreases with increasing coupling constant. (classical areas of phenomenology)

  12. Comparison of junctionless and inversion-mode p-type metal-oxide-semiconductor field-effect transistors in presence of hole-phonon interactions

    Energy Technology Data Exchange (ETDEWEB)

    Dib, E., E-mail: elias.dib@for.unipi.it [Dipartimento di Ingegneria dell' Informazione, Università di Pisa, 56122 Pisa (Italy); Carrillo-Nuñez, H. [Integrated Systems Laboratory ETH Zürich, Gloriastrasse 35, 8092 Zürich (Switzerland); Cavassilas, N.; Bescond, M. [IM2NP, UMR CNRS 6242, Bât. IRPHE, Technopôle de Château-Gombert, 13384 Marseille Cedex 13 (France)

    2016-01-28

    Junctionless transistors are being considered as one of the alternatives to conventional metal-oxide field-effect transistors. In this work, it is then presented a simulation study of silicon double-gated p-type junctionless transistors compared with its inversion-mode counterpart. The quantum transport problem is solved within the non-equilibrium Green's function formalism, whereas hole-phonon interactions are tackled by means of the self-consistent Born approximation. Our findings show that junctionless transistors should perform as good as a conventional transistor only for ultra-thin channels, with the disadvantage of requiring higher supply voltages in thicker channel configurations.

  13. Comparison of junctionless and inversion-mode p-type metal-oxide-semiconductor field-effect transistors in presence of hole-phonon interactions

    International Nuclear Information System (INIS)

    Dib, E.; Carrillo-Nuñez, H.; Cavassilas, N.; Bescond, M.

    2016-01-01

    Junctionless transistors are being considered as one of the alternatives to conventional metal-oxide field-effect transistors. In this work, it is then presented a simulation study of silicon double-gated p-type junctionless transistors compared with its inversion-mode counterpart. The quantum transport problem is solved within the non-equilibrium Green's function formalism, whereas hole-phonon interactions are tackled by means of the self-consistent Born approximation. Our findings show that junctionless transistors should perform as good as a conventional transistor only for ultra-thin channels, with the disadvantage of requiring higher supply voltages in thicker channel configurations

  14. DC Voltage Droop Control Structures and its Impact on the Interaction Modes in Interconnected AC-HVDC Systems

    DEFF Research Database (Denmark)

    Thams, Florian; Chatzivasileiadis, Spyros; Eriksson, Robert

    2017-01-01

    Different dc voltage droop control structures for future multi-terminal HVDC systems have been proposed in literature. This paper contributes to the evaluation of those structures by an analysis of their impact on the coupling of the interconnected subsystems. In particular, the modes...... of the systems are classified in different subsets according to the participation of the various subsystems. Those subsets are then evaluated qualitatively and quantitatively indicating which impact the choice of the droop control structure has on the degree of coupling between the connected ac and dc systems...

  15. Quantification of cytosolic interactions identifies Ede1 oligomers as key organizers of endocytosis.

    Science.gov (United States)

    Boeke, Dominik; Trautmann, Susanne; Meurer, Matthias; Wachsmuth, Malte; Godlee, Camilla; Knop, Michael; Kaksonen, Marko

    2014-11-03

    Clathrin-mediated endocytosis is a highly conserved intracellular trafficking pathway that depends on dynamic protein-protein interactions between up to 60 different proteins. However, little is known about the spatio-temporal regulation of these interactions. Using fluorescence (cross)-correlation spectroscopy in yeast, we tested 41 previously reported interactions in vivo and found 16 to exist in the cytoplasm. These detected cytoplasmic interactions included the self-interaction of Ede1, homolog of mammalian Eps15. Ede1 is the crucial scaffold for the organization of the early stages of endocytosis. We show that oligomerization of Ede1 through its central coiled coil domain is necessary for its localization to the endocytic site and we link the oligomerization of Ede1 to its function in locally concentrating endocytic adaptors and organizing the endocytic machinery. Our study sheds light on the importance of the regulation of protein-protein interactions in the cytoplasm for the assembly of the endocytic machinery in vivo. © 2014 The Authors. Published under the terms of the CC BY 4.0 license.

  16. Preparation, characterization and application of a reversed phase liquid chromatography/hydrophilic interaction chromatography mixed-mode C18-DTT stationary phase.

    Science.gov (United States)

    Wang, Qing; Long, Yao; Yao, Lin; Xu, Li; Shi, Zhi-Guo; Xu, Lanying

    2016-01-01

    A mixed-mode chromatographic stationary phase, C18-DTT (dithiothreitol) silica (SiO2) was prepared through "thiol-ene" click chemistry. The obtained material was characterized by fourier transform infrared spectroscope, nitrogen adsorption analysis and contact angle analysis. Chromatographic performance of the C18-DTT was systemically evaluated by studying the effect of acetonitrile content, pH, buffer concentration of the mobile phase and column temperature. It was demonstrated that the novel stationary phase possessed reversed phase liquid chromatography (RPLC)/hydrophilic interaction liquid chromatography (HILIC) mixed-mode property. The stop-flow test revealed that C18-DTT exhibited excellent compatibility with 100% aqueous mobile phase. Additionally, the stability and column-to-column reproducibility of the C18-DTT material were satisfactory, with relative standard deviations of retention factor of the tested analytes (verapamil, fenbufen, guanine, tetrandrine and nicotinic acid) in the range of 1.82-3.72% and 0.85-1.93%, respectively. Finally, the application of C18-DTT column was demonstrated in the separation of non-steroidal anti-inflammatory drugs, aromatic carboxylic acids, alkaloids, nucleo-analytes and polycyclic aromatic hydrocarbons. It had great resolving power in the analysis of various compounds in HILIC and RPLC chromatographic conditions and was a promising RPLC/HILIC mixed-mode stationary phase. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. “Weak direct” and “Strong indirect” interactions are the mode of action of food factors

    Directory of Open Access Journals (Sweden)

    Tetsuya Konishi

    2014-06-01

    Full Text Available Age-dependent and lifestyle related diseases such as metabolic syndromes have become a social problem worldwide. Since these disorders are closely related to dietary lifestyle, the old saying “foods are medicine” is now being re-evaluated. Thus, dietary protection against these diseases is attracting much attention. As research into functional foods advances, a book of knowledge is being accumulated on the active ingredients, termed “food factors”, present in food resources. Identifying such molecules usually follows the conventional methodology used for finding drug candidates from natural resources. The question has arisen as to whether the mode of action of food factors as molecules is the same as that of drugs. In this article, the functional properties of food factors and drugs are comparatively reviewed and the characteristic features of food factor function is discussed, based on the idea of “weak direct” and “strong indirect” actions of food factors to their receptors

  18. Two-dimensional spectroscopy for harmonic vibrational modes with nonlinear system-bath interactions. I. Gaussian-white case

    NARCIS (Netherlands)

    Steffen, T; Tanimura, Y

    The quantum Fokker-Planck equation is derived for a system nonlinearly coupled to a harmonic oscillator bath. The system-bath interaction is assumed to be linear in the bath coordinates but quadratic in the system coordinate. The relaxation induced dynamics of a harmonic system are investigated by

  19. Normal modes and possibility of spatially inhomogeneous phases for a 2D ferromagnet with biquadratic and magnetoelastic interactions

    International Nuclear Information System (INIS)

    Fridman, Yu.A.; Klevets, Ph.N.; Matyunin, D.A.

    2006-01-01

    Influence of the magnetodipolar interaction on the phase states of a 2D non-Heisenberg ferromagnet is investigated. It is shown that in the system considered both the homogeneous states (ferromagnetic or quadrupolar) and the spatially inhomogeneous ones can be realized. At this the spatial inhomogeneity is related with the distribution of the quadrupolar order parameters

  20. The effect of polymerization mode on monomer conversion, free radical entrapment, and interaction with hydroxyapatite of commercial self-adhesive cements.

    Science.gov (United States)

    D'Alpino, Paulo Henrique Perlatti; Silva, Marília Santos; Vismara, Marcus Vinícius Gonçalves; Di Hipólito, Vinicius; Miranda González, Alejandra Hortencia; de Oliveira Graeff, Carlos Frederico

    2015-06-01

    This study evaluated the degree of conversion, the free radical entrapment, and the chemical interaction of self-adhesive resin cements mixed with pure hydroxyapatite, as a function of the polymerization activation mode among a variety of commercial self-adhesive cements. Four cements (Embrace WetBond, MaxCem Elite, Bifix SE, and RelyX U200) were mixed, combined with hydroxyapatite, dispensed into molds, and distributed into three groups, according to polymerization protocols: IP (photoactivation for 40s); DP (delayed photoactivation, 10 min self-curing plus 40s light-activated); and CA (chemical activation, no light exposure). Infrared (IR) spectra were obtained and monomer conversion (%) was calculated by comparing the aliphatic-to-aromatic IR absorption peak ratio before and after polymerization (n=10). The free radical entrapment values of the resin cements were characterized using Electron Paramagnetic Resonance (EPR) and the concentration of spins (number of spins/mass) calculated (n=3). Values were compared using two-way ANOVA and Tukey's post-hoc test (α=5%). X-ray diffraction (XRD) characterized the crystallinity of hydroxyapatite as a function of the chemical interactions with the resin cements. The tested parameters varied as a function of resin cement and polymerization protocol. Embrace WetBond and RelyX U200 demonstrated dependence on photoactivation (immediate or delayed), whereas MaxCem Elite exhibited dependence on the chemical activation mode. Bifix SE presented the best balance based on the parameters analyzed, irrespective of the activation protocol. Choice of polymerization protocol affects the degree of conversion, free radical entrapment, and the chemical interaction between hydroxyapatite and self-adhesive resin cement mixtures. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. A new protein-protein interaction sensor based on tripartite split-GFP association.

    Science.gov (United States)

    Cabantous, Stéphanie; Nguyen, Hau B; Pedelacq, Jean-Denis; Koraïchi, Faten; Chaudhary, Anu; Ganguly, Kumkum; Lockard, Meghan A; Favre, Gilles; Terwilliger, Thomas C; Waldo, Geoffrey S

    2013-10-04

    Monitoring protein-protein interactions in living cells is key to unraveling their roles in numerous cellular processes and various diseases. Previously described split-GFP based sensors suffer from poor folding and/or self-assembly background fluorescence. Here, we have engineered a micro-tagging system to monitor protein-protein interactions in vivo and in vitro. The assay is based on tripartite association between two twenty amino-acids long GFP tags, GFP10 and GFP11, fused to interacting protein partners, and the complementary GFP1-9 detector. When proteins interact, GFP10 and GFP11 self-associate with GFP1-9 to reconstitute a functional GFP. Using coiled-coils and FRB/FKBP12 model systems we characterize the sensor in vitro and in Escherichia coli. We extend the studies to mammalian cells and examine the FK-506 inhibition of the rapamycin-induced association of FRB/FKBP12. The small size of these tags and their minimal effect on fusion protein behavior and solubility should enable new experiments for monitoring protein-protein association by fluorescence.

  2. Physiologically-Relevant Modes of Membrane Interactions by the Human Antimicrobial Peptide, LL-37, Revealed by SFG Experiments

    Science.gov (United States)

    Ding, Bei; Soblosky, Lauren; Nguyen, Khoi; Geng, Junqing; Yu, Xinglong; Ramamoorthy, Ayyalusamy; Chen, Zhan

    2013-05-01

    Antimicrobial peptides (AMPs) could become the next generation antibiotic compounds which can overcome bacterial resistance by disrupting cell membranes and it is essential to determine the factors underlying its mechanism of action. Although high-resolution NMR and other biological studies have provided valuable insights, it has been a major challenge to follow the AMP-membrane interactions at physiologically-relevant low peptide concentrations. In this study, we demonstrate a novel approach to overcome this major limitation by performing Sum Frequency Generation (SFG) vibrational spectroscopic experiments on lipid bilayers containing an AMP, LL-37. Our results demonstrate the power of SFG to study non-linear helical peptides and also infer that lipid-peptide interaction and the peptide orientation depend on the lipid membrane composition. The observed SFG signal changes capture the aggregating process of LL-37 on membrane. In addition, our SFG results on cholesterol-containing lipid bilayers indicate the inhibition effect of cholesterol on peptide-induced membrane permeation process.

  3. Interaction of the elytra and hind wing of a rhinoceros beetle (Trypoxylus dichotomus) during a take-off mode

    Science.gov (United States)

    Oh, Seungyoung; Oh, Sehyeong; Choi, Haecheon; Lee, Boogeon; Park, Hyungmin; Kim, Sun-Tae

    2015-11-01

    The elytra are a pair of hardened wings that cover the abdomen of a beetle to protect beetle's hind wings. During the take-off, these elytra open and flap in phase with the hind wings. We investigate the effect of the elytra flapping on beetle's aerodynamic performance. Numerical simulations are performed at Re=10,000 (based on the wingtip mean velocity and mean chord length of the hind wing) using an immersed boundary method. The simulations are focused on a take-off, and the wing kinematics used is directly obtained from the experimental observations using high speed cameras. The simulation result shows three-dimensional vortical structures generated by the hind wing of the beetle and their interaction with the elytra. The presence of elytra has a negative effect on the lift generation by the hind wings, but the lift force on the elytra themselves is negligible. Further discussions on the elytra - hind wing interaction will be provided during the presentation. Supported by UD130070ID.

  4. Magnetoencephalographic alpha band connectivity reveals differential default mode network interactions during focused attention and open monitoring meditation

    Science.gov (United States)

    Marzetti, Laura; Di Lanzo, Claudia; Zappasodi, Filippo; Chella, Federico; Raffone, Antonino; Pizzella, Vittorio

    2014-01-01

    According to several conceptualizations of meditation, the interplay between brain systems associated to self-related processing, attention and executive control is crucial for meditative states and related traits. We used magnetoencephalography (MEG) to investigate such interplay in a highly selected group of “virtuoso” meditators (Theravada Buddhist monks), with long-term training in the two main meditation styles: focused attention (FA) and open monitoring (OM) meditation. Specifically, we investigated the differences between FA meditation, OM meditation and resting state in the coupling between the posterior cingulate cortex, core node of the Default Mode Network (DMN) implicated in mind wandering and self-related processing, and the whole brain, with a recently developed phase coherence approach. Our findings showed a state dependent coupling of posterior cingulate cortex (PCC) to nodes of the DMN and of the executive control brain network in the alpha frequency band (8–12 Hz), related to different attentional and cognitive control processes in FA and OM meditation, consistently with the putative role of alpha band synchronization in the functional mechanisms for attention and consciousness. The coupling of PCC with left medial prefrontal cortex (lmPFC) and superior frontal gyrus characterized the contrast between the two meditation styles in a way that correlated with meditation expertise. These correlations may be related to a higher mindful observing ability and a reduced identification with ongoing mental activity in more expert meditators. Notably, different styles of meditation and different meditation expertise appeared to modulate the dynamic balance between fronto-parietal (FP) and DMN networks. Our results support the idea that the interplay between the DMN and the FP network in the alpha band is crucial for the transition from resting state to different meditative states. PMID:25360102

  5. Inhibition and Larvicidal Activity of Phenylpropanoids from Piper sarmentosum on Acetylcholinesterase against Mosquito Vectors and Their Binding Mode of Interaction.

    Directory of Open Access Journals (Sweden)

    Arshia Hematpoor

    Full Text Available Aedes aegypti, Aedes albopictus and Culex quinquefasciatus are vectors of dengue fever and West Nile virus diseases. This study was conducted to determine the toxicity, mechanism of action and the binding interaction of three active phenylpropanoids from Piper sarmentosum (Piperaceae toward late 3rd or early 4th larvae of above vectors. A bioassay guided-fractionation on the hexane extract from the roots of Piper sarmentosum led to the isolation and identification of three active phenylpropanoids; asaricin 1, isoasarone 2 and trans-asarone 3. The current study involved evaluation of the toxicity and acetylcholinesterase (AChE inhibition of these compounds against Aedes aegypti, Aedes albopictus and Culex quinquefasciatus larvae. Asaricin 1 and isoasarone 2 were highly potent against Aedes aegypti, Aedes albopictus and Culex quinquefasciatus larvae causing up to 100% mortality at ≤ 15 μg/mL concentration. The ovicidal activity of asaricin 1, isoasarone 2 and trans-asarone 3 were evaluated through egg hatching. Asaricin 1 and isoasarone 2 showed potent ovicidal activity. Ovicidal activity for both compounds was up to 95% at 25μg/mL. Asaricin 1 and isoasarone 2 showed strong inhibition on acetylcholinesterase with relative IC50 values of 0.73 to 1.87 μg/mL respectively. These findings coupled with the high AChE inhibition may suggest that asaricin 1 and isoasarone 2 are neuron toxic compounds toward Aedes aegypti, Aedes albopictus and Culex quinquefasciatus. Further computational docking with Autodock Vina elaborates the possible interaction of asaricin 1 and isoasarone 2 with three possible binding sites of AChE which includes catalytic triads (CAS: S238, E367, H480, the peripheral sites (PAS: E72, W271 and anionic binding site (W83. The binding affinity of asaricin 1 and isoasarone 2 were relatively strong with asaricin 1 showed a higher binding affinity in the anionic pocket.

  6. Inhibition and Larvicidal Activity of Phenylpropanoids from Piper sarmentosum on Acetylcholinesterase against Mosquito Vectors and Their Binding Mode of Interaction.

    Science.gov (United States)

    Hematpoor, Arshia; Liew, Sook Yee; Chong, Wei Lim; Azirun, Mohd Sofian; Lee, Vannajan Sanghiran; Awang, Khalijah

    2016-01-01

    Aedes aegypti, Aedes albopictus and Culex quinquefasciatus are vectors of dengue fever and West Nile virus diseases. This study was conducted to determine the toxicity, mechanism of action and the binding interaction of three active phenylpropanoids from Piper sarmentosum (Piperaceae) toward late 3rd or early 4th larvae of above vectors. A bioassay guided-fractionation on the hexane extract from the roots of Piper sarmentosum led to the isolation and identification of three active phenylpropanoids; asaricin 1, isoasarone 2 and trans-asarone 3. The current study involved evaluation of the toxicity and acetylcholinesterase (AChE) inhibition of these compounds against Aedes aegypti, Aedes albopictus and Culex quinquefasciatus larvae. Asaricin 1 and isoasarone 2 were highly potent against Aedes aegypti, Aedes albopictus and Culex quinquefasciatus larvae causing up to 100% mortality at ≤ 15 μg/mL concentration. The ovicidal activity of asaricin 1, isoasarone 2 and trans-asarone 3 were evaluated through egg hatching. Asaricin 1 and isoasarone 2 showed potent ovicidal activity. Ovicidal activity for both compounds was up to 95% at 25μg/mL. Asaricin 1 and isoasarone 2 showed strong inhibition on acetylcholinesterase with relative IC50 values of 0.73 to 1.87 μg/mL respectively. These findings coupled with the high AChE inhibition may suggest that asaricin 1 and isoasarone 2 are neuron toxic compounds toward Aedes aegypti, Aedes albopictus and Culex quinquefasciatus. Further computational docking with Autodock Vina elaborates the possible interaction of asaricin 1 and isoasarone 2 with three possible binding sites of AChE which includes catalytic triads (CAS: S238, E367, H480), the peripheral sites (PAS: E72, W271) and anionic binding site (W83). The binding affinity of asaricin 1 and isoasarone 2 were relatively strong with asaricin 1 showed a higher binding affinity in the anionic pocket.

  7. Linear entropy and collapse–revival phenomenon for a general formalism N-type four-level atom interacting with a single-mode field

    Science.gov (United States)

    Eied, A. A.

    2018-05-01

    In this paper, the linear entropy and collapse-revival phenomenon through the relation ( -{\\bar{n}}) in a system of N-configuration four-level atom interacting with a single-mode field with additional forms of nonlinearities of both the field and the intensity-dependent atom-field coupling functional are investigated. A factorization of the initial density operator is assumed, considering the field to be initially in a squeezed coherent states and the atom initially in its most upper excited state. The dynamical behavior of the linear entropy and the time evolution of ( -{\\bar{n}}) are analyzed. In particular, the effects of the mean photon number, detuning, Kerr-like medium and the intensity-dependent coupling functional on the entropy and the evolution of ( -{\\bar{n}}) are examined.

  8. Selecting Molecular Recognition. What Can Existing Aptamers Tell Us about Their Inherent Recognition Capabilities and Modes of Interaction?

    Directory of Open Access Journals (Sweden)

    Ralf Landgraf

    2012-05-01

    Full Text Available The use of nucleic acid derived aptamers has rapidly expanded since the introduction of SELEX in 1990. Nucleic acid aptamers have demonstrated their ability to target a broad range of molecules in ways that rival antibodies, but advances have been very uneven for different biochemical classes of targets, and clinical applications have been slow to emerge. What sets different aptamers apart from each other and from rivaling molecular recognition platforms, specifically proteins? What advantages do aptamers as a reagent class offer, and how do the chemical properties and selection procedures of aptamers influence their function? Do the building blocks of nucleic acid aptamers dictate inherent limitations in the nature of molecular targets, and do existing aptamers give us insight in how these challenges might be overcome? This review is written as an introduction for potential endusers of aptamer technology who are evaluating the advantages of aptamers as a versatile, affordable, yet highly expandable platform to target a broad range of biological processes or interactions.

  9. TH-C-12A-12: Veritas: An Open Source Tool to Facilitate User Interaction with TrueBeam Developer Mode

    Energy Technology Data Exchange (ETDEWEB)

    Mishra, P [Brigham and Women' s Hospital, Harvard Medical School, Boston, MA (United States); Varian Medical Systems, Palo Alto, CA (United States); Lewis, J [Brigham and Women' s Hospital, Harvard Medical School, Boston, MA (United States); Etmektzoglou, T; Svatos, M [Varian Medical Systems, Palo Alto, CA (United States)

    2014-06-15

    Purpose: To address the challenges of creating delivery trajectories and imaging sequences with TrueBeam Developer Mode, a new open-source graphical XML builder, Veritas, has been developed, tested and made freely available. Veritas eliminates most of the need to understand the underlying schema and write XML scripts, by providing a graphical menu for each control point specifying the state of 30 mechanical/dose axes. All capabilities of Developer Mode are accessible in Veritas. Methods: Veritas was designed using QT Designer, a ‘what-you-is-what-you-get’ (WYSIWIG) tool for building graphical user interfaces (GUI). Different components of the GUI are integrated using QT's signals and slots mechanism. Functionalities are added using PySide, an open source, cross platform Python binding for the QT framework. The XML code generated is immediately visible, making it an interactive learning tool. A user starts from an anonymized DICOM file or XML example and introduces delivery modifications, or begins their experiment from scratch, then uses the GUI to modify control points as desired. The software automatically generates XML plans following the appropriate schema. Results: Veritas was tested by generating and delivering two XML plans at Brigham and Women's Hospital. The first example was created to irradiate the letter ‘B’ with a narrow MV beam using dynamic couch movements. The second was created to acquire 4D CBCT projections for four minutes. The delivery of the letter ‘B’ was observed using a 2D array of ionization chambers. Both deliveries were generated quickly in Veritas by non-expert Developer Mode users. Conclusion: We introduced a new open source tool Veritas for generating XML plans (delivery trajectories and imaging sequences). Veritas makes Developer Mode more accessible by reducing the learning curve for quick translation of research ideas into XML plans. Veritas is an open source initiative, creating the possibility for future

  10. TH-C-12A-12: Veritas: An Open Source Tool to Facilitate User Interaction with TrueBeam Developer Mode

    International Nuclear Information System (INIS)

    Mishra, P; Lewis, J; Etmektzoglou, T; Svatos, M

    2014-01-01

    Purpose: To address the challenges of creating delivery trajectories and imaging sequences with TrueBeam Developer Mode, a new open-source graphical XML builder, Veritas, has been developed, tested and made freely available. Veritas eliminates most of the need to understand the underlying schema and write XML scripts, by providing a graphical menu for each control point specifying the state of 30 mechanical/dose axes. All capabilities of Developer Mode are accessible in Veritas. Methods: Veritas was designed using QT Designer, a ‘what-you-is-what-you-get’ (WYSIWIG) tool for building graphical user interfaces (GUI). Different components of the GUI are integrated using QT's signals and slots mechanism. Functionalities are added using PySide, an open source, cross platform Python binding for the QT framework. The XML code generated is immediately visible, making it an interactive learning tool. A user starts from an anonymized DICOM file or XML example and introduces delivery modifications, or begins their experiment from scratch, then uses the GUI to modify control points as desired. The software automatically generates XML plans following the appropriate schema. Results: Veritas was tested by generating and delivering two XML plans at Brigham and Women's Hospital. The first example was created to irradiate the letter ‘B’ with a narrow MV beam using dynamic couch movements. The second was created to acquire 4D CBCT projections for four minutes. The delivery of the letter ‘B’ was observed using a 2D array of ionization chambers. Both deliveries were generated quickly in Veritas by non-expert Developer Mode users. Conclusion: We introduced a new open source tool Veritas for generating XML plans (delivery trajectories and imaging sequences). Veritas makes Developer Mode more accessible by reducing the learning curve for quick translation of research ideas into XML plans. Veritas is an open source initiative, creating the possibility for future

  11. RNF41 interacts with the VPS52 subunit of the GARP and EARP complexes.

    Science.gov (United States)

    Masschaele, Delphine; De Ceuninck, Leentje; Wauman, Joris; Defever, Dieter; Stenner, Frank; Lievens, Sam; Peelman, Frank; Tavernier, Jan

    2017-01-01

    RNF41 (Ring Finger Protein 41) is an E3 ubiquitin ligase involved in the intracellular sorting and function of a diverse set of substrates. Next to BRUCE and Parkin, RNF41 can directly ubiquitinate ErbB3, IL-3, EPO and RARα receptors or downstream signaling molecules such as Myd88, TBK1 and USP8. In this way it can regulate receptor signaling and routing. To further elucidate the molecular mechanism behind the role of RNF41 in intracellular transport we performed an Array MAPPIT (Mammalian Protein-Protein Interaction Trap) screen using an extensive set of proteins derived from the human ORFeome collection. This paper describes the identification of VPS52, a subunit of the GARP (Golgi-Associated Retrograde Protein) and the EARP (Endosome-Associated Recycling Protein) complexes, as a novel interaction partner of RNF41. Through interaction via their coiled coil domains, RNF41 ubiquitinates and relocates VPS52 away from VPS53, a common subunit of the GARP and EARP complexes, towards RNF41 bodies.

  12. RNF41 interacts with the VPS52 subunit of the GARP and EARP complexes.

    Directory of Open Access Journals (Sweden)

    Delphine Masschaele

    Full Text Available RNF41 (Ring Finger Protein 41 is an E3 ubiquitin ligase involved in the intracellular sorting and function of a diverse set of substrates. Next to BRUCE and Parkin, RNF41 can directly ubiquitinate ErbB3, IL-3, EPO and RARα receptors or downstream signaling molecules such as Myd88, TBK1 and USP8. In this way it can regulate receptor signaling and routing. To further elucidate the molecular mechanism behind the role of RNF41 in intracellular transport we performed an Array MAPPIT (Mammalian Protein-Protein Interaction Trap screen using an extensive set of proteins derived from the human ORFeome collection. This paper describes the identification of VPS52, a subunit of the GARP (Golgi-Associated Retrograde Protein and the EARP (Endosome-Associated Recycling Protein complexes, as a novel interaction partner of RNF41. Through interaction via their coiled coil domains, RNF41 ubiquitinates and relocates VPS52 away from VPS53, a common subunit of the GARP and EARP complexes, towards RNF41 bodies.

  13. Direct molecular interactions between Beclin 1 and the canonical NFκB activation pathway.

    Science.gov (United States)

    Niso-Santano, Mireia; Criollo, Alfredo; Malik, Shoaib Ahmad; Michaud, Michael; Morselli, Eugenia; Mariño, Guillermo; Lachkar, Sylvie; Galluzzi, Lorenzo; Maiuri, Maria Chaira; Kroemer, Guido

    2012-02-01

    General (macro)autophagy and the activation of NFκB constitute prominent responses to a large array of intracellular and extracellular stress conditions. The depletion of any of the three subunits of the inhibitor of NFκB (IκB) kinase (IKKα, IKKβ, IKKγ/NEMO), each of which is essential for the canonical NFκB activation pathway, limits autophagy induction by physiological or pharmacological triggers, while constitutive active IKK subunits suffice to stimulate autophagy. The activation of IKK usually relies on TGFβ-activated kinase 1 (TAK1), which is also necessary for the optimal induction of autophagy in multiple settings. TAK1 interacts with two structurally similar co-activators, TAK1-binding proteins 2 and 3 (TAB2 and TAB3). Importantly, in resting conditions both TAB2 and TAB3 bind the essential autophagic factor Beclin 1, but not TAK1. In response to pro-autophagic stimuli, TAB2 and TAB3 dissociate from Beclin 1 and engage in stimulatory interactions with TAK1. The inhibitory interaction between TABs and Beclin 1 is mediated by their coiled-coil domains (CCDs). Accordingly, the overexpression of either TAB2 or TAB3 CCD stimulates Beclin 1- and TAK1-dependent autophagy. These results point to the existence of a direct molecular crosstalk between the canonical NFκB activation pathway and the autophagic core machinery that guarantees the coordinated induction of these processes in response to stress.

  14. Age-Related Differences in Dynamic Interactions Among Default Mode, Frontoparietal Control, and Dorsal Attention Networks during Resting-State and Interference Resolution

    Science.gov (United States)

    Avelar-Pereira, Bárbara; Bäckman, Lars; Wåhlin, Anders; Nyberg, Lars; Salami, Alireza

    2017-01-01

    Resting-state fMRI (rs-fMRI) can identify large-scale brain networks, including the default mode (DMN), frontoparietal control (FPN) and dorsal attention (DAN) networks. Interactions among these networks are critical for supporting complex cognitive functions, yet the way in which they are modulated across states is not well understood. Moreover, it remains unclear whether these interactions are similarly affected in aging regardless of cognitive state. In this study, we investigated age-related differences in functional interactions among the DMN, FPN and DAN during rest and the Multi-Source Interference task (MSIT). Networks were identified using independent component analysis (ICA), and functional connectivity was measured during rest and task. We found that the FPN was more coupled with the DMN during rest and with the DAN during the MSIT. The degree of FPN-DMN connectivity was lower in older compared to younger adults, whereas no age-related differences were observed in FPN-DAN connectivity in either state. This suggests that dynamic interactions of the FPN are stable across cognitive states. The DMN and DAN were anti correlated and age-sensitive during the MSIT only, indicating variation in a task-dependent manner. Increased levels of anticorrelation from rest to task also predicted successful interference resolution. Additional analyses revealed that the degree of DMN-DAN anticorrelation during the MSIT was associated to resting cerebral blood flow (CBF) within the DMN. This suggests that reduced DMN neural activity during rest underlies an impaired ability to achieve higher levels of anticorrelation during a task. Taken together, our results suggest that only parts of age-related differences in connectivity are uncovered at rest and thus, should be studied in the functional connectome across multiple states for a more comprehensive picture. PMID:28588476

  15. Dual-Mode Combustor

    Science.gov (United States)

    Trefny, Charles J (Inventor); Dippold, Vance F (Inventor)

    2013-01-01

    A new dual-mode ramjet combustor used for operation over a wide flight Mach number range is described. Subsonic combustion mode is usable to lower flight Mach numbers than current dual-mode scramjets. High speed mode is characterized by supersonic combustion in a free-jet that traverses the subsonic combustion chamber to a variable nozzle throat. Although a variable combustor exit aperture is required, the need for fuel staging to accommodate the combustion process is eliminated. Local heating from shock-boundary-layer interactions on combustor walls is also eliminated.

  16. Interaction Pattern of Arg 62 in the A-Pocket of Differentially Disease-Associated HLA-B27 Subtypes Suggests Distinct TCR Binding Modes

    Science.gov (United States)

    Cauli, Alberto; Mathieu, Alessandro; Tedeschi, Valentina; Caristi, Silvana; Sorrentino, Rosa; Böckmann, Rainer A.; Fiorillo, Maria Teresa

    2012-01-01

    The single amino acid replacement Asp116His distinguishes the two subtypes HLA-B*2705 and HLA-B*2709 which are, respectively, associated and non-associated with Ankylosing Spondylitis, an autoimmune chronic inflammatory disease. The reason for this differential association is so far poorly understood and might be related to subtype-specific HLA:peptide conformations as well as to subtype/peptide-dependent dynamical properties on the nanoscale. Here, we combine functional experiments with extensive molecular dynamics simulations to investigate the molecular dynamics and function of the conserved Arg62 of the α1-helix for both B27 subtypes in complex with the self-peptides pVIPR (RRKWRRWHL) and TIS (RRLPIFSRL), and the viral peptides pLMP2 (RRRWRRLTV) and NPflu (SRYWAIRTR). Simulations of HLA:peptide systems suggest that peptide-stabilizing interactions of the Arg62 residue observed in crystal structures are metastable for both B27 subtypes under physiological conditions, rendering this arginine solvent-exposed and, probably, a key residue for TCR interaction more than peptide-binding. This view is supported by functional experiments with conservative (R62K) and non-conservative (R62A) B*2705 and B*2709 mutants that showed an overall reduction in their capability to present peptides to CD8+ T cells. Moreover, major subtype-dependent differences in the peptide recognition suggest distinct TCR binding modes for the B*2705 versus the B*2709 subtype. PMID:22403718

  17. Divergent and convergent modes of interaction between wheat and Puccinia graminis f. sp. tritici isolates revealed by the comparative gene co-expression network and genome analyses.

    Science.gov (United States)

    Rutter, William B; Salcedo, Andres; Akhunova, Alina; He, Fei; Wang, Shichen; Liang, Hanquan; Bowden, Robert L; Akhunov, Eduard

    2017-04-12

    Two opposing evolutionary constraints exert pressure on plant pathogens: one to diversify virulence factors in order to evade plant defenses, and the other to retain virulence factors critical for maintaining a compatible interaction with the plant host. To better understand how the diversified arsenals of fungal genes promote interaction with the same compatible wheat line, we performed a comparative genomic analysis of two North American isolates of Puccinia graminis f. sp. tritici (Pgt). The patterns of inter-isolate divergence in the secreted candidate effector genes were compared with the levels of conservation and divergence of plant-pathogen gene co-expression networks (GCN) developed for each isolate. Comprative genomic analyses revealed substantial level of interisolate divergence in effector gene complement and sequence divergence. Gene Ontology (GO) analyses of the conserved and unique parts of the isolate-specific GCNs identified a number of conserved host pathways targeted by both isolates. Interestingly, the degree of inter-isolate sub-network conservation varied widely for the different host pathways and was positively associated with the proportion of conserved effector candidates associated with each sub-network. While different Pgt isolates tended to exploit similar wheat pathways for infection, the mode of plant-pathogen interaction varied for different pathways with some pathways being associated with the conserved set of effectors and others being linked with the diverged or isolate-specific effectors. Our data suggest that at the intra-species level pathogen populations likely maintain divergent sets of effectors capable of targeting the same plant host pathways. This functional redundancy may play an important role in the dynamic of the "arms-race" between host and pathogen serving as the basis for diverse virulence strategies and creating conditions where mutations in certain effector groups will not have a major effect on the pathogen

  18. p53 inhibits autophagy by interacting with the human ortholog of yeast Atg17, RB1CC1/FIP200.

    Science.gov (United States)

    Morselli, Eugenia; Shen, Shensi; Ruckenstuhl, Christoph; Bauer, Maria Anna; Mariño, Guillermo; Galluzzi, Lorenzo; Criollo, Alfredo; Michaud, Mickael; Maiuri, Maria Chiara; Chano, Tokuhiro; Madeo, Frank; Kroemer, Guido

    2011-08-15

    The tumor suppressor protein p53 tonically suppresses autophagy when it is present in the cytoplasm. This effect is phylogenetically conserved from mammals to nematodes, and human p53 can inhibit autophagy in yeast, as we show here. Bioinformatic investigations of the p53 interactome in relationship to the autophagy-relevant protein network underscored the possible relevance of a direct molecular interaction between p53 and the mammalian ortholog of the essential yeast autophagy protein Atg17, namely RB1-inducible coiled-coil protein 1 (RB1CC1), also called FAK family kinase-interacting protein of 200 KDa (FIP200). Mutational analyses revealed that a single point mutation in p53 (K382R) abolished its capacity to inhibit autophagy upon transfection into p53-deficient human colon cancer or yeast cells. In conditions in which wild-type p53 co-immunoprecipitated with RB1CC1/FIP200, p53 (K382R) failed to do so, underscoring the importance of the physical interaction between these proteins for the control of autophagy. In conclusion, p53 regulates autophagy through a direct molecular interaction with RB1CC1/FIP200, a protein that is essential for the very apical step of autophagy initiation.

  19. Interaction of the amyloid precursor protein-like protein 1 (APLP1) E2 domain with heparan sulfate involves two distinct binding modes

    Energy Technology Data Exchange (ETDEWEB)

    Dahms, Sven O., E-mail: sdahms@fli-leibniz.de [Leibniz Institute for Age Research (FLI), Beutenbergstrasse 11, 07745 Jena (Germany); Mayer, Magnus C. [Freie Universität Berlin, Thielallee 63, 14195 Berlin (Germany); Miltenyi Biotec GmbH, Robert-Koch-Strasse 1, 17166 Teterow (Germany); Roeser, Dirk [Leibniz Institute for Age Research (FLI), Beutenbergstrasse 11, 07745 Jena (Germany); Multhaup, Gerd [McGill University Montreal, Montreal, Quebec H3G 1Y6 (Canada); Than, Manuel E., E-mail: sdahms@fli-leibniz.de [Leibniz Institute for Age Research (FLI), Beutenbergstrasse 11, 07745 Jena (Germany)

    2015-03-01

    Two X-ray structures of APLP1 E2 with and without a heparin dodecasaccharide are presented, revealing two distinct binding modes of the protein to heparan sulfate. The data provide a mechanistic explanation of how APP-like proteins bind to heparan sulfates and how they specifically recognize nonreducing structures of heparan sulfates. Beyond the pathology of Alzheimer’s disease, the members of the amyloid precursor protein (APP) family are essential for neuronal development and cell homeostasis in mammals. APP and its paralogues APP-like protein 1 (APLP1) and APP-like protein 2 (APLP2) contain the highly conserved heparan sulfate (HS) binding domain E2, which effects various (patho)physiological functions. Here, two crystal structures of the E2 domain of APLP1 are presented in the apo form and in complex with a heparin dodecasaccharide at 2.5 Å resolution. The apo structure of APLP1 E2 revealed an unfolded and hence flexible N-terminal helix αA. The (APLP1 E2){sub 2}–(heparin){sub 2} complex structure revealed two distinct binding modes, with APLP1 E2 explicitly recognizing the heparin terminus but also interacting with a continuous heparin chain. The latter only requires a certain register of the sugar moieties that fits to a positively charged surface patch and contributes to the general heparin-binding capability of APP-family proteins. Terminal binding of APLP1 E2 to heparin specifically involves a structure of the nonreducing end that is very similar to heparanase-processed HS chains. These data reveal a conserved mechanism for the binding of APP-family proteins to HS and imply a specific regulatory role of HS modifications in the biology of APP and APP-like proteins.

  20. Identification of human and mouse CatSper3 and CatSper4 genes: Characterisation of a common interaction domain and evidence for expression in testis

    Directory of Open Access Journals (Sweden)

    Reynolds Lindsey

    2003-08-01

    Full Text Available Abstract Background CatSper1 and CatSper2 are two recently identified channel-like proteins, which show sperm specific expression patterns. Through targeted mutagenesis in the mouse, CatSper1 has been shown to be required for fertility, sperm motility and for cAMP induced Ca2+ current in sperm. Both channels resemble a single pore forming repeat from a four repeat voltage dependent Ca2+ /Na+ channel. However, neither CatSper1 or CatSper2 have been shown to function as cation channels when transfected into cells, singly or in conjunction. As the pore forming units of voltage gated cation channels form a tetramer it has been suggested that the known CatSper proteins require additional subunits and/or interaction partners to function. Results Using in silico gene identification and prediction techniques, we have identified two further members of the CatSper family, CatSper3 and Catsper4. Each carries a single channel-forming domain with the predicted pore-loop containing the consensus sequence T×D×W. Each of the new CatSper genes has evidence for expression in the testis. Furthermore we identified coiled-coil protein-protein interaction domains in the C-terminal tails of each of the CatSper channels, implying that CatSper channels 1,2,3 and 4 may interact directly or indirectly to form a functional tetramer. Conclusions The topological and sequence relationship of CatSper1 and CatSper2 to the four repeat Ca2+ /Na+ channels suggested other members of this family may exist. We have identified a further two novel CatSper genes, conserved in both the human and mouse genomes. Furthermore, all four of the CatSper proteins are predicted to contain a common coiled-coil protein-protein interaction domain in their C-terminal tail. Coupled with expression data this leads to the hypothesis that the CatSper proteins form a functional hetero-tetrameric channel in sperm.

  1. GEMC1 is a TopBP1-interacting protein required for chromosomal DNA replication.

    Science.gov (United States)

    Balestrini, Alessia; Cosentino, Claudia; Errico, Alessia; Garner, Elizabeth; Costanzo, Vincenzo

    2010-05-01

    Many of the factors required for chromosomal DNA replication have been identified in unicellular eukaryotes. However, DNA replication is poorly understood in multicellular organisms. Here, we report the identification of GEMC1 (geminin coiled-coil containing protein 1), a novel vertebrate protein required for chromosomal DNA replication. GEMC1 is highly conserved in vertebrates and is preferentially expressed in proliferating cells. Using Xenopus laevis egg extract we show that Xenopus GEMC1 (xGEMC1) binds to the checkpoint and replication factor TopBP1, which promotes binding of xGEMC1 to chromatin during pre-replication complex (pre-RC) formation. We demonstrate that xGEMC1 interacts directly with replication factors such as Cdc45 and the kinase Cdk2-CyclinE, through which it is heavily phosphorylated. Phosphorylated xGEMC1 stimulates initiation of DNA replication, whereas depletion of xGEMC1 prevents the onset of DNA replication owing to the impairment of Cdc45 loading onto chromatin. Similarly, inhibition of GEMC1 expression with morpholino and siRNA oligos prevents DNA replication in embryonic and somatic vertebrate cells. These data suggest that GEMC1 promotes initiation of chromosomal DNA replication in multicellular organisms by mediating TopBP1- and Cdk2-dependent recruitment of Cdc45 onto replication origins.

  2. Neuronal Calcium Sensor-1 Binds the D2 Dopamine Receptor and G-protein-coupled Receptor Kinase 1 (GRK1) Peptides Using Different Modes of Interactions.

    Science.gov (United States)

    Pandalaneni, Sravan; Karuppiah, Vijaykumar; Saleem, Muhammad; Haynes, Lee P; Burgoyne, Robert D; Mayans, Olga; Derrick, Jeremy P; Lian, Lu-Yun

    2015-07-24

    Neuronal calcium sensor-1 (NCS-1) is the primordial member of the neuronal calcium sensor family of EF-hand Ca(2+)-binding proteins. It interacts with both the G-protein-coupled receptor (GPCR) dopamine D2 receptor (D2R), regulating its internalization and surface expression, and the cognate kinases GRK1 and GRK2. Determination of the crystal structures of Ca(2+)/NCS-1 alone and in complex with peptides derived from D2R and GRK1 reveals that the differential recognition is facilitated by the conformational flexibility of the C-lobe-binding site. We find that two copies of the D2R peptide bind within the hydrophobic crevice on Ca(2+)/NCS-1, but only one copy of the GRK1 peptide binds. The different binding modes are made possible by the C-lobe-binding site of NCS-1, which adopts alternative conformations in each complex. C-terminal residues Ser-178-Val-190 act in concert with the flexible EF3/EF4 loop region to effectively form different peptide-binding sites. In the Ca(2+)/NCS-1·D2R peptide complex, the C-terminal region adopts a 310 helix-turn-310 helix, whereas in the GRK1 peptide complex it forms an α-helix. Removal of Ser-178-Val-190 generated a C-terminal truncation mutant that formed a dimer, indicating that the NCS-1 C-terminal region prevents NCS-1 oligomerization. We propose that the flexible nature of the C-terminal region is essential to allow it to modulate its protein-binding sites and adapt its conformation to accommodate both ligands. This appears to be driven by the variability of the conformation of the C-lobe-binding site, which has ramifications for the target specificity and diversity of NCS-1. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  3. Entanglement and Other Nonclassical Properties of Two Two-Level Atoms Interacting with a Two-Mode Binomial Field: Constant and Intensity-Dependent Coupling Regimes

    International Nuclear Information System (INIS)

    Tavassoly, M.K.; Hekmatara, H.

    2015-01-01

    In this paper, we consider the interaction between two two-level atoms and a two-mode binomial field with a general intensity-dependent coupling regime. The outlined dynamical problem has explicit analytical solution, by which we can evaluate a few of its physical features of interest. To achieve the purpose of the paper, after choosing a particular nonlinearity function, we investigate the quantum statistics, atomic population inversion and at last the linear entropy of the atom-field system which is a good measure for the degree of entanglement. In detail, the effects of binomial field parameters, in addition to different initial atomic states on the temporal behavior of the mentioned quantities have been analyzed. The results show that, the values of binomial field parameters and the initial state of the two atoms influence on the nonclassical effects in the obtained states through which one can tune the nonclassicality criteria appropriately. Setting intensity-dependent coupling function equal to 1 reduces the results to the constant coupling case. By comparing the latter case with the nonlinear regime, we will observe that the nonlinearity disappears the pattern of collapse-revival phenomenon in the evolution of Mandel parameter and population inversion (which can be seen in the linear case with constant coupling), however, more typical collapse-revivals will be appeared for the cross-correlation function in the nonlinear case. Finally, in both linear and nonlinear regime, the entropy remains less than (but close to) 0.5. In other words the particular chosen nonlinearity does not critically affect on the entropy of the system. (paper)

  4. DIFFICULTY OF MODE OF ACTION DETERMINATION FOR TRICHLOROETHYLENE: AN EXAMPLE OF COMPLEX INTERACTIONS OF METABOLITES AND OTHER CHEMICAL EXPOSURES (Journal Article)

    Science.gov (United States)

    The mode(s) of action (MOA) of a pollutant for adverse health effects may be dependent on the mixture of metabolites resulting from exposure to a single agent and may also be affected by co-exposure to pollutants that have similar targets or affected pathways. Trichloroethylene ...

  5. Plasma Modes

    Science.gov (United States)

    Dubin, D. H. E.

    This chapter explores several aspects of the linear electrostatic normal modes of oscillation for a single-species non-neutral plasma in a Penning trap. Linearized fluid equations of motion are developed, assuming the plasma is cold but collisionless, which allow derivation of the cold plasma dielectric tensor and the electrostatic wave equation. Upper hybrid and magnetized plasma waves in an infinite uniform plasma are described. The effect of the plasma surface in a bounded plasma system is considered, and the properties of surface plasma waves are characterized. The normal modes of a cylindrical plasma column are discussed, and finally, modes of spheroidal plasmas, and finite temperature effects on the modes, are briefly described.

  6. INTERACT

    DEFF Research Database (Denmark)

    Jochum, Elizabeth; Borggreen, Gunhild; Murphey, TD

    This paper considers the impact of visual art and performance on robotics and human-computer interaction and outlines a research project that combines puppetry and live performance with robotics. Kinesics—communication through movement—is the foundation of many theatre and performance traditions ...

  7. C2360, a nuclear protein expressed in human proliferative cytotrophoblasts, is a representative member of a novel protein family with a conserved coiled coil-helix-coiled coil-helix domain.

    NARCIS (Netherlands)

    Westerman, B.A.; Poutsma, A; Steegers, EA; Oudejans, C.B.M.

    2004-01-01

    In this study, we describe the identification of nine novel genes isolated from a unique human first-trimester cDNA library generated from the placental bed. One of these clones, called C2360 and located on chromosome 10q22, was selected as it showed restricted expression in placental bed tissue as

  8. C2360, a nuclear protein expressed in human proliferative cytotrophoblasts, is a representative member of a novel protein family with a conserved coiled coil-helix-coiled coil-helix domain

    NARCIS (Netherlands)

    Westerman, Bart A.; Poutsma, Ankie; Steegers, Eric A. P.; Oudejans, Cees B. M.

    2004-01-01

    In this study, we describe the identification of nine novel genes isolated from a unique human first-trimester cDNA library generated from the placental bed. One of these clones, called C2360 and located on chromosome 10q22, was selected as it showed restricted expression in placental bed tissue as

  9. Evaluation of mode equivalence of the MSKCC Bowel Function Instrument, LASA Quality of Life, and Subjective Significance Questionnaire items administered by Web, interactive voice response system (IVRS), and paper.

    Science.gov (United States)

    Bennett, Antonia V; Keenoy, Kathleen; Shouery, Marwan; Basch, Ethan; Temple, Larissa K

    2016-05-01

    To assess the equivalence of patient-reported outcome (PRO) survey responses across Web, interactive voice response system (IVRS), and paper modes of administration. Postoperative colorectal cancer patients with home Web/e-mail and phone were randomly assigned to one of the eight study groups: Groups 1-6 completed the survey via Web, IVRS, and paper, in one of the six possible orders; Groups 7-8 completed the survey twice, either by Web or by IVRS. The 20-item survey, including the MSKCC Bowel Function Instrument (BFI), the LASA Quality of Life (QOL) scale, and the Subjective Significance Questionnaire (SSQ) adapted to bowel function, was completed from home on consecutive days. Mode equivalence was assessed by comparison of mean scores across modes and intraclass correlation coefficients (ICCs) and was compared to the test-retest reliability of Web and IVRS. Of 170 patients, 157 completed at least one survey and were included in analysis. Patients had mean age 56 (SD = 11), 53% were male, 81% white, 53% colon, and 47% rectal cancer; 78% completed all assigned surveys. Mean scores for BFI total score, BFI subscale scores, LASA QOL, and adapted SSQ varied by mode by less than one-third of a score point. ICCs across mode were: BFI total score (Web-paper = 0.96, Web-IVRS = 0.97, paper-IVRS = 0.97); BFI subscales (range = 0.88-0.98); LASA QOL (Web-paper = 0.98, Web-IVRS = 0.78, paper-IVRS = 0.80); and SSQ (Web-paper = 0.92, Web-IVRS = 0.86, paper-IVRS = 0.79). Mode equivalence was demonstrated for the BFI total score, BFI subscales, LASA QOL, and adapted SSQ, supporting the use of multiple modes of PRO data capture in clinical trials.

  10. TCS1, a Microtubule-Binding Protein, Interacts with KCBP/ZWICHEL to Regulate Trichome Cell Shape in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Liangliang Chen

    2016-10-01

    Full Text Available How cell shape is controlled is a fundamental question in developmental biology, but the genetic and molecular mechanisms that determine cell shape are largely unknown. Arabidopsis trichomes have been used as a good model system to investigate cell shape at the single-cell level. Here we describe the trichome cell shape 1 (tcs1 mutants with the reduced trichome branch number in Arabidopsis. TCS1 encodes a coiled-coil domain-containing protein. Pharmacological analyses and observations of microtubule dynamics show that TCS1 influences the stability of microtubules. Biochemical analyses and live-cell imaging indicate that TCS1 binds to microtubules and promotes the assembly of microtubules. Further results reveal that TCS1 physically associates with KCBP/ZWICHEL, a microtubule motor involved in the regulation of trichome branch number. Genetic analyses indicate that kcbp/zwi is epistatic to tcs1 with respect to trichome branch number. Thus, our findings define a novel genetic and molecular mechanism by which TCS1 interacts with KCBP to regulate trichome cell shape by influencing the stability of microtubules.

  11. A reassessment of the potential for an alpha-mode containment failure and a review of the current understanding of broader fuel-coolant interaction issues. Second steam explosion review group workshop

    Energy Technology Data Exchange (ETDEWEB)

    Basu, S. [Nuclear Regulatory Commission, Washington, DC (United States); Ginsberg, T. [Brookhaven National Lab., Upton, NY (United States)

    1996-08-01

    This report summarizes the review and evaluation by experts of the current understanding of the molten fuel-coolant interaction (FCI) issues covering the complete spectrum of interactions, i.e., from mild quenching to very energetic interactions including those that could lead to the alpha-mode containment failure. Of the eleven experts polled, all but two concluded that the alpha-mode failure issue was resolved from a risk perspective, meaning that this mode of failure is of very low probability, that it is of little or no significance to the overall risk from a nuclear power plant, and that any further reduction in residual uncertainties is not likely to change the probability in an appreciable manner. To a lesser degree, discussions also took place on the broader FCI issues such as mild quenching of core melt during non-explosive FCI, and shock loading of lower head and ex-vessel support structures arising from explosive localized FCIs. These latter issues are relevant with regard to determining the efficacy of certain accident management strategies for operating reactors as well as for advanced light water reactors. The experts reviewed the status of understanding of the FCI phenomena in the context of these broader issues, identified residual uncertainties in the understanding, and recommended future research (both experimental and analytical) to reduce the uncertainties.

  12. A reassessment of the potential for an alpha-mode containment failure and a review of the current understanding of broader fuel-coolant interaction issues. Second steam explosion review group workshop

    International Nuclear Information System (INIS)

    Basu, S.; Ginsberg, T.

    1996-08-01

    This report summarizes the review and evaluation by experts of the current understanding of the molten fuel-coolant interaction (FCI) issues covering the complete spectrum of interactions, i.e., from mild quenching to very energetic interactions including those that could lead to the alpha-mode containment failure. Of the eleven experts polled, all but two concluded that the alpha-mode failure issue was resolved from a risk perspective, meaning that this mode of failure is of very low probability, that it is of little or no significance to the overall risk from a nuclear power plant, and that any further reduction in residual uncertainties is not likely to change the probability in an appreciable manner. To a lesser degree, discussions also took place on the broader FCI issues such as mild quenching of core melt during non-explosive FCI, and shock loading of lower head and ex-vessel support structures arising from explosive localized FCIs. These latter issues are relevant with regard to determining the efficacy of certain accident management strategies for operating reactors as well as for advanced light water reactors. The experts reviewed the status of understanding of the FCI phenomena in the context of these broader issues, identified residual uncertainties in the understanding, and recommended future research (both experimental and analytical) to reduce the uncertainties

  13. A coiled coil trigger site is essential for rapid binding of synaptobrevin to the SNARE acceptor complex

    DEFF Research Database (Denmark)

    Wiederhold, Katrin; Kloepper, Tobias H; Walter, Alexander M

    2010-01-01

    Exocytosis from synaptic vesicles is driven by stepwise formation of a tight alpha-helical complex between the fusing membranes. The complex is composed of the three SNAREs: synaptobrevin 2, SNAP-25, and syntaxin 1a. An important step in complex formation is fast binding of vesicular synaptobrevi...

  14. Tacoma mode

    International Nuclear Information System (INIS)

    Courant, E.D.; Ruth, R.D.; Wang, J.M.

    1979-01-01

    The name Tacoma refers to the Tacoma Narrows Bridge which collapsed on November 8, 1940 due to massive oscillations caused by high winds. One of the destructive modes was a torsion mode which was excited by transverse wind, a dipole force, and continued until the bridge collapsed. The name is used to refer to a coherent mode of oscillation of a spectrum of oscillators in which the amplitude vs frequency graph contains one node, where the node occurs near the driving frequency and a ω is not symmetric about zero. When this result is applied to vertical instabilities in coasting beams, it implies the existence of a coherent skew quadrupole moment, Q/sub xy/, whenever a coherent dipole oscillation exists

  15. Tacoma mode

    International Nuclear Information System (INIS)

    Courant, E.D.; Ruth, R.D.; Wang, J.M.

    1979-01-01

    The name Tacoma refers to the Tacoma Narrows Bridge which collapsed on November 8, 1940 due to massive oscillations caused by high winds. One of the destructive modes was a torsion mode which was excited by transverse wind, a dipole force, and continued until the bridge collapsed. The name is used to refer to a coherent mode of oscillation of a spectrum of oscillators in which the amplitude vs frequency graph contains one node, where the node occurs near the driving frequency and a(ω) is not symmetric about zero. When this result is applied to vertical instabilities in coasting beams, it implies the existence of a coherent skew quadrupole moment, whenever a coherent dipole oscillation exists

  16. Studies in interactive communication. I - The effects of four communication modes on the behavior of teams during cooperative problem-solving.

    Science.gov (United States)

    Chapanis, A.; Ochsman, R. B.; Parrish, R. N.; Weeks, G. D.

    1972-01-01

    Two-man teams solved credible, 'real-world' problems for which computer assistance has been or could be useful. Conversations were carried on in one of four modes of communication: (1) typewriting, (2) handwriting, (3) voice, and (4) natural, unrestricted communication. Two groups of subjects (experienced and inexperienced typists) were tested in the typewriting mode. Performance was assessed on three classes of dependent measures: time to solution, behavioral measures of activity, and linguistic measures. Significant and meaningful differences among the communication modes were found in each of the three classes of dependent variable. This paper is concerned mainly with the results of the activity analyses. Behavior was recorded in 15 different categories. The analyses of variance yielded 34 statistically significant terms of which 27 were judged to be practically significant as well. When the data were transformed to eliminate heterogeneity, the analyses of variance yielded 35 statistically significant terms of which 26 were judged to be practically significant.

  17. Keratins are the widely distributed fibrous proteins of our ...

    African Journals Online (AJOL)

    SAJID DANWAR

    2013-01-17

    Jan 17, 2013 ... Keratins, due to the presence of the disulfide linkages, coiled-coil in the structure, hydrophobic interactions, and hydrogen bonds, are highly resistant to acids and some protease enzymes ..... (2010) where slight reduction in.

  18. Tapping mode microwave impedance microscopy

    KAUST Repository

    Lai, K.; Kundhikanjana, W.; Peng, H.; Cui, Y.; Kelly, M. A.; Shen, Z. X.

    2009-01-01

    We report tapping mode microwave impedance imaging based on atomic force microscope platforms. The shielded cantilever probe is critical to localize the tip-sample interaction near the tip apex. The modulated tip-sample impedance can be accurately

  19. Failure Modes

    DEFF Research Database (Denmark)

    Jakobsen, K. P.; Burcharth, H. F.; Ibsen, Lars Bo

    1999-01-01

    The present appendix contains the derivation of ten different limit state equations divided on three different failure modes. Five of the limit state equations can be used independently of the characteristics of the subsoil, whereas the remaining five can be used for either drained or undrained s...

  20. Accurate mode characterization of two-mode optical fibers by in-fiber acousto-optics.

    Science.gov (United States)

    Alcusa-Sáez, E; Díez, A; Andrés, M V

    2016-03-07

    Acousto-optic interaction in optical fibers is exploited for the accurate and broadband characterization of two-mode optical fibers. Coupling between LP 01 and LP 1m modes is produced in a broadband wavelength range. Difference in effective indices, group indices, and chromatic dispersions between the guided modes, are obtained from experimental measurements. Additionally, we show that the technique is suitable to investigate the fine modes structure of LP modes, and some other intriguing features related with modes' cut-off.

  1. Interaction between shock coils increased the incidence of inappropriate therapies and lead failure in implantable cardioverter defibrillator.

    Science.gov (United States)

    El Garhy, Mohammad; Ohlow, Marc-Alexander; Lauer, Bernward

    Shock coil interaction in patients with multiple implantable cardioverter defibrillator (ICD) leads is occasionally observed. We aimed to evaluate the incidence of shock coil interaction and its clinical relevance. All ICD patients (646 patients) who came to follow up control in our ICD ambulance between January 1, 2011, and December 31, 2011 in the department of cardiology in Bad Berka hospital were retrospectively evaluated in this study. All baseline demographic, clinical, and procedural characteristics and postoperative chest x ray in postero-anterior and lateral view as well as clinical and ICD follow up data were evaluated. Among 646 patients 42 had multiple ICD leads (6.5%) of whom 36 patients (5.5% of total cohort patients and 85.7% of patients with multiple ICD leads) had shock coil interaction and presented the study group (Group I). The control group (Group II) consisted of 610 patients without coil-coil interaction including patients with single shock lead (604 patients) or patients with multiple leads but without interaction between shock coils (6 patients). Inappropriate anti-tachycardia therapies and RV lead revisions were more frequent in patients with interaction between shock coils (Group I vs Group II: 27.7% and 5.7%; p = 0.049 and 30.6% vs 6.4; p = 0.0001, respectively). Interaction between shock coils may be one of possible causes of lead failure and resulted in inappropriate therapies and subsequent lead revision. Copyright © 2018 Indian Heart Rhythm Society. Production and hosting by Elsevier B.V. All rights reserved.

  2. Quantum entanglement and position–momentum entropic squeezing of a moving Lambda-type three-level atom interacting with a single-mode quantized field with intensity-dependent coupling

    International Nuclear Information System (INIS)

    Faghihi, M J; Tavassoly, M K

    2013-01-01

    In this paper, we study the interaction between a moving Λ-type three-level atom and a single-mode cavity field in the presence of intensity-dependent atom–field coupling. After obtaining the state vector of the entire system explicitly, we study the nonclassical features of the system such as quantum entanglement, position–momentum entropic squeezing, quadrature squeezing and sub-Poissonian statistics. According to the obtained numerical results we illustrate that the squeezed period, the duration of entropy squeezing and the maximal squeezing can be controlled by choosing the appropriate nonlinearity function together with entering the atomic motion effect by the suitable selection of the field-mode structure parameter. Also, the atomic motion, as well as the nonlinearity function, leads to the oscillatory behaviour of the degree of entanglement between the atom and field. (paper)

  3. Quantum entanglement and position-momentum entropic squeezing of a moving Lambda-type three-level atom interacting with a single-mode quantized field with intensity-dependent coupling

    Science.gov (United States)

    Faghihi, M. J.; Tavassoly, M. K.

    2013-07-01

    In this paper, we study the interaction between a moving Λ-type three-level atom and a single-mode cavity field in the presence of intensity-dependent atom-field coupling. After obtaining the state vector of the entire system explicitly, we study the nonclassical features of the system such as quantum entanglement, position-momentum entropic squeezing, quadrature squeezing and sub-Poissonian statistics. According to the obtained numerical results we illustrate that the squeezed period, the duration of entropy squeezing and the maximal squeezing can be controlled by choosing the appropriate nonlinearity function together with entering the atomic motion effect by the suitable selection of the field-mode structure parameter. Also, the atomic motion, as well as the nonlinearity function, leads to the oscillatory behaviour of the degree of entanglement between the atom and field.

  4. Research and practice on building social interactive learning based open course platform and teaching mode%社交互动式高职网络公开课平台和教学模式的构建

    Institute of Scientific and Technical Information of China (English)

    王静; 汪昀

    2012-01-01

    通过将积木块技术和项目化教学方式引入到专业共享型网络公开课平台的建设,探索适合高职的网络公开课课程的社交互动学习模式,同时通过对学习模式的研究完善网络公开课平台的构建。%Practical research on Dynamic modular designed Open Course platform based on building blocks technology and project teaching mode is to explore a social interactive learning mode of High Vocational Education. The exploration is also for improving the construction of open course platform and breaking local resources sharing barriers.

  5. Propagating annular modes

    Science.gov (United States)

    Sheshadri, A.; Plumb, R. A.

    2017-12-01

    The leading "annular mode", defined as the dominant EOF of surface pressure or of zonal mean zonal wind variability, appears as a dipolar structure straddling the mean midlatitude jet and thus seems to describe north-south wobbling of the jet latitude. However, extratropical zonal wind anomalies frequently tend to migrate poleward. This behavior can be described by the first two EOFs, the first (AM1) being the dipolar structure, and the second (AM2) having a tripolar structure centered on the mean jet. Taken in isolation, AM1 thus describes a north-south wobbling of the jet position, while AM2 describes a strengthening and narrowing of the jet. However, despite the fact that they are spatially orthogonal, and their corresponding time series temporally orthogonal, AM1 and AM2 are not independent, but show significant lag-correlations which reveal the propagation. The EOFs are not modes of the underlying dynamical system governing the zonal flow evolution. The true modes can be estimated using principal oscillation pattern (POP) analysis. In the troposphere, the leading POPs manifest themselves as a pair of complex conjugate structures with conjugate eigenvalues thus, in reality, constituting a single, complex, mode that describes propagating anomalies. Even though the principal components associated with the two leading EOFs decay at different rates, each decays faster than the true mode. These facts have implications for eddy feedback and the susceptibility of the mode to external perturbations. If one interprets the annular modes as the modes of the system, then simple theory predicts that the response to steady forcing will usually be dominated by AM1 (with the longest time scale). However, such arguments should really be applied to the true modes. Experiments with a simplified GCM show that climate response to perturbations do not necessarily have AM1 structures. Implications of these results for stratosphere-troposphere interactions are explored. The POP

  6. Fatty acids bind tightly to the N-terminal domain of angiopoietin-like protein 4 and modulate its interaction with lipoprotein lipase.

    Science.gov (United States)

    Robal, Terje; Larsson, Mikael; Martin, Miina; Olivecrona, Gunilla; Lookene, Aivar

    2012-08-24

    Angiopoietin-like protein 4 (Angptl4), a potent regulator of plasma triglyceride metabolism, binds to lipoprotein lipase (LPL) through its N-terminal coiled-coil domain (ccd-Angptl4) inducing dissociation of the dimeric enzyme to inactive monomers. In this study, we demonstrate that fatty acids reduce the inactivation of LPL by Angptl4. This was the case both with ccd-Angptl4 and full-length Angptl4, and the effect was seen in human plasma or in the presence of albumin. The effect decreased in the sequence oleic acid > palmitic acid > myristic acid > linoleic acid > linolenic acid. Surface plasmon resonance, isothermal titration calorimetry, fluorescence, and chromatography measurements revealed that fatty acids bind with high affinity to ccd-Angptl4. The interactions were characterized by fast association and slow dissociation rates, indicating formation of stable complexes. The highest affinity for ccd-Angptl4 was detected for oleic acid with a subnanomolar equilibrium dissociation constant (K(d)). The K(d) values for palmitic and myristic acid were in the nanomolar range. Linoleic and linolenic acid bound with much lower affinity. On binding of fatty acids, ccd-Angptl4 underwent conformational changes resulting in a decreased helical content, weakened structural stability, dissociation of oligomers, and altered fluorescence properties of the Trp-38 residue that is located close to the putative LPL-binding region. Based on these results, we propose that fatty acids play an important role in modulating the effects of Angptl4.

  7. Characterization of a 65 kDa NIF in the nuclear matrix of the monocot Allium cepa that interacts with nuclear spectrin-like proteins.

    Science.gov (United States)

    Pérez-Munive, Clara; Blumenthal, Sonal S D; de la Espina, Susana Moreno Díaz

    2012-01-01

    Plant cells have a well organized nucleus and nuclear matrix, but lack orthologues of the main structural components of the metazoan nuclear matrix. Although data is limited, most plant nuclear structural proteins are coiled-coil proteins, such as the NIFs (nuclear intermediate filaments) in Pisum sativum that cross-react with anti-intermediate filament and anti-lamin antibodies, form filaments 6-12 nm in diameter in vitro, and may play the role of lamins. We have investigated the conservation and features of NIFs in a monocot species, Allium cepa, and compared them with onion lamin-like proteins. Polyclonal antisera against the pea 65 kDa NIF were used in 1D and 2D Western blots, ICM (imunofluorescence confocal microscopy) and IEM (immunoelectron microscopy). Their presence in the nuclear matrix was analysed by differential extraction of nuclei, and their association with structural spectrin-like proteins by co-immunoprecipitation and co-localization in ICM. NIF is a conserved structural component of the nucleus and its matrix in monocots with Mr and pI values similar to those of pea 65 kDa NIF, which localized to the nuclear envelope, perichromatin domains and foci, and to the nuclear matrix, interacting directly with structural nuclear spectrin-like proteins. Its similarities with some of the proteins described as onion lamin-like proteins suggest that they are highly related or perhaps the same proteins.

  8. Majorana zero modes and long range edge correlation in interacting Kitaev chains: analytic solutions and density-matrix-renormalization-group study.

    Science.gov (United States)

    Miao, Jian-Jian; Jin, Hui-Ke; Zhang, Fu-Chun; Zhou, Yi

    2018-01-11

    We study Kitaev model in one-dimension with open boundary condition by using exact analytic methods for non-interacting system at zero chemical potential as well as in the symmetric case of Δ = t, and by using density-matrix-renormalization-group method for interacting system with nearest neighbor repulsion interaction. We suggest and examine an edge correlation function of Majorana fermions to characterize the long range order in the topological superconducting states and study the phase diagram of the interating Kitaev chain.

  9. Spin modes

    International Nuclear Information System (INIS)

    Gaarde, C.

    1985-01-01

    An analysis of spectra of (p,n) reactions showed that they were very selective in exciting spin modes. Charge exchange reactions at intermediate energies give important new understanding of the M1-type of excitations and of the spin structure of continuum p spectra in general. In this paper, the author discusses three charge exchange reactions: (p,n); ( 3 H,t); and (d,2p) at several targets. Low-lying states and the Δ region are discussed separately. Finally, the charge exchange reaction with heavy ion beams is briefly discussed. (G.J.P./Auth.)

  10. Microtearing modes

    International Nuclear Information System (INIS)

    Garbet, X.; Mourgues, F.; Samain, A.; Zou, X.

    1990-01-01

    A serious degradation of confinement with additional heating is commonly observed on most tokamaks. The microtearing modes could provide an explanation for this experimental fact. They are driven linearly unstable by diamagnetism in collisional regimes, but it may be shown that the collisions in non linear regimes provide a small diffusion coefficient which can be only significant at the plasme edge. In the bulk of the plasma, the microtearing turbulence could play a basic role if it is unstable in the collisionless regime. While it is linearly stable without collisions, it could be driven unstable in realistic regimes by the radial diffusion it induces. To study this effect, we have used a model where the non linear action of the modes on a given helicity component is represented by a diffusion operator. They are found unstable for reasonable β p =2μ o nT/B 2 p , with a special radial profile of the potential vector A. The problem arises the validity of this model where non linearities in the trajectories behaviour are replaced by the diffusion which broadens resonances. To test this procedure, we calculate the actual electron distribution function when it is determined by the ergodicity of the field lines. We compute the correlations of the distribution function with the magnetic perturbation and compare them with the analytical expressions derived from the resonance broadening model. (author) 3 refs., 2 figs

  11. Targeting Signaling to YAP for the Therapy of NF2

    Science.gov (United States)

    2016-12-01

    confocal microscopy for beta- arrestin-green fluorescent protein translocation G protein-coupled receptor assays using the Evotec Opera. Methods...Facility of MSKCC along the lines described in Accomplishments below. Notably, this Facility is equipped for High Throughput Confocal Imaging and...interacts through its coiled-coil segment with the central coiled-coil segment of AMOT proteins, which localize to Adherens Junctions (AJs) and

  12. Mycobacterium tuberculosis class II apurinic/apyrimidinic-endonuclease/3'-5' exonuclease III exhibits DNA regulated modes of interaction with the sliding DNA β-clamp.

    Science.gov (United States)

    Khanam, Taran; Rai, Niyati; Ramachandran, Ravishankar

    2015-10-01

    The class-II AP-endonuclease (XthA) acts on abasic sites of damaged DNA in bacterial base excision repair. We identified that the sliding DNA β-clamp forms in vivo and in vitro complexes with XthA in Mycobacterium tuberculosis. A novel 239 QLRFPKK245 motif in the DNA-binding domain of XthA was found to be important for the interactions. Likewise, the peptide binding-groove (PBG) and the C-terminal of β-clamp located on different domains interact with XthA. The β-clamp-XthA complex can be disrupted by clamp binding peptides and also by a specific bacterial clamp inhibitor that binds at the PBG. We also identified that β-clamp stimulates the activities of XthA primarily by increasing its affinity for the substrate and its processivity. Additionally, loading of the β-clamp onto DNA is required for activity stimulation. A reduction in XthA activity stimulation was observed in the presence of β-clamp binding peptides supporting that direct interactions between the proteins are necessary to cause stimulation. Finally, we found that in the absence of DNA, the PBG located on the second domain of the β-clamp is important for interactions with XthA, while the C-terminal domain predominantly mediates functional interactions in the substrate's presence. © 2015 John Wiley & Sons Ltd.

  13. Substituent and noncovalent interaction effects in the reactivity of purine derivatives with tetracarboxylato-dirhodium(II) units. Rationalization of a rare binding mode via N3.

    Science.gov (United States)

    Amo-Ochoa, Pilar; Castillo, Oscar; Harrington, Ross W; Zamora, Félix; Houlton, Andrew

    2013-02-18

    Reactions between [Rh(2)(CH(3)COO)(4)] with 2,6-diaminopurine (HDap) or 6-chloro-2-aminopurine (HClap) and [Rh(2)((CH(3))(3)CCOO)(4)] with HClap produce, three new dirhodium(II) carboxylate complexes of the general form, [Rh(2)(RCOO)(4)(Purine)(2)] (R = CH(3), (CH(3))(3)C). Single crystal X-ray diffraction studies confirm that in all cases the purine coordinates to the axial position of the dirhodium(II)tetracarboxylate unit. However, while the complex obtained with HDap features the typical purine binding mode via N(7), complexes containing HClap show unusual N3 coordination. This is an extremely rare instance of an unrestricted purine binding via N3. Some rationalization of these data is offered based on a series of DFT calculations.

  14. A Unique Mdm2-Binding Mode of the 3-Pyrrolin-2-one- and 2-Furanone-Based Antagonists of the p53-Mdm2 Interaction

    NARCIS (Netherlands)

    Surmiak, Ewa; Twarda-Clapa, Aleksandra; Zak, Krzysztof M.; Musielak, Bogdan; Tomala, Marcin D.; Kubica, Katarzyna; Grudnik, Przemyslaw; Madej, Mariusz; Jablonski, Mateusz; Potempa, Jan; Kalinowska-Tluscik, Justyna; Dömling, Alexander; Dubin, Grzegorz; Holak, Tad A.

    2016-01-01

    The p53 pathway is inactivated in almost all types of cancer by mutations in the p53 encoding gene or overexpression of the p53 negative regulators, Mdm2 and/or Mdmx. Restoration of the p53 function by inhibition of the p53-Mdm2/Mdmx interaction opens up a prospect for a nongenotoxic anticancer

  15. The Interactive Modes of Non-Native Speakers in International Chinese Language Distance Class Discussions: An Analysis of Smiling as a Facial Cue

    Science.gov (United States)

    Sunaoka, Kazuko

    2018-01-01

    The focus of this research is on an international distance discussion class carried out in Chinese between university students in Japan, China and Taiwan using videoconferencing. Smiling was used as an interactional index in an analysis of the archival footage of the recordings of the discussion between native speakers (NS) of Chinese and…

  16. Renormalized modes in cuprate superconductors

    Science.gov (United States)

    Gupta, Anushri; Kumari, Anita; Verma, Sanjeev K.; Indu, B. D.

    2018-04-01

    The renormalized mode frequencies are obtained with the help of quantum dynamical approach of many body phonon Green's function technique via a general Hamiltonian (excluding BCS Hamiltonian) including the effects of phonons and electrons, anharmonicities and electron-phonon interactions. The numerical estimates have been carried out to study the renormalized mode frequency of high temperature cuprate superconductor (HTS) YBa2Cu3O7-δ using modified Born-Mayer-Huggins interaction potential (MBMHP) best applicable to study the dynamical properties of all HTS.

  17. The Dynamics of a Five-level (Double Λ)-type Atom Interacting with Two-mode Field in a Cross Kerr-like Medium

    Science.gov (United States)

    Obada, A.-S. F.; Ahmed, M. M. A.; Farouk, Ahmed M.

    2018-04-01

    In this paper, we propose a new transition scheme (Double Λ) for the interaction between a five-level atom and an electromagnetic field and study its dynamics in the presence of a cross Kerr-like medium in the exact-resonance case. The wave function is derived when the atom is initially prepared in its upper most state, and the field is initially prepared in the coherent state. We studied the atomic population inversion, the coherence degree by studying the second-order correlation function, Cauchy-Schwartz inequality (CSI) and the relation with P-function. Finally, we investigate the effect of Kerr-like medium on the evolution of Husimi Q-function of the considered system.

  18. Physics of resistive wall modes

    International Nuclear Information System (INIS)

    Igochine, V.

    2012-01-01

    The advanced tokamak regime is a promising candidate for steady-state tokamak operation which is desirable for a fusion reactor. This regime is characterized by a high bootstrap current fraction and a flat or reversed safety factor profile, which leads to operation close to the pressure limit. At this limit, an external kink mode becomes unstable. This external kink is converted into the slowly growing resistive wall mode (RWM) by the presence of a conducting wall. Reduction of the growth rate allows one to act on the mode and to stabilize it. There are two main factors which determine the stability of the RWM. The first factor comes from external magnetic perturbations (error fields, resistive wall, feedback coils, etc). This part of RWM physics is the same for tokamaks and reversed field pinch configurations. The physics of this interaction is relatively well understood and based on classical electrodynamics. The second ingredient of RWM physics is the interaction of the mode with plasma flow and fast particles. These interactions are particularly important for tokamaks, which have higher plasma flow and stronger trapped particle effects. The influence of the fast particles will also be increasingly more important in ITER and DEMO which will have a large fraction of fusion born alpha particles. These interactions have kinetic origins which make the computations challenging since not only particles influence the mode, but also the mode acts on the particles. Correct prediction of the ‘plasma–RWM’ interaction is an important ingredient which has to be combined with external field's influence (resistive wall, error fields and feedback) to make reliable predictions for RWM behaviour in tokamaks. All these issues are reviewed in this paper. (special topic)

  19. Number-phase entropic squeezing and nonclassical properties of a three-level atom interacting with a two-mode field: intensity-dependent coupling, deformed Kerr medium, and detuning effects

    Science.gov (United States)

    Faghihi, Mohammad Javad; Tavassoly, Mohammad Kazem

    2013-11-01

    In this paper, we follow our presented model in J. Opt. Soc. Am. B {\\bf 30}, 1109--1117 (2013), in which the interaction between a $\\Lambda$-type three-level atom and a quantized two-mode radiation field in a cavity in the presence of nonlinearities is studied. After giving a brief review on the procedure of obtaining the state vector of the atom-field system, some further interesting and important physical features (which are of particular interest in the quantum optics field of research) of the whole system state, i.e., the number-phase entropic uncertainty relation (based on the two-mode Pegg-Barnett formalism) and some of the nonclassicality signs consist of sub-Poissonian statistics, Cauchy-Schwartz inequality and two kinds of squeezing phenomenon are investigated. During our presentation, the effects of intensity-dependent coupling, deformed Kerr medium and the detuning parameters on the depth and domain of each of the mentioned nonclassical criteria of the considered quantum system are studied, in detail. It is shown that each of the mentioned nonclassicality aspects can be obtained by appropriately choosing the related parameters.

  20. Entanglement dynamics and position-momentum entropic uncertainty relation of a Λ-type three-level atom interacting with a two-mode cavity field in the presence of nonlinearities

    Science.gov (United States)

    Faghihi, M. J.; Tavassoly, M. K.; Hooshmandasl, M. R.

    2013-05-01

    In this paper, the interaction between a $\\Lambda$-type three-level atom and two-mode cavity field is discussed. The detuning parameters and cross-Kerr nonlinearity are taken into account and it is assumed that atom-field coupling and Kerr medium to be $f$-deformed. Even though the system seems to be complicated, the analytical form of the state vector of the entire system for considered model is exactly obtained. The time evolution of nonclassical properties such as quantum entanglement and position-momentum entropic uncertainty relation (entropy squeezing) of the field are investigated. In each case, the influences of the detuning parameters, generalized Kerr medium and intensity-dependent coupling on the latter nonclassicality signs are analyzed, in detail.

  1. Depth of interaction and bias voltage depenence of the spectral response in a pixellated CdTe detector operating in time-over-threshold mode subjected to monochromatic X-rays

    Science.gov (United States)

    Fröjdh, E.; Fröjdh, C.; Gimenez, E. N.; Maneuski, D.; Marchal, J.; Norlin, B.; O'Shea, V.; Stewart, G.; Wilhelm, H.; Modh Zain, R.; Thungström, G.

    2012-03-01

    High stopping power is one of the most important figures of merit for X-ray detectors. CdTe is a promising material but suffers from: material defects, non-ideal charge transport and long range X-ray fluorescence. Those factors reduce the image quality and deteriorate spectral information. In this project we used a monochromatic pencil beam collimated through a 20μm pinhole to measure the detector spectral response in dependance on the depth of interaction. The sensor was a 1mm thick CdTe detector with a pixel pitch of 110μm, bump bonded to a Timepix readout chip operating in Time-Over-Threshold mode. The measurements were carried out at the Extreme Conditions beamline I15 of the Diamond Light Source. The beam was entering the sensor at an angle of \\texttildelow20 degrees to the surface and then passed through \\texttildelow25 pixels before leaving through the bottom of the sensor. The photon energy was tuned to 77keV giving a variation in the beam intensity of about three orders of magnitude along the beam path. Spectra in Time-over-Threshold (ToT) mode were recorded showing each individual interaction. The bias voltage was varied between -30V and -300V to investigate how the electric field affected the spectral information. For this setup it is worth noticing the large impact of fluorescence. At -300V the photo peak and escape peak are of similar height. For high bias voltages the spectra remains clear throughout the whole depth but for lower voltages as -50V, only the bottom part of the sensor carries spectral information. This is an effect of the low hole mobility and the longer range the electrons have to travel in a low field.

  2. Preparation of a long-alkyl-chain-based hybrid monolithic column with mixed-mode interactions using a "one-pot" process for pressurized capillary electrochromatography.

    Science.gov (United States)

    Lyu, Haixia; Zhao, Heqing; Qin, Wenfei; Xie, Zenghong

    2017-12-01

    A simple "one-pot" approach for the preparation of a new vinyl-functionalized organic-inorganic hybrid monolithic column is described. In this improved method, the hydrolyzed alkoxysilanes of tetramethoxysilane and triethoxyvinylsilane were used as precursors for the synthesis of a silica-based monolith, while 1-hexadecene and sodium ethylenesulfonate were used as vinyl functional monomers along with azobisisobutyronitrile as an initiator. The effects of reaction temperature, urea content, and composition of organic monomers on the column properties (e.g. morphology, mechanical stability, and chromatographic performance) were investigated. The monolithic column was used for the separation of neutral solutes by reversed-phase pressurized capillary. Furthermore, the monolith can separate various aromatic amines, which indicated its excellent cation-exchange capability and hydrophobic interactions. The baseline separation of the aromatic amines was obtained with a column efficiency of up to 78 000 plates/m. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Two distinct binding modes define the interaction of Brox with the C-terminal tails of CHMP5 and CHMP4B.

    Science.gov (United States)

    Mu, Ruiling; Dussupt, Vincent; Jiang, Jiansheng; Sette, Paola; Rudd, Victoria; Chuenchor, Watchalee; Bello, Nana F; Bouamr, Fadila; Xiao, Tsan Sam

    2012-05-09

    Interactions of the CHMP protein carboxyl terminal tails with effector proteins play important roles in retroviral budding, cytokinesis, and multivesicular body biogenesis. Here we demonstrate that hydrophobic residues at the CHMP4B C-terminal amphipathic α helix bind a concave surface of Brox, a mammalian paralog of Alix. Unexpectedly, CHMP5 was also found to bind Brox and specifically recruit endogenous Brox to detergent-resistant membrane fractions through its C-terminal 20 residues. Instead of an α helix, the CHMP5 C-terminal tail adopts a tandem β-hairpin structure that binds Brox at the same site as CHMP4B. Additional Brox:CHMP5 interface is furnished by a unique CHMP5 hydrophobic pocket engaging the Brox residue Y348 that is not conserved among the Bro1 domains. Our studies thus unveil a β-hairpin conformation of the CHMP5 protein C-terminal tail, and provide insights into the overlapping but distinct binding profiles of ESCRT-III and the Bro1 domain proteins. Copyright © 2012 Elsevier Ltd. All rights reserved.

  4. Interactions of L-3,5,3'-Triiodothyronine [corrected], Allopregnanolone, and Ivermectin with the GABAA Receptor: Evidence for Overlapping Intersubunit Binding Modes.

    Science.gov (United States)

    Westergard, Thomas; Salari, Reza; Martin, Joseph V; Brannigan, Grace

    2015-01-01

    Structural mechanisms of modulation of γ-aminobutyric acid (GABA) type A receptors by neurosteroids and hormones remain unclear. The thyroid hormone L-3,5,3'-triiodothyronine (T3) inhibits GABAA receptors at micromolar concentrations and has common features with neurosteroids such as allopregnanolone (ALLOP). Here we use functional experiments on α2β1γ2 GABAA receptors expressed in Xenopus oocytes to detect competitive interactions between T3 and an agonist (ivermectin, IVM) with a crystallographically determined binding site at subunit interfaces in the transmembrane domain of a homologous receptor (glutamate-gated chloride channel, GluCl). T3 and ALLOP also show competitive effects, supporting the presence of both a T3 and ALLOP binding site at one or more subunit interfaces. Molecular dynamics (MD) simulations over 200 ns are used to investigate the dynamics and energetics of T3 in the identified intersubunit sites. In these simulations, T3 molecules occupying all intersubunit sites (with the exception of the α-β interface) display numerous energetically favorable conformations with multiple hydrogen bonding partners, including previously implicated polar/acidic sidechains and a structurally conserved deformation in the M1 backbone.

  5. Interactions of L-3,5,3'-Triiodothyronine, Allopregnanolone, and Ivermectin with the GABAA Receptor: Evidence for Overlapping Intersubunit Binding Modes

    Science.gov (United States)

    Westergard, Thomas; Salari, Reza; Martin, Joseph V.; Brannigan, Grace

    2015-01-01

    Structural mechanisms of modulation of γ-aminobutyric acid (GABA) type A receptors by neurosteroids and hormones remain unclear. The thyroid hormone L-3,5,3’-triiodothyronine (T3) inhibits GABAA receptors at micromolar concentrations and has common features with neurosteroids such as allopregnanolone (ALLOP). Here we use functional experiments on α2β1γ2 GABAA receptors expressed in Xenopus oocytes to detect competitive interactions between T3 and an agonist (ivermectin, IVM) with a crystallographically determined binding site at subunit interfaces in the transmembrane domain of a homologous receptor (glutamate-gated chloride channel, GluCl). T3 and ALLOP also show competitive effects, supporting the presence of both a T3 and ALLOP binding site at one or more subunit interfaces. Molecular dynamics (MD) simulations over 200 ns are used to investigate the dynamics and energetics of T3 in the identified intersubunit sites. In these simulations, T3 molecules occupying all intersubunit sites (with the exception of the α-β interface) display numerous energetically favorable conformations with multiple hydrogen bonding partners, including previously implicated polar/acidic sidechains and a structurally conserved deformation in the M1 backbone. PMID:26421724

  6. Parametric Landau damping of space charge modes

    Energy Technology Data Exchange (ETDEWEB)

    Macridin, Alexandru [Fermilab; Burov, Alexey [Fermilab; Stern, Eric [Fermilab; Amundson, James [Fermilab; Spentzouris, Panagiotis [Fermilab

    2016-09-23

    Landau damping is the mechanism of plasma and beam stabilization; it arises through energy transfer from collective modes to the incoherent motion of resonant particles. Normally this resonance requires the resonant particle's frequency to match the collective mode frequency. We have identified an important new damping mechanism, parametric Landau damping, which is driven by the modulation of the mode-particle interaction. This opens new possibilities for stability control through manipulation of both particle and mode-particle coupling spectra. We demonstrate the existence of parametric Landau damping in a simulation of transverse coherent modes of bunched accelerator beams with space charge.

  7. Nonlinear coupling of kink modes in Tokamaks

    International Nuclear Information System (INIS)

    Dagazian, R.Y.

    1975-07-01

    The m = 2, n = 1 kink mode is shown to be capable of destabilizing the m = 1, n = 1 internal kink. A nonlinear Lagrangian theory is developed for the coupling of modes of different pitch, and it is applied to the interaction of these modes. The coupling to the m = 2 mode provides sufficient additional destabilization to the internal mode to permit it to account even quantitatively (where it had failed when considered by itself) for many of the features of the disruptive instability. (U.S.)

  8. Investigation on heat transfer analysis and its effect on a multi-mode, beam-wave interaction for a 140 GHz, MW-class gyrotron

    Science.gov (United States)

    Liu, Qiao; Liu, Yinghui; Chen, Zhaowei; Niu, Xinjian; Li, Hongfu; Xu, Jianhua

    2018-04-01

    The interaction cavity of a 140 GHz, 1 MW continuous wave gyrotron developed in UESTC will be loaded with a very large heat load in the inner surface during operation. In order to reduce the heat, the axial wedge grooves of the outside surface of the cavity are considered and employed as the heat radiation structure. Thermoanalysis and structural analysis were discussed in detail to obtain the effects of heat on the cavity. In thermoanalysis, the external coolant-flow rates ranging from 20 L/min to 50 L/min were considered, and the distribution of wall loading was loaded as the heat flux source. In structural analysis, the cavity's deformation caused by the loads of heat and pressure was calculated. Compared with a non-deformed cavity, the effects of deformation on the performance of a cavity were discussed. For a cold-cavity, the results show that the quality factor would be reduced by 72, 89, 99 and 171 at the flow rates of 50 L/min, 40 L/min, 30 L/min and 20 L/min, respectively. Correspondingly, the cold-cavity frequencies would be decreased by 0.13 GHz, 0.15 GHz, 0.19 GHz and 0.38 GHz, respectively. For a hot-cavity, the results demonstrate that the output port frequencies would be dropped down, but the offset would be gradually decreased with increasing coolant-flow rate. Meanwhile, the output powers would be reduced dramatically with decreasing coolant-flow rate. In addition, when the coolant-flow rate reaches 40 L/min, the output power and the frequency are just reduced by 30 kW and 0.151 GHz, respectively.

  9. Mode structure of active resonators

    NARCIS (Netherlands)

    Ernst, G.J.; Witteman, W.J.

    1973-01-01

    An analysis is made of the mode structure of lasers when the interaction with the active medium is taken into account. We consider the combined effect of gain and refractive-index variations for arbitrary mirror configurations. Using a dimensionless round-trip matrix for a medium with a quadratic

  10. Modes and Mode Volumes for Leaky Optical Cavities and Plasmonic Nanoresonators

    DEFF Research Database (Denmark)

    Hughes, Stephen; Kristensen, Philip Trøst

    2013-01-01

    Electromagnetic cavity modes in photonic and plasmonic resonators offer rich and attractive regimes for tailoring the properties of light–matter interactions, yet there is a disturbing lack of a precise definition for what constitutes a cavity mode, and as a result their mathematical properties r...... methods for quasinormal modes of both photonic and plasmonic resonators and the concept of a generalized effective mode volume, and we illustrate the theory with several representative cavity structures from the fields of photonic crystals and nanoplasmonics....

  11. Biophysical and Structural Characterization of the Thioredoxin-binding Domain of Protein Kinase ASK1 and Its Interaction with Reduced Thioredoxin

    Czech Academy of Sciences Publication Activity Database

    Košek, Dalibor; Kylarová, Salome; Pšenáková, Katarína; Řežábková, L.; Herman, P.; Večeř, J.; Obšilová, Veronika; Obšil, T.

    2014-01-01

    Roč. 289, č. 35 (2014), s. 24463-24474 ISSN 0021-9258 R&D Projects: GA ČR(CZ) GA14-10061S Institutional support: RVO:67985823 Keywords : ASK1 * thioredoxin * AUC * SAXS * coiled-coiled domain Subject RIV: CE - Biochemistry Impact factor: 4.573, year: 2014

  12. Nonlinear mode coupling in rotating stars and the r-mode instability in neutron stars

    International Nuclear Information System (INIS)

    Schenk, A.K.; Arras, P.; Flanagan, E.E.; Teukolsky, S.A.; Wasserman, I.

    2002-01-01

    We develop the formalism required to study the nonlinear interaction of modes in rotating Newtonian stars, assuming that the mode amplitudes are only mildly nonlinear. The formalism is simpler than previous treatments of mode-mode interactions for spherical stars, and simplifies and corrects previous treatments for rotating stars. At linear order, we elucidate and extend slightly a formalism due to Schutz, show how to decompose a general motion of a rotating star into a sum over modes, and obtain uncoupled equations of motion for the mode amplitudes under the influence of an external force. Nonlinear effects are added perturbatively via three-mode couplings, which suffices for moderate amplitude modal excitations; the formalism is easy to extend to higher order couplings. We describe a new, efficient way to compute the modal coupling coefficients, to zeroth order in the stellar rotation rate, using spin-weighted spherical harmonics. The formalism is general enough to allow computation of the initial trends in the evolution of the spin frequency and differential rotation of the background star. We apply this formalism to derive some properties of the coupling coefficients relevant to the nonlinear interactions of unstable r modes in neutron stars, postponing numerical integrations of the coupled equations of motion to a later paper. First, we clarify some aspects of the expansion in stellar rotation frequency Ω that is often used to compute approximate mode functions. We show that, in zero-buoyancy stars, the rotational modes (those modes whose frequencies vanish as Ω→0) are orthogonal to zeroth order in Ω. From an astrophysical viewpoint, the most interesting result of this paper is that many couplings of r modes to other rotational modes are small: either they vanish altogether because of various selection rules, or they vanish to lowest order in Ω or in compressibility. In particular, in zero-buoyancy stars, the coupling of three r modes is forbidden

  13. ALDH16A1 is a novel non-catalytic enzyme that may be involved in the etiology of gout via protein-protein interactions with HPRT1.

    Science.gov (United States)

    Vasiliou, Vasilis; Sandoval, Monica; Backos, Donald S; Jackson, Brian C; Chen, Ying; Reigan, Philip; Lanaspa, Miguel A; Johnson, Richard J; Koppaka, Vindhya; Thompson, David C

    2013-02-25

    Gout, a common form of inflammatory arthritis, is strongly associated with elevated uric acid concentrations in the blood (hyperuricemia). A recent study in Icelanders identified a rare missense single nucleotide polymorphism (SNP) in the ALDH16A1 gene, ALDH16A1*2, to be associated with gout and serum uric acid levels. ALDH16A1 is a novel and rather unique member of the ALDH superfamily in relation to its gene and protein structures. ALDH16 genes are present in fish, amphibians, protista, bacteria but absent from archaea, fungi and plants. In most mammalian species, two ALDH16A1 spliced variants (ALDH16A1, long form and ALDH16A1_v2, short form) have been identified and both are expressed in HepG-2, HK-2 and HK-293 human cell lines. The ALDH16 proteins contain two ALDH domains (as opposed to one in the other members of the superfamily), four transmembrane and one coiled-coil domains. The active site of ALDH16 proteins from bacterial, frog and lower animals contain the catalytically important cysteine residue (Cys-302); this residue is absent from the mammalian and fish orthologs. Molecular modeling predicts that both the short and long forms of human ALDH16A1 protein would lack catalytic activity but may interact with the hypoxanthine-guanine phosphoribosyltransferase (HPRT1) protein, a key enzyme involved in uric acid metabolism and gout. Interestingly, such protein-protein interactions with HPRT1 are predicted to be impaired for the long or short forms of ALDH16A1*2. These results lead to the intriguing possibility that association between ALDH16A1 and HPRT1 may be required for optimal HPRT activity with disruption of this interaction possibly contributing to the hyperuricemia seen in ALDH16A1*2 carriers. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  14. Mode Contributions to the Casimir Effect

    Science.gov (United States)

    Intravaia, F.; Henkel, C.

    2010-04-01

    Applying a sum-over-modes approach to the Casimir interaction between two plates with finite conductivity, we isolate and study the contributions of surface plasmons and Foucault (eddy current) modes. We show in particular that for the TE-polarization eddy currents provide a repulsive force that cancels, at high temperatures, the Casimir free energy calculated with the plasma model.

  15. Spin and isospin modes

    International Nuclear Information System (INIS)

    Suzuki, T.; Sagawa, H.

    2000-01-01

    Complete text of publication follows. Spin and isospin modes in nuclei are investigated. We discuss some of the following topics. 1. Spin-dipole excitations in 12 C and 16 O are studied (1). Effects of tensor and spin-orbit interactions on the distribution of the strengths are investigated, and neutral current neutrino scattering cross sections in 16 O are obtained for heavy-flavor neutrinos from the supernovae. 2. Gamow-Teller (GT) and spin-dipole (SD) modes in 208 Bi are investigated. Quenching and fragmentation of the GT strength are discussed (2). SD excitations and electric dipole (E1) transitions between the GT and SD states are studied (3). Calculated E1 strengths are compared with the sum rule values obtained within the 1p-1h and 1p-1h + 2p-2h configuration spaces. 3. Coulomb displacement energy (CDE) of the IAS of 14 Be is calculated, and the effects of the halo on the CDE and the configuration of the halo state are investigated. 4. Spreading width of IAS and isospin dependence of the width are investigated (4). Our formula for the width explains very well the observed isospin dependence (5). (author)

  16. Mode Medium Interaction. A Theoretical Study.

    Science.gov (United States)

    1980-09-01

    matrix form our coupled equations become A j/go = 0 (66) AVCO f-r VIH f I U U u Where S -Cgo -- 2L U - r-l r T b3 2 vI goo 2 ge) ° 3 2 (r1-) + _(r+l...may result in other significant mec OC7 c l. ,. The chemical laser cons; ists of at series1 flame sheets (Figure 541). The jets from)- the1 Tr0 ::(- IL...backward traveling waves. If such interference e:: ists , t:t effect is to shift the overall value of intelisit’’v s ia ill amount. See G. Agrawal and M

  17. H-mode physics

    International Nuclear Information System (INIS)

    Itoh, Sanae.

    1991-06-01

    After the discovery of the H-mode in ASDEX ( a tokamak in Germany ) the transition between the L-mode ( Low confinement mode ) and H-mode ( High confinement mode ) has been observed in many tokamaks in the world. The H-mode has made a breakthrough in improving the plasma parameters and has been recognized to be a universal phenomena. Since its discovery, the extensive studies both in experiments and in theory have been made. The research on H-mode has been casting new problems of an anomalous transport across the magnetic surface. This series of lectures will provide a brief review of experiments for explaining H-mode and a model theory of H-mode transition based on the electric field bifurcation. If the time is available, a new theoretical model of the temporal evolution of the H-mode will be given. (author)

  18. Playful Interaction

    DEFF Research Database (Denmark)

    2003-01-01

    The video Playful Interaction describes a future architectural office, and envisions ideas and concepts for playful interactions between people, materials and appliances in a pervasive and augmented working environment. The video both describes existing developments, technologies and designs...... as well as ideas not yet implemented such as playful modes of interaction with an augmented ball. Playful Interaction has been used as a hybrid of a vision video and a video prototype (1). Externally the video has been used to visualising our new ideas, and internally the video has also worked to inspire...

  19. Multispectroscopic methods reveal different modes of interaction of anti cancer drug mitoxantrone with Poly(dG-dC).Poly(dG-dC) and Poly(dA-dT).Poly(dA-dT).

    Science.gov (United States)

    Awasthi, Pamita; Dogra, Shilpa; Barthwal, Ritu

    2013-10-05

    The interaction of mitoxantrone with alternating Poly(dG-dC).Poly(dG-dC) and Poly(dA-dT).Poly(dA-dT) duplex has been studied by absorption, fluorescence and Circular Dichroism (CD) spectroscopy at Drug to Phosphate base pair ratios D/P=20.0-0.04. Binding to GC polymer occurs in two distinct modes: partial stacking characterized by red shifts of 18-23nm at D/P=0.2-0.8 and external binding at D/P=1.0-20.0 whereas that to AT polymer occurs externally in the entire range of D/P. The binding constant and number of binding sites is 3.7×10(5)M(-1), 0.3 and 1.3× 10(4)M(-1), 1.5 in GC and AT polymers, respectively at low D/P ratios. CD binding isotherms show breakpoints at D/P=0.1, 0.5 and 0.25, 0.5 in GC and AT polymers, respectively. The intrinsic CD bands indicate that the distortions in GC polymer are significantly higher than that in AT polymer. Docking studies show partial insertion of mitoxantrone rings between to GC base pairs in alternating GC polymer. Side chains of mitoxantrone interact specifically with base pairs and DNA backbone. The studies are relevant to the understanding of suppression or inhibition of DNA cleavage on formation of ternary complex with topoisomerase-II enzyme and hence the anti cancer action. Copyright © 2013 Elsevier B.V. All rights reserved.

  20. Biochemistry and biophysics of HIV-1 gp41 - membrane interactions and implications for HIV-1 envelope protein mediated viral-cell fusion and fusion inhibitor design.

    Science.gov (United States)

    Cai, Lifeng; Gochin, Miriam; Liu, Keliang

    2011-12-01

    Human immunodeficiency virus type 1 (HIV-1), the pathogen of acquired immunodeficiency syndrome (AIDS), causes ~2 millions death every year and still defies an effective vaccine. HIV-1 infects host cells through envelope protein - mediated virus-cell fusion. The transmembrane subunit of envelope protein, gp41, is the molecular machinery which facilitates fusion. Its ectodomain contains several distinguishing functional domains, fusion peptide (FP), Nterminal heptad repeat (NHR), C-terminal heptad repeat (CHR) and membrane proximal extracellular region (MPER). During the fusion process, FP inserts into the host cell membrane, and an extended gp41 prehairpin conformation bridges the viral and cell membranes through MPER and FP respectively. Subsequent conformational change of the unstable prehairpin results in a coiled-coil 6-helix bundle (6HB) structure formed between NHR and CHR. The energetics of 6HB formation drives membrane apposition and fusion. Drugs targeting gp41 functional domains to prevent 6HB formation inhibit HIV-1 infection. T20 (enfuvirtide, Fuzeon) was approved by the US FDA in 2003 as the first fusion inhibitor. It is a 36-residue peptide from the gp41 CHR, and it inhibits 6HB formation by targeting NHR and lipids. Development of new fusion inhibitors, especially small molecule drugs, is encouraged to overcome the shortcomings of T20 as a peptide drug. Hydrophobic characteristics and membrane association are critical for gp41 function and mechanism of action. Research in gp41-membrane interactions, using peptides corresponding to specific functional domains, or constructs including several interactive domains, are reviewed here to get a better understanding of gp41 mediated virus-cell fusion that can inform or guide the design of new HIV-1 fusion inhibitors.

  1. Tapping mode microwave impedance microscopy

    KAUST Repository

    Lai, K.

    2009-01-01

    We report tapping mode microwave impedance imaging based on atomic force microscope platforms. The shielded cantilever probe is critical to localize the tip-sample interaction near the tip apex. The modulated tip-sample impedance can be accurately simulated by the finite-element analysis and the result agrees quantitatively to the experimental data on a series of thin-film dielectric samples. The tapping mode microwave imaging is also superior to the contact mode in that the thermal drift in a long time scale is totally eliminated and an absolute measurement on the dielectric properties is possible. We demonstrated tapping images on working nanodevices, and the data are consistent with the transport results. © 2009 American Institute of Physics.

  2. Dynamics of entropy and nonclassical properties of the state of a Λ-type three-level atom interacting with a single-mode cavity field with intensity-dependent coupling in a Kerr medium

    International Nuclear Information System (INIS)

    Faghihi, M J; Tavassoly, M K

    2012-01-01

    In this paper, we study the interaction between a three-level atom and a quantized single-mode field with ‘intensity-dependent coupling’ in a ‘Kerr medium’. The three-level atom is considered to be in a Λ-type configuration. Under particular initial conditions, which may be prepared for the atom and the field, the dynamical state vector of the entire system will be explicitly obtained, for the arbitrary nonlinearity function f(n) associated with any physical system. Then, after evaluating the variation of the field entropy against time, we will investigate the quantum statistics as well as some of the nonclassical properties of the introduced state. During our calculations we investigate the effects of intensity-dependent coupling, Kerr medium and detuning parameters on the depth and domain of the nonclassicality features of the atom–field state vector. Finally, we compare our obtained results with those of V-type three-level atoms. (paper)

  3. Dynamics of entropy and nonclassical properties of the state of a Λ-type three-level atom interacting with a single-mode cavity field with intensity-dependent coupling in a Kerr medium

    Science.gov (United States)

    Faghihi, M. J.; Tavassoly, M. K.

    2012-02-01

    In this paper, we study the interaction between a three-level atom and a quantized single-mode field with ‘intensity-dependent coupling’ in a ‘Kerr medium’. The three-level atom is considered to be in a Λ-type configuration. Under particular initial conditions, which may be prepared for the atom and the field, the dynamical state vector of the entire system will be explicitly obtained, for the arbitrary nonlinearity function f(n) associated with any physical system. Then, after evaluating the variation of the field entropy against time, we will investigate the quantum statistics as well as some of the nonclassical properties of the introduced state. During our calculations we investigate the effects of intensity-dependent coupling, Kerr medium and detuning parameters on the depth and domain of the nonclassicality features of the atom-field state vector. Finally, we compare our obtained results with those of V-type three-level atoms.

  4. The structure of salt bridges between Arg(+) and Glu(-) in peptides investigated with 2D-IR spectroscopy: Evidence for two distinct hydrogen-bond geometries.

    Science.gov (United States)

    Huerta-Viga, Adriana; Amirjalayer, Saeed; Domingos, Sérgio R; Meuzelaar, Heleen; Rupenyan, Alisa; Woutersen, Sander

    2015-06-07

    Salt bridges play an important role in protein folding and in supramolecular chemistry, but they are difficult to detect and characterize in solution. Here, we investigate salt bridges between glutamate (Glu(-)) and arginine (Arg(+)) using two-dimensional infrared (2D-IR) spectroscopy. The 2D-IR spectrum of a salt-bridged dimer shows cross peaks between the vibrational modes of Glu(-) and Arg(+), which provide a sensitive structural probe of Glu(-)⋯Arg(+) salt bridges. We use this probe to investigate a β-turn locked by a salt bridge, an α-helical peptide whose structure is stabilized by salt bridges, and a coiled coil that is stabilized by intra- and intermolecular salt bridges. We detect a bidentate salt bridge in the β-turn, a monodentate one in the α-helical peptide, and both salt-bridge geometries in the coiled coil. To our knowledge, this is the first time 2D-IR has been used to probe tertiary side chain interactions in peptides, and our results show that 2D-IR spectroscopy is a powerful method for investigating salt bridges in solution.

  5. Yeast Interacting Proteins Database: YOL069W, YIL144W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available complex (Ndc80p-Nuf2p-Spc24p-Spc25p); involved in chromosome segregation, spindle checkpoint activity and kinetochore clustering...vity, kinetochore assembly and clustering Rows with this prey as prey (2) Rows with this prey as bait (0) 12...-Nuf2p-Spc24p-Spc25p); involved in chromosome segregation, spindle checkpoint activity and kinetochore clustering...d coiled-coil protein involved in chromosome segregation, spindle checkpoint activity, kinetochore assembly and clustering

  6. Mode coupling in spin torque oscillators

    International Nuclear Information System (INIS)

    Zhang, Steven S.-L.; Zhou, Yan; Li, Dong; Heinonen, Olle

    2016-01-01

    A number of recent experimental works have shown that the dynamics of a single spin torque oscillator can exhibit complex behavior that stems from interactions between two or more modes of the oscillator, such as observed mode-hopping or mode coexistence. There has been some initial work indicating how the theory for a single-mode (macro-spin) spin torque oscillator should be generalized to include several modes and the interactions between them. In the present work, we rigorously derive such a theory starting with the Landau–Lifshitz–Gilbert equation for magnetization dynamics by expanding up to third-order terms in deviation from equilibrium. Our results show how a linear mode coupling, which is necessary for observed mode-hopping to occur, arises through coupling to a magnon bath. The acquired temperature dependence of this coupling implies that the manifold of orbits and fixed points may shift with temperature. - Highlights: • Deriving equations for coupled modes in spin torque oscillators. • Including Hamiltonian formalism and elimination of three–magnon processes. • Thermal bath of magnons central to mode coupling. • Numerical examples of circular and elliptical devices.

  7. Mode coupling in spin torque oscillators

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Steven S.-L., E-mail: ZhangShule@missouri.edu [Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211 (United States); Zhou, Yan, E-mail: yanzhou@hku.hk [Department of Physics, The University of Hong Kong, Hong Kong (China); Center of Theoretical and Computational Physics, University of Hong Kong, Hong Kong (China); Li, Dong, E-mail: geodesic.ld@gmail.com [Department of Physics, Centre for Nonlinear Studies, and Beijing-Hong Kong-Singapore Joint Centre for Nonlinear and Complex Systems, Hong Kong Baptist University, Kowloon Tong, Hong Kong (China); Heinonen, Olle, E-mail: heinonen@anl.gov [Material Science Division, Argonne National Laboratory, Lemont, IL 60439 (United States); Northwestern-Argonne Institute of Science and Technology, 2145 Sheridan Road, Evanston, IL 60208 (United States); Computation Institute, The Unversity of Chicago, 5735 S Ellis Avenue, Chicago, IL 60637 (United States)

    2016-09-15

    A number of recent experimental works have shown that the dynamics of a single spin torque oscillator can exhibit complex behavior that stems from interactions between two or more modes of the oscillator, such as observed mode-hopping or mode coexistence. There has been some initial work indicating how the theory for a single-mode (macro-spin) spin torque oscillator should be generalized to include several modes and the interactions between them. In the present work, we rigorously derive such a theory starting with the Landau–Lifshitz–Gilbert equation for magnetization dynamics by expanding up to third-order terms in deviation from equilibrium. Our results show how a linear mode coupling, which is necessary for observed mode-hopping to occur, arises through coupling to a magnon bath. The acquired temperature dependence of this coupling implies that the manifold of orbits and fixed points may shift with temperature. - Highlights: • Deriving equations for coupled modes in spin torque oscillators. • Including Hamiltonian formalism and elimination of three–magnon processes. • Thermal bath of magnons central to mode coupling. • Numerical examples of circular and elliptical devices.

  8. The energy spectrum of electromagnetic normal modes in dissipative media: modes between two metal half spaces

    International Nuclear Information System (INIS)

    Sernelius, Bo E

    2008-01-01

    The energy spectrum of electromagnetic normal modes plays a central role in the theory of the van der Waals and Casimir interaction. Here we study the modes in connection with the van der Waals interaction between two metal half spaces. Neglecting dissipation leads to distinct normal modes with real-valued frequencies. Including dissipation seems to have the effect that these distinct modes move away from the real axis into the complex frequency plane. The summation of the zero-point energies of these modes render a complex-valued result. Using the contour integration, resulting from the use of the generalized argument principle, gives a real-valued and different result. We resolve this contradiction and show that the spectrum of true normal modes forms a continuum with real frequencies

  9. Impact of peptide clustering on unbinding forces in the context of fusion mimetics

    International Nuclear Information System (INIS)

    Pähler, Gesa; Lorenz, Bärbel; Janshoff, Andreas

    2013-01-01

    Highlights: ► Coiled-coil peptides as SNARE mimetics for membrane fusion. ► Interaction forces assessed by colloidal probe microscopy. ► Lateral organization of lipopeptides visualized by atomic force microscopy. -- Abstract: Coiled-coil zipping and unzipping is a pivotal process in SNARE-regulated membrane fusion. In this study we examine this process mediated by a minimal model for coiled-coil formation employing force spectroscopy in the context of membrane-coated surfaces and probes. The interaction forces of several hundred pN are surprisingly low considering the proposed amount of molecular bonds in the contact zone. However, by means of high-resolution imaging employing atomic force microscopy and studying the lateral mobility of lipids and peptides as a function of coiled-coil formation, we are able to supply a detailed view on processes occurring on the membrane surfaces during force measurements. The interaction forces determined here are not only dependent on the peptide concentration on the surface, but also on the regional organization of lateral peptide clusters found prior to coiled-coil formation

  10. Nonlinear simulation of tearing mode and m=1 kink mode based on kinetic RMHD model

    International Nuclear Information System (INIS)

    Yagi, M.; Yoshida, S.; Itoh, S.-I.; Naitou, H.; Nagahara, H.; Leboeuf, J.-N.; Itoh, K.; Matsumoto, T.; Tokuda, S.; Azumi, M.

    2005-01-01

    In this paper, we investigate dynamics of sawtooth oscillation and neoclassical tearing modes based on kinetic RMHD model, putting an emphasis on interaction with microscopic and transport processes. The simulation results show that the assumption in the conventional theory of neoclassical tearing mode is rather rude. (author)

  11. Streaming tearing mode

    Science.gov (United States)

    Shigeta, M.; Sato, T.; Dasgupta, B.

    1985-01-01

    The magnetohydrodynamic stability of streaming tearing mode is investigated numerically. A bulk plasma flow parallel to the antiparallel magnetic field lines and localized in the neutral sheet excites a streaming tearing mode more strongly than the usual tearing mode, particularly for the wavelength of the order of the neutral sheet width (or smaller), which is stable for the usual tearing mode. Interestingly, examination of the eigenfunctions of the velocity perturbation and the magnetic field perturbation indicates that the streaming tearing mode carries more energy in terms of the kinetic energy rather than the magnetic energy. This suggests that the streaming tearing mode instability can be a more feasible mechanism of plasma acceleration than the usual tearing mode instability.

  12. Single-Mode VCSELs

    Science.gov (United States)

    Larsson, Anders; Gustavsson, Johan S.

    The only active transverse mode in a truly single-mode VCSEL is the fundamental mode with a near Gaussian field distribution. A single-mode VCSEL produces a light beam of higher spectral purity, higher degree of coherence and lower divergence than a multimode VCSEL and the beam can be more precisely shaped and focused to a smaller spot. Such beam properties are required in many applications. In this chapter, after discussing applications of single-mode VCSELs, we introduce the basics of fields and modes in VCSELs and review designs implemented for single-mode emission from VCSELs in different materials and at different wavelengths. This includes VCSELs that are inherently single-mode as well as inherently multimode VCSELs where higher-order modes are suppressed by mode selective gain or loss. In each case we present the current state-of-the-art and discuss pros and cons. At the end, a specific example with experimental results is provided and, as a summary, the most promising designs based on current technologies are identified.

  13. Effects of Different Student Response Modes on Science Learning

    Science.gov (United States)

    Kho, Lee Sze; Chen, Chwen Jen

    2017-01-01

    Student response systems (SRSs) are wireless answering devices that enable students to provide simple real-time feedback to instructors. This study aims to evaluate the effects of different SRS interaction modes on elementary school students' science learning. Three interaction modes which include SRS Individual, SRS Collaborative, and Classroom…

  14. Nuclear scissors mode with pairing

    International Nuclear Information System (INIS)

    Balbutsev, E. B.; Malov, L. A.; Schuck, P.; Urban, M.; Vinas, X.

    2008-01-01

    The coupled dynamics of the scissors mode and the isovector giant quadrupole resonance are studied using a generalized Wigner function moments method, taking into account pair correlations. Equations of motion for angular momentum, quadrupole moment, and other relevant collective variables are derived on the basis of the time-dependent Hartree-Fock-Bogolyubov equations. Analytical expressions for energy centroids and transition probabilities are found for the harmonic-oscillator model with the quadrupole-quadrupole residual interaction and monopole pairing force. Deformation dependences of energies and B(M1) values are correctly reproduced. The inclusion of pair correlations leads to a drastic improvement in the description of qualitative and quantitative characteristics of the scissors mode.

  15. Double-mode pulsation

    International Nuclear Information System (INIS)

    Cox, A.N.

    1982-01-01

    Double mode pulsation is a very pervasive phenomenon in stars all over the Hertzsprung-Russell diagram. In order of increasing radius, examples are: ZZ Ceti stars, the sun, the delta Scuti stars, RR Lyrae variables, the β Cephei variables and those related to them, Cepheids, and maybe even the Mira stars. These many modes have been interpreted as both radial and nonradial modes, but in many cases the actual mode has not been clearly identified. Yellow giants seem to be the most simple pulsators with a large majority of the RR Lyrae variables and Cepheids showing only one pulsation period. We limit this review to those very few cases for classical Cepheids and RR Lyrae variables which display two modes. For these we know many facts about these stars, but the actual cause of the pulsation in two modes simultaneously remains unknown

  16. Streaming gravity mode instability

    International Nuclear Information System (INIS)

    Wang Shui.

    1989-05-01

    In this paper, we study the stability of a current sheet with a sheared flow in a gravitational field which is perpendicular to the magnetic field and plasma flow. This mixing mode caused by a combined role of the sheared flow and gravity is named the streaming gravity mode instability. The conditions of this mode instability are discussed for an ideal four-layer model in the incompressible limit. (author). 5 refs

  17. The soybean-Phytophthora resistance locus Rps1-k encompasses coiled coil-nucleotide binding-leucine rich repeat-like genes and repetitive sequences

    Directory of Open Access Journals (Sweden)

    Bhattacharyya Madan K

    2008-03-01

    Full Text Available Abstract Background A series of Rps (resistance to Pytophthora sojae genes have been protecting soybean from the root and stem rot disease caused by the Oomycete pathogen, Phytophthora sojae. Five Rps genes were mapped to the Rps1 locus located near the 28 cM map position on molecular linkage group N of the composite genetic soybean map. Among these five genes, Rps1-k was introgressed from the cultivar, Kingwa. Rps1-k has been providing stable and broad-spectrum Phytophthora resistance in the major soybean-producing regions of the United States. Rps1-k has been mapped and isolated. More than one functional Rps1-k gene was identified from the Rps1-k locus. The clustering feature at the Rps1-k locus might have facilitated the expansion of Rps1-k gene numbers and the generation of new recognition specificities. The Rps1-k region was sequenced to understand the possible evolutionary steps that shaped the generation of Phytophthora resistance genes in soybean. Results Here the analyses of sequences of three overlapping BAC clones containing the 184,111 bp Rps1-k region are reported. A shotgun sequencing strategy was applied in sequencing the BAC contig. Sequence analysis predicted a few full-length genes including two Rps1-k genes, Rps1-k-1 and Rps1-k-2. Previously reported Rps1-k-3 from this genomic region 1 was evolved through intramolecular recombination between Rps1-k-1 and Rps1-k-2 in Escherichia coli. The majority of the predicted genes are truncated and therefore most likely they are nonfunctional. A member of a highly abundant retroelement, SIRE1, was identified from the Rps1-k region. The Rps1-k region is primarily composed of repetitive sequences. Sixteen simple repeat and 63 tandem repeat sequences were identified from the locus. Conclusion These data indicate that the Rps1 locus is located in a gene-poor region. The abundance of repetitive sequences in the Rps1-k region suggested that the location of this locus is in or near a heterochromatic region. Poor recombination frequencies combined with presence of two functional Rps genes at this locus has been providing stable Phytophthora resistance in soybean.

  18. Conformational plasticity of the coiled coil domain of BmrR is required for bmr operator binding - the structure of unliganded BmrR

    OpenAIRE

    Kumaraswami, Muthiah; Newberry, Kate J.; Brennan, Richard G.

    2010-01-01

    The multidrug-binding transcription regulator, BmrR, from Bacillus subtilis is a MerR family member that binds to a wide array of cationic lipophilic toxins to activate transcription of the multidrug efflux pump gene, bmr. Transcription activation from the σA-dependent bmr operator requires BmrR to remodel the nonoptimal 19 base pair spacer between the −10 and −35 promoter elements in order to facilitate productive RNA polymerase binding. Despite the availability of several structures of BmrR...

  19. Algebraic description of intrinsic modes in nuclei

    International Nuclear Information System (INIS)

    Leviatan, A.

    1989-01-01

    We present a procedure for extracting normal modes in algebraic number-conserving systems of interacting bosons relevant for collective states in even-even nuclei. The Hamiltonian is resolved into intrinsic (bandhead related) and collective (in-band related) parts. Shape parameters are introduced through non-spherical boson bases. Intrinsic modes decoupled from the spurious modes are obtained from the intinsic part of the Hamiltonian in the limit of large number of bosons. Intrinsic states are constructed and serve to evaluate electromagnetic transition rates. The method is illustrated for systems with one type of boson as well as with proton-neutron bosons. 28 refs., 1 fig

  20. Normal modes of weak colloidal gels

    Science.gov (United States)

    Varga, Zsigmond; Swan, James W.

    2018-01-01

    The normal modes and relaxation rates of weak colloidal gels are investigated in calculations using different models of the hydrodynamic interactions between suspended particles. The relaxation spectrum is computed for freely draining, Rotne-Prager-Yamakawa, and accelerated Stokesian dynamics approximations of the hydrodynamic mobility in a normal mode analysis of a harmonic network representing several colloidal gels. We find that the density of states and spatial structure of the normal modes are fundamentally altered by long-ranged hydrodynamic coupling among the particles. Short-ranged coupling due to hydrodynamic lubrication affects only the relaxation rates of short-wavelength modes. Hydrodynamic models accounting for long-ranged coupling exhibit a microscopic relaxation rate for each normal mode, λ that scales as l-2, where l is the spatial correlation length of the normal mode. For the freely draining approximation, which neglects long-ranged coupling, the microscopic relaxation rate scales as l-γ, where γ varies between three and two with increasing particle volume fraction. A simple phenomenological model of the internal elastic response to normal mode fluctuations is developed, which shows that long-ranged hydrodynamic interactions play a central role in the viscoelasticity of the gel network. Dynamic simulations of hard spheres that gel in response to short-ranged depletion attractions are used to test the applicability of the density of states predictions. For particle concentrations up to 30% by volume, the power law decay of the relaxation modulus in simulations accounting for long-ranged hydrodynamic interactions agrees with predictions generated by the density of states of the corresponding harmonic networks as well as experimental measurements. For higher volume fractions, excluded volume interactions dominate the stress response, and the prediction from the harmonic network density of states fails. Analogous to the Zimm model in polymer

  1. Mode competition and hopping in optomechanical nano-oscillators

    Science.gov (United States)

    Zhang, Xingwang; Lin, Tong; Tian, Feng; Du, Han; Zou, Yongchao; Chau, Fook Siong; Zhou, Guangya

    2018-04-01

    We investigate the inter-mode nonlinear interaction in the multi-mode optomechanical nano-oscillator which consists of coupled silicon nanocantilevers, where the integrated photonic crystal nanocavities provide the coupling between the optical and mechanical modes. Due to the self-saturation and cross-saturation of the mechanical gain, the inter-mode competition is observed, which leads to the bistable operation of the optomechanical nano-oscillator: only one of the mechanical modes can oscillate at any one time, and the oscillation of one mode extremely suppresses that of the other with a side mode suppression ratio (SMSR) up to 40 dB. In the meantime, mode hopping, i.e., the optomechanical oscillation switches from one mode to the other, is also observed and found to be able to be provoked by excitation laser fluctuations.

  2. Antipastorialism : Resistant Georgic Mode

    National Research Council Canada - National Science Library

    Zimmerman, Donald

    2000-01-01

    .... Abolitionists, women, Afro-British slaves, and those who protested land enclosure developed a multivalent, resistant mode of writing, which I name 'antipastoralism', that countered orthodox, poetical...

  3. Nonlinear drift tearing mode

    International Nuclear Information System (INIS)

    Zelenyj, L.M.; Kuznetsova, M.M.

    1989-01-01

    Nonlinear study of magnetic perturbation development under single-mode conditions in collision-free plasma in configurations with the magnetic field shear is investigated. Results are obtained with regard of transverse component of electrical field and its effect on ion dynamics within wide range of ion Larmor radius value and values of magnetic field shear. Increments of nonlinear drift tearing mode are obtained and it is shown that excitation drastic conditions of even linearly stable modes are possible. Mechanism of instability nonlinear stabilization is considered and the value of magnetic island at the saturation threshold is estimeted. Energy of nonlinear drift tearing mode is discussed

  4. Microwave plasma mode conversion

    International Nuclear Information System (INIS)

    Torres, H.S.; Sakanaka, P.H.; Villarroel, C.H.

    1985-01-01

    The behavior of hot electrons during the process of laser-produced plasma is studied. The basic equations of mode conversion from electromagnetic waves to electrostatic waves are presented. It is shown by mode conversion, that, the resonant absorption and parametric instabilities appear simultaneously, but in different plasma regions. (M.C.K.) [pt

  5. Effects of mode coupling between low-mode radiation flux asymmetry and intermediate-mode ablator roughness on ignition capsule implosions

    Directory of Open Access Journals (Sweden)

    Jianfa Gu

    2017-01-01

    Full Text Available The low-mode shell asymmetry and high-mode hot spot mixing appear to be the main reasons for the performance degradation of the National Ignition Facility (NIF implosion experiments. The effects of the mode coupling between low-mode P2 radiation flux asymmetry and intermediate-mode L = 24 capsule roughness on the implosion performance of ignition capsule are investigated by two-dimensional radiation hydrodynamic simulations. It is shown that the amplitudes of new modes generated by the mode coupling are in good agreement with the second-order mode coupling equation during the acceleration phase. The later flow field not only shows large areal density P2 asymmetry in the main fuel, but also generates large-amplitude spikes and bubbles. In the deceleration phase, the increasing mode coupling generates more new modes, and the perturbation spectrum on the hot spot boundary is mainly from the strong mode interactions rather than the initial perturbation conditions. The combination of the low-mode and high-mode perturbations breaks up the capsule shell, resulting in a significant reduction of the hot spot temperature and implosion performance.

  6. Excursions through KK modes

    Energy Technology Data Exchange (ETDEWEB)

    Furuuchi, Kazuyuki [Manipal Centre for Natural Sciences, Manipal University,Manipal, Karnataka 576104 (India)

    2016-07-07

    In this article we study Kaluza-Klein (KK) dimensional reduction of massive Abelian gauge theories with charged matter fields on a circle. Since local gauge transformations change position dependence of the charged fields, the decomposition of the charged matter fields into KK modes is gauge dependent. While whole KK mass spectrum is independent of the gauge choice, the mode number depends on the gauge. The masses of the KK modes also depend on the field value of the zero-mode of the extra dimensional component of the gauge field. In particular, one of the KK modes in the KK tower of each massless 5D charged field becomes massless at particular values of the extra-dimensional component of the gauge field. When the extra-dimensional component of the gauge field is identified with the inflaton, this structure leads to recursive cosmological particle productions.

  7. Excursions through KK modes

    International Nuclear Information System (INIS)

    Furuuchi, Kazuyuki

    2016-01-01

    In this article we study Kaluza-Klein (KK) dimensional reduction of massive Abelian gauge theories with charged matter fields on a circle. Since local gauge transformations change position dependence of the charged fields, the decomposition of the charged matter fields into KK modes is gauge dependent. While whole KK mass spectrum is independent of the gauge choice, the mode number depends on the gauge. The masses of the KK modes also depend on the field value of the zero-mode of the extra dimensional component of the gauge field. In particular, one of the KK modes in the KK tower of each massless 5D charged field becomes massless at particular values of the extra-dimensional component of the gauge field. When the extra-dimensional component of the gauge field is identified with the inflaton, this structure leads to recursive cosmological particle productions.

  8. Surface modes in physics

    CERN Document Server

    Sernelius, Bo E

    2011-01-01

    Electromagnetic surface modes are present at all surfaces and interfaces between material of different dielectric properties. These modes have very important effects on numerous physical quantities: adhesion, capillary force, step formation and crystal growth, the Casimir effect etc. They cause surface tension and wetting and they give rise to forces which are important e.g. for the stability of colloids.This book is a useful and elegant approach to the topic, showing how the concept of electromagnetic modes can be developed as a unifying theme for a range of condensed matter physics. The

  9. Study of complex modes

    International Nuclear Information System (INIS)

    Pastrnak, J.W.

    1986-01-01

    This eighteen-month study has been successful in providing the designer and analyst with qualitative guidelines on the occurrence of complex modes in the dynamics of linear structures, and also in developing computer codes for determining quantitatively which vibration modes are complex and to what degree. The presence of complex modes in a test structure has been verified. Finite element analysis of a structure with non-proportional dumping has been performed. A partial differential equation has been formed to eliminate possible modeling errors

  10. Switch mode power supply

    International Nuclear Information System (INIS)

    Kim, Hui Jun

    1993-06-01

    This book concentrates on switch mode power supply. It has four parts, which are introduction of switch mode power supply with DC-DC converter such as Buck converter boost converter, Buck-boost converter and PWM control circuit, explanation for SMPS with DC-DC converter modeling and power mode control, resonance converter like resonance switch, converter, multi resonance converter and series resonance and parallel resonance converters, basic test of SMPS with PWM control circuit, Buck converter, Boost converter, flyback converter, forward converter and IC for control circuit.

  11. Nonlinear evolution of Mack modes in a hypersonic boundary layer

    Science.gov (United States)

    Chokani, Ndaona

    2005-01-01

    In hypersonic boundary layer flows the nonlinear disturbance evolution occurs relatively slowly over a very long length scale and has a profound effect on boundary layer transition. In the case of low-level freestream disturbances and negligible surface roughness, the transition is due to the modal growth of exponentially growing Mack modes that are destabilized by wall cooling. Cross-bicoherence measurements, derived from hot-wire data acquired in a quiet hypersonic tunnel, are used to identify and quantify phase-locked, quadratic sum and difference interactions involving the Mack modes. In the early stages of the nonlinear disturbance evolution, cross-bicoherence measurements indicate that the energy exchange between the Mack mode and the mean flow first occurs to broaden the sidebands; this is immediately followed by a sum interaction of the Mack mode to generate the first harmonic. In the next stages of the nonlinear disturbance evolution, there is a difference interaction of the first harmonic, which is also thought to contribute to the mean flow distortion. This difference interaction, in the latter stages, is also accompanied by a difference interaction between Mack mode and first harmonic, and a sum interaction, which forces the second harmonic. Analysis using the digital complex demodulation technique, shows that the low-frequency, phase-locked interaction that is identified in the cross bicoherence when the Mack mode and first harmonic have large amplitudes, arises due to the amplitude modulation of Mack mode and first harmonic.

  12. Nuclear scissors modes and hidden angular momenta

    Energy Technology Data Exchange (ETDEWEB)

    Balbutsev, E. B., E-mail: balbuts@theor.jinr.ru; Molodtsova, I. V. [Joint Institute for Nuclear Research (Russian Federation); Schuck, P. [Université Paris-Sud, Institut de Physique Nucléaire, IN2P3–CNRS (France)

    2017-01-15

    The coupled dynamics of low-lying modes and various giant resonances are studied with the help of the Wigner Function Moments method generalized to take into account spin degrees of freedom and pair correlations simultaneously. The method is based on Time-Dependent Hartree–Fock–Bogoliubov equations. The model of the harmonic oscillator including spin–orbit potential plus quadrupole–quadrupole and spin–spin interactions is considered. New low-lying spin-dependent modes are analyzed. Special attention is paid to the scissors modes. A new source of nuclear magnetism, connected with counter-rotation of spins up and down around the symmetry axis (hidden angular momenta), is discovered. Its inclusion into the theory allows one to improve substantially the agreement with experimental data in the description of energies and transition probabilities of scissors modes.

  13. Influence of toroidal rotation on tearing modes

    Science.gov (United States)

    Cai, Huishan; Cao, Jintao; Li, Ding

    2017-10-01

    Tearing modes stability analysis including toroidal rotation is studied. It is found that rotation affects the stability of tearing modes mainly through the interaction with resistive inner region of tearing mode. The coupling of magnetic curvature with centrifugal force and Coriolis force provides a perturbed perpendicular current, and a return parallel current is induced to affect the stability of tearing modes. Toroidal rotation plays a stable role, which depends on the magnitude of Mach number and adiabatic index Γ, and is independent on the direction of toroidal rotation. For Γ >1, the scaling of growth rate is changed for typical Mach number in present tokamaks. For Γ = 1 , the scaling keeps unchanged, and the effect of toroidal rotation is much less significant, compared with that for Γ >1. National Magnetic Confinement Fusion Science Program and National Science Foundation of China under Grants No. 2014GB106004, No. 2013GB111000, No. 11375189, No. 11075161 and No. 11275260, and Youth Innovation Promotion Association CAS.

  14. Higher Order Mode Fibers

    DEFF Research Database (Denmark)

    Israelsen, Stine Møller

    This PhD thesis considers higher order modes (HOMs) in optical fibers. That includes their excitation and characteristics. Within the last decades, HOMs have been applied both for space multiplexing in optical communications, group velocity dispersion management and sensing among others......-radial polarization as opposed to the linear polarization of the LP0X modes. The effect is investigated numerically in a double cladding fiber with an outer aircladding using a full vectorial modesolver. Experimentally, the bowtie modes are excited using a long period grating and their free space characteristics...... and polarization state are investigated. For this fiber, the onset of the bowtie effect is shown numerically to be LP011. The characteristics usually associated with Bessel-likes modes such as long diffraction free length and selfhealing are shown to be conserved despite the lack of azimuthal symmetry...

  15. Compression modes and the nuclear matter incompressibility ...

    Indian Academy of Sciences (India)

    We review the current status of the nuclear matter ( = and no Coulomb interaction) incompressibility coefficient, , and describe the theoretical and the experimental methods used to determine from properties of compression modes in nuclei. In particular we consider the long standing problem of the conflicting ...

  16. Plasmon Modes of Vertically Aligned Superlattices

    DEFF Research Database (Denmark)

    Filonenko, Konstantin; Duggen, Lars; Willatzen, Morten

    2017-01-01

    By using the Finite Element Method we visualize the modes of vertically aligned superlattice composed of gold and dielectric nanocylinders and investigate the emitter-plasmon interaction in approximation of weak coupling. We find that truncated vertically aligned superlattice can function...

  17. Population of collective modes in light scattering by many atoms

    Science.gov (United States)

    Guerin, William; Kaiser, Robin

    2017-05-01

    The interaction of light with an atomic sample containing a large number of particles gives rise to many collective (or cooperative) effects, such as multiple scattering, superradiance, and subradiance, even if the atomic density is low and the incident optical intensity weak (linear optics regime). Tracing over the degrees of freedom of the light field, the system can be well described by an effective atomic Hamiltonian, which contains the light-mediated dipole-dipole interaction between atoms. This long-range interaction is at the origin of the various collective effects, or of collective excitation modes of the system. Even though an analysis of the eigenvalues and eigenfunctions of these collective modes does allow distinguishing superradiant modes, for instance, from other collective modes, this is not sufficient to understand the dynamics of a driven system, as not all collective modes are significantly populated. Here, we study how the excitation parameters, i.e., the driving field, determines the population of the collective modes. We investigate in particular the role of the laser detuning from the atomic transition, and demonstrate a simple relation between the detuning and the steady-state population of the modes. This relation allows understanding several properties of cooperative scattering, such as why superradiance and subradiance become independent of the detuning at large enough detuning without vanishing, and why superradiance, but not subradiance, is suppressed near resonance. We also show that the spatial properties of the collective modes allow distinguishing diffusive modes, responsible for radiation trapping, from subradiant modes.

  18. Perspective gyrotron with mode converter for co- and counter-rotation operating modes

    International Nuclear Information System (INIS)

    Chirkov, A. V.; Kuftin, A. N.; Denisov, G. G.

    2015-01-01

    A gyrotron oscillator operating efficiently at modes of both rotations was developed and tested. The gyrotron operation can be switched between two modes: co- and counter rotating ones with respect to electron rotation in a resonance magnetic field. A synthesized mode converter provides output of both waves in the form of two different paraxial wave beams corresponding to direction of the mode rotation. Measured gyrotron power (up to 2 MW), interaction efficiency (34%), and diffraction losses in the mode converter (≈2%) agree well with the design values. The proposed gyrotron scheme alloys principal enhancement in the device parameters—possibility of electronic switching of output wave beam direction and possibility to arrange an effective scheme to provide frequency/phase locking of a gyrotron-oscillator

  19. Perspective gyrotron with mode converter for co- and counter-rotation operating modes

    Energy Technology Data Exchange (ETDEWEB)

    Chirkov, A. V.; Kuftin, A. N. [Institute of Applied Physics, Russian Academy of Sciences, 46 Ul' yanov Street, 603950 Nizhny Novgorod (Russian Federation); Denisov, G. G. [Institute of Applied Physics, Russian Academy of Sciences, 46 Ul' yanov Street, 603950 Nizhny Novgorod (Russian Federation); University of Nizhny Novgorod, 23 Prospekt Gagarina, 603950 Nizhny Novgorod (Russian Federation)

    2015-06-29

    A gyrotron oscillator operating efficiently at modes of both rotations was developed and tested. The gyrotron operation can be switched between two modes: co- and counter rotating ones with respect to electron rotation in a resonance magnetic field. A synthesized mode converter provides output of both waves in the form of two different paraxial wave beams corresponding to direction of the mode rotation. Measured gyrotron power (up to 2 MW), interaction efficiency (34%), and diffraction losses in the mode converter (≈2%) agree well with the design values. The proposed gyrotron scheme alloys principal enhancement in the device parameters—possibility of electronic switching of output wave beam direction and possibility to arrange an effective scheme to provide frequency/phase locking of a gyrotron-oscillator.

  20. Mode coupling in nonlinear Rayleigh--Taylor instability

    International Nuclear Information System (INIS)

    Ofer, D.; Shvarts, D.; Zinamon, Z.; Orszag, S.A.

    1992-01-01

    This paper studies the interaction of a small number of modes in the two-fluid Rayleigh--Taylor instability at relatively late stages of development, i.e., the nonlinear regime, using a two-dimensional hydrodynamic code incorporating a front-tracking scheme. It is found that the interaction of modes can greatly affect the amount of mixing and may even reduce the width of the mixing region. This interaction is both relatively long range in wave-number space and also acts in both directions, i.e., short wavelengths affect long wavelengths and vice versa. Three distinct stages of interaction have been identified, including substantial interaction among modes some of which may still be in their classical (single mode) ''linear'' phase

  1. Role of the N-terminal activation domain of coactivator CoCoA in mediating transcriptional activation by β-catenin*

    OpenAIRE

    Yang, Catherine K.; Kim, Jeong Hoon; Stallcup, Michael R.

    2006-01-01

    The coiled-coil coactivator (CoCoA) is involved in transcriptional activation of target genes by nuclear receptors and the xenobiotic aryl hydrocarbon receptor, as well as target genes of the Wnt signaling pathway, which is mediated by the lymphocyte enhancer factor (LEF)/T cell factor transcription factors and the coactivator β-catenin. The recruitment of CoCoA by nuclear receptors is accomplished by the interaction of the central coiled-coiled domain of CoCoA with p160 coactivators; the C-t...

  2. Constructing petal modes from the coherent superposition of Laguerre-Gaussian modes

    Science.gov (United States)

    Naidoo, Darryl; Forbes, Andrew; Ait-Ameur, Kamel; Brunel, Marc

    2011-03-01

    An experimental approach in generating Petal-like transverse modes, which are similar to what is seen in porro-prism resonators, has been successfully demonstrated. We hypothesize that the petal-like structures are generated from a coherent superposition of Laguerre-Gaussian modes of zero radial order and opposite azimuthal order. To verify this hypothesis, visually based comparisons such as petal peak to peak diameter and the angle between adjacent petals are drawn between experimental data and simulated data. The beam quality factor of the Petal-like transverse modes and an inner product interaction is also experimentally compared to numerical results.

  3. From dressed particle to dressed mode in plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Itoh, Sanae-I. [Kyushu Univ., Research Inst. for Applied Mechanics, Kasuga, Fukuoka (Japan); Itoh, Kimitaka [National Inst. for Fusion Science, Toki, Gifu (Japan)

    2002-05-01

    A theoretical method to analyze the strong turbulence in far-nonequilibrium plasma is discussed. In this approach, a test mode is treated being dressed with interactions with other modes. Nonlinear dispersion relation of the dressed mode and statistical treatment of turbulence is briefly explained. Analogue to the method of dressed particle, which has given Balescu-Lenard collision operator for inter-particle collisions, is mentioned. (author)

  4. Collective Lyapunov modes

    International Nuclear Information System (INIS)

    Takeuchi, Kazumasa A; Chaté, Hugues

    2013-01-01

    We show, using covariant Lyapunov vectors in addition to standard Lyapunov analysis, that there exists a set of collective Lyapunov modes in large chaotic systems exhibiting collective dynamics. Associated with delocalized Lyapunov vectors, they act collectively on the trajectory and hence characterize the instability of its collective dynamics. We further develop, for globally coupled systems, a connection between these collective modes and the Lyapunov modes in the corresponding Perron–Frobenius equation. We thereby address the fundamental question of the effective dimension of collective dynamics and discuss the extensivity of chaos in the presence of collective dynamics. This article is part of a special issue of Journal of Physics A: Mathematical and Theoretical devoted to ‘Lyapunov analysis: from dynamical systems theory to applications’. (paper)

  5. Sliding mode control and observation

    CERN Document Server

    Shtessel, Yuri; Fridman, Leonid; Levant, Arie

    2014-01-01

    The sliding mode control methodology has proven effective in dealing with complex dynamical systems affected by disturbances, uncertainties and unmodeled dynamics. Robust control technology based on this methodology has been applied to many real-world problems, especially in the areas of aerospace control, electric power systems, electromechanical systems, and robotics. Sliding Mode Control and Observation represents the first textbook that starts with classical sliding mode control techniques and progresses toward newly developed higher-order sliding mode control and observation algorithms and their applications. The present volume addresses a range of sliding mode control issues, including: *Conventional sliding mode controller and observer design *Second-order sliding mode controllers and differentiators *Frequency domain analysis of conventional and second-order sliding mode controllers *Higher-order sliding mode controllers and differentiators *Higher-order sliding mode observers *Sliding mode disturbanc...

  6. Mode selection laser

    DEFF Research Database (Denmark)

    2014-01-01

    spatial reflector variations, may be combined to generate a laser beam containing a plurality of orthogonal modes. The laser beam may be injected into a few- mode optical fiber, e.g. for the purpose of optical communication. The VCSEL may have intra-cavity contacts (31,37) and a Tunnel junction (33......) for current confinement into the active layer (34). An air-gap layer (102) may be provided between the upper reflector (15) and the SOI wafer (50) acting as a substrate. The lower reflector may be designed as a high-contrast grating (51) by etching....

  7. Component mode synthesis in structural dynamics

    International Nuclear Information System (INIS)

    Reddy, G.R.; Vaze, K.K.; Kushwaha, H.S.

    1993-01-01

    In seismic analysis of Nuclear Reactor Structures and equipments eigen solution requires large computer time. Component mode synthesis is an efficient technique with which one can evaluate dynamic characteristics of a large structure with minimum computer time. Due to this reason it is possible to do a coupled analysis of structure and equipment which takes into account the interaction effects. Basically in this the method large size structure is divided into small substructures and dynamic characteristics of individual substructure are determined. The dynamic characteristics of entire structure are evaluated by synthesising the individual substructure characteristics. Component mode synthesis has been applied in this paper to the analysis of a tall heavy water upgrading tower. Use of fixed interface normal modes, constrained modes, attachment modes in the component mode synthesis using energy principle and using Ritz vectors have been discussed. The validity of this method is established by solving fixed-fixed beam and comparing the results obtained by conventional and classical method. The eigen value problem has been solved using simultaneous iteration method. (author)

  8. Particle Distribution Modification by Low Amplitude Modes

    International Nuclear Information System (INIS)

    White, R.B.; Gorelenkov, N.; Heidbrink, W.W.; Van Zeeland, M.A.

    2009-01-01

    Modification of a high energy particle distribution by a spectrum of low amplitude modes is investigated using a guiding center code. Only through resonance are modes effective in modifying the distribution. Diagnostics are used to illustrate the mode-particle interaction and to find which effects are relevant in producing significant resonance, including kinetic Poincare plots and plots showing those orbits with time averaged mode-particle energy transfer. Effects of pitch angle scattering and drag are studied, as well as plasma rotation and time dependence of the equilibrium and mode frequencies. A specific example of changes observed in a DIII-D deuterium beam distribution in the presence of low amplitude experimentally validated Toroidal Alfven (TAE) eigenmodes and Reversed Shear Alfven (RSAE) eigenmodes is examined in detail. Comparison with experimental data shows that multiple low amplitude modes can account for significant modification of high energy beam particle distributions. It is found that there is a stochastic threshold for beam profile modification, and that the experimental amplitudes are only slightly above this threshold.

  9. Higher order modes of coupled optical fibres

    International Nuclear Information System (INIS)

    Alexeyev, C N; Yavorsky, M A; Boklag, N A

    2010-01-01

    The structure of hybrid higher order modes of two coupled weakly guiding identical optical fibres is studied. On the basis of perturbation theory with degeneracy for the vector wave equation expressions for modes with azimuthal angular number l ≥ 1 are obtained that allow for the spin–orbit interaction. The spectra of polarization corrections to the scalar propagation constants are calculated in a wide range of distances between the fibres. The limiting cases of widely and closely spaced fibres are studied. The obtained results can be used for studying the tunnelling of optical vortices in directional couplers and in matters concerned with information security

  10. Failure modes of composite sandwich beams

    Directory of Open Access Journals (Sweden)

    Gdoutos E.

    2008-01-01

    Full Text Available A thorough investigation of failure behavior of composite sandwich beams under three-and four-point bending was undertaken. The beams were made of unidirectional carbon/epoxy facings and a PVC closed-cell foam core. The constituent materials were fully characterized and in the case of the foam core, failure envelopes were developed for general two-dimensional states of stress. Various failure modes including facing wrinkling, indentation failure and core failure were observed and compared with analytical predictions. The initiation, propagation and interaction of failure modes depend on the type of loading, constituent material properties and geometrical dimensions.

  11. Estimation of the binding modes with important human cytochrome P450 enzymes, drug interaction potential, pharmacokinetics, and hepatotoxicity of ginger components using molecular docking, computational, and pharmacokinetic modeling studies.

    Science.gov (United States)

    Qiu, Jia-Xuan; Zhou, Zhi-Wei; He, Zhi-Xu; Zhang, Xueji; Zhou, Shu-Feng; Zhu, Shengrong

    2015-01-01

    Ginger is one of the most commonly used herbal medicines for the treatment of numerous ailments and improvement of body functions. It may be used in combination with prescribed drugs. The coadministration of ginger with therapeutic drugs raises a concern of potential deleterious drug interactions via the modulation of the expression and/or activity of drug-metabolizing enzymes and drug transporters, resulting in unfavorable therapeutic outcomes. This study aimed to determine the molecular interactions between 12 main active ginger components (6-gingerol, 8-gingerol, 10-gingerol, 6-shogaol, 8-shogaol, 10-shogaol, ar-curcumene, β-bisabolene, β-sesquiphelandrene, 6-gingerdione, (-)-zingiberene, and methyl-6-isogingerol) and human cytochrome P450 (CYP) 1A2, 2C9, 2C19, 2D6, and 3A4 and to predict the absorption, distribution, metabolism, excretion, and toxicity (ADMET) of the 12 ginger components using computational approaches and comprehensive literature search. Docking studies showed that ginger components interacted with a panel of amino acids in the active sites of CYP1A2, 2C9, 2C19, 2D6, and 3A4 mainly through hydrogen bond formation, to a lesser extent, via π-π stacking. The pharmacokinetic simulation studies showed that the [I]/[Ki ] value for CYP2C9, 2C19, and 3A4 ranged from 0.0002 to 19.6 and the R value ranged from 1.0002 to 20.6 and that ginger might exhibit a high risk of drug interaction via inhibition of the activity of human CYP2C9 and CYP3A4, but a low risk of drug interaction toward CYP2C19-mediated drug metabolism. Furthermore, it has been evaluated that the 12 ginger components possessed a favorable ADMET profiles with regard to the solubility, absorption, permeability across the blood-brain barrier, interactions with CYP2D6, hepatotoxicity, and plasma protein binding. The validation results showed that there was no remarkable effect of ginger on the metabolism of warfarin in humans, whereas concurrent use of ginger and nifedipine exhibited a

  12. Magnetic modes in superlattices

    International Nuclear Information System (INIS)

    Oliveira, F.A.

    1990-04-01

    A first discussion of reciprocal propagation of magnetic modes in a superlattice is presented. In the absence of an applied external magnetic field a superllatice made of alternate layers of the type antiferromagnetic-non-magnetic materials presents effects similar to those of phonons in a dielectric superlattice. (A.C.A.S.) [pt

  13. Thermodynamics of Radiation Modes

    Science.gov (United States)

    Pina, Eduardo; de la Selva, Sara Maria Teresa

    2010-01-01

    We study the equilibrium thermodynamics of the electromagnetic radiation in a cavity of a given volume and temperature. We found three levels of description, the thermodynamics of one mode, the thermodynamics of the distribution of frequencies in a band by summing over the frequencies in it and the global thermodynamics by summing over all the…

  14. Thermal Operating Modes

    International Nuclear Information System (INIS)

    Bechtel SAIC Company

    2002-01-01

    Higher and lower temperature operating modes (e.g., above and below the boiling point of water) are alternative approaches to managing the heat produced by the radioactive decay of spent nuclear fuel. Current analyses indicate that a repository at the Yucca Mountain site is likely to comply with applicable safety standards regardless of the particular thermal operating mode. Both modes have potential advantages and disadvantages. With a higher temperature operating mode (HTOM), waste packages (WPs) can be placed closer together. This reduces the number of drifts, the required emplacement area, construction costs, and occupational risks to construction workers. In addition, the HTOM would minimize the amount of water that might contact the waste for hundreds of years after closure. On the other hand, higher temperatures introduce uncertainties in the understanding of the long-term performance of the repository because of uncertainties in the thermal effects on WP lifetime and the near-field environment around the drifts. A lower temperature operating mode (LTOM) has the potential to reduce uncertainties in long-term performance of the repository by limiting the effects of temperature on WP lifetime and on the near-field environment around the drifts. Depending on the combination of operating parameters, a LTOM could require construction of additional drifts, a larger emplacement area, increased construction costs, increased occupational risks to construction works, and a longer period of ventilation than a HTOM. The repository design for the potential Yucca Mountain site is flexible and can be constructed and operated in various operating modes to achieve specific technical objectives, accommodate future policy decisions, and use of new information. For example, the flexible design can be operated across a range of temperatures and can be tailored to achieve specific thermal requirements in the future. To accommodate future policy decisions, the repository can be

  15. Nonlinear saturation of the trapped-ion mode by mode coupling in two dimensions

    International Nuclear Information System (INIS)

    Cohen, B.I.; Tang, W.M.

    1977-01-01

    A study of the nonlinear saturation by mode coupling of the dissipative trapped-ion mode is presented in which both radial and poloidal variations are considered. The saturation mechanism consists of the nonlinear coupling via E x B convection of energy from linearly unstable modes to stable modes. Stabilization is provided at short poloidal wavelengths by Landau damping from trapped and circulating ions, at short radial wavelengths by effects associated with the finite ion banana excursions and at long wavelengths by ion collisions. A one-dimensional, nonlinear partial differential equation for the electrostatic potential derived in earlier work is extended to two dimensions and to third order in amplitude. Included systematically are kinetic effects, e.g., Landau damping and its spatial dependence due to magnetic shear. The stability and accessibility of equilibria are considered in detail for cases far from as well as close to marginal stability. In the first case three-wave interactions are found to be important when the spectrum of unstable modes is sufficiently narrow. In the latter case, it is found that for a single unstable mode, a four-wave interaction can provide the dominant saturation mechanism. Cross-field transport is calculated, and the scaling of results is considered for tokamak parameters

  16. Interference of Multi-Mode Gaussian States and "non Appearance" of Quantum Correlations

    Science.gov (United States)

    Olivares, Stefano

    2012-01-01

    We theoretically investigate bilinear, mode-mixing interactions involving two modes of uncorrelated multi-mode Gaussian states. In particular, we introduce the notion of "locally the same states" (LSS) and prove that two uncorrelated LSS modes are invariant under the mode mixing, i.e. the interaction does not lead to the birth of correlations between the outgoing modes. We also study the interference of orthogonally polarized Gaussian states by means of an interferometric scheme based on a beam splitter, rotators of polarization and polarization filters.

  17. Default mode contributions to automated information processing.

    Science.gov (United States)

    Vatansever, Deniz; Menon, David K; Stamatakis, Emmanuel A

    2017-11-28

    Concurrent with mental processes that require rigorous computation and control, a series of automated decisions and actions govern our daily lives, providing efficient and adaptive responses to environmental demands. Using a cognitive flexibility task, we show that a set of brain regions collectively known as the default mode network plays a crucial role in such "autopilot" behavior, i.e., when rapidly selecting appropriate responses under predictable behavioral contexts. While applying learned rules, the default mode network shows both greater activity and connectivity. Furthermore, functional interactions between this network and hippocampal and parahippocampal areas as well as primary visual cortex correlate with the speed of accurate responses. These findings indicate a memory-based "autopilot role" for the default mode network, which may have important implications for our current understanding of healthy and adaptive brain processing.

  18. Coupling of tearing modes in tokamaks

    International Nuclear Information System (INIS)

    Finn, J.M.

    1977-01-01

    The simultaneous presence of tearing modes of different helical pitches leads to the destruction of magnetic surfaces, which has been suggested as the mechanism leading to the onset of the disruptive instability in tokamaks. For current profiles in which the m = 2 mode is unstable, but the m = 3 is stable, the coupling of the m = 3 to the m = 2 through the poloidal variation of the toroidal field can drive the m = 3 amplitude psi 3 to order psi 2 times the inverse aspect ratio. Detailed calculations, both analytical and numerical, have been performed for two models for the equilibrium and m = 2 mode structure. A slab model and incompressible m = 3 perturbations are assumed. The m = 3 amplitude increases with shear, up to a point, showing that as the current channel shrinks, overlap of resonances becomes more likely. The results also apply qualitatively to other m, m +- 1 interactions

  19. Magnetohydrodynamic waves driven by p-modes

    International Nuclear Information System (INIS)

    Khomenko, Elena; Santamaria, Irantzu Calvo

    2013-01-01

    Waves are observed at all layers of the solar atmosphere and the magnetic field plays a key role in their propagation. While deep down in the atmosphere the p-modes are almost entirely of acoustic nature, in the upper layers magnetic forces are dominating, leading to a large variety of new wave modes. Significant advances have been made recently in our understanding of the physics of waves interaction with magnetic structures, with the help of analytical theories, numerical simulations, as well as high-resolution observations. In this contribution, we review recent observational findings and current theoretical ideas in the field, with an emphasis on the following questions: (i) Peculiarities of the observed wave propagation in network, plage and facular regions; (ii) Role of the mode transformation and observational evidences of this process: (iii) Coupling of the photosphere, chromosphere, and above by means of waves propagating in magnetic structures.

  20. Single-mode coherent synchrotron radiation instability

    Directory of Open Access Journals (Sweden)

    S. Heifets

    2003-06-01

    Full Text Available The microwave instability driven by the coherent synchrotron radiation (CSR has been previously studied [S. Heifets and G. V. Stupakov, Phys. Rev. ST Accel. Beams 5, 054402 (2002] neglecting effect of the shielding caused by the finite beam pipe aperture. In practice, the unstable mode can be close to the shielding threshold where the spectrum of the radiation in a toroidal beam pipe is discrete. In this paper, the CSR instability is studied in the case when it is driven by a single synchronous mode. A system of equations for the beam-wave interaction is derived and its similarity to the 1D free-electron laser theory is demonstrated. In the linear regime, the growth rate of the instability is obtained and a transition to the case of continuous spectrum is discussed. The nonlinear evolution of the single-mode instability, both with and without synchrotron damping and quantum diffusion, is also studied.

  1. Estimation of the binding modes with important human cytochrome P450 enzymes, drug interaction potential, pharmacokinetics, and hepatotoxicity of ginger components using molecular docking, computational, and pharmacokinetic modeling studies

    Directory of Open Access Journals (Sweden)

    Qiu JX

    2015-02-01

    Full Text Available Jia-Xuan Qiu,1,2 Zhi-Wei Zhou,3 Zhi-Xu He,4 Xueji Zhang,5 Shu-Feng Zhou,3 Shengrong Zhu11Department of Stomatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People’s Republic of China; 2Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People’s Republic of China; 3Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, USA; 4Guizhou Provincial Key Laboratory for Regenerative Medicine, Stem Cell and Tissue Engineering Research Center and Sino-US Joint Laboratory for Medical Sciences, Guiyang Medical University, Guiyang, Guizhou, People’s Republic of China; 5Research Center for Bioengineering and Sensing Technology, University of Science and Technology Beijing, Beijing, People’s Republic of ChinaAbstract: Ginger is one of the most commonly used herbal medicines for the treatment of numerous ailments and improvement of body functions. It may be used in combination with prescribed drugs. The coadministration of ginger with therapeutic drugs raises a concern of potential deleterious drug interactions via the modulation of the expression and/or activity of drug-metabolizing enzymes and drug transporters, resulting in unfavorable therapeutic outcomes. This study aimed to determine the molecular interactions between 12 main active ginger components (6-gingerol, 8-gingerol, 10-gingerol, 6-shogaol, 8-shogaol, 10-shogaol, ar-curcumene, ß-bisabolene, ß-sesquiphelandrene, 6-gingerdione, (--zingiberene, and methyl-6-isogingerol and human cytochrome P450 (CYP 1A2, 2C9, 2C19, 2D6, and 3A4 and to predict the absorption, distribution, metabolism, excretion, and toxicity (ADMET of the 12 ginger components using computational approaches and comprehensive literature search. Docking studies showed that ginger components interacted with a panel of amino acids in the active sites of CYP1A

  2. Experimental studies of tearing mode and resistive wall mode dynamics in the reversed field pinch configuration

    International Nuclear Information System (INIS)

    Malmberg, Jenny-Ann

    2003-06-01

    It is relatively straightforward to establish equilibrium in magnetically confined plasmas, but the plasma is frequently susceptible to a variety of instabilities that are driven by the free energy in the magnetic field or in the pressure gradient. These unstable modes exhibit effects that affect the particle, momentum and heat confinement properties of the configuration. Studies of the dynamics of several of the most important modes are the subject of this thesis. The studies are carried out on plasmas in the reversed field pinch (RFP) configuration. One phenomenon commonly observed in RFPs is mode wall locking. The localized nature of these phase- and wall locked structures results in localized power loads on the wall which are detrimental for confinement. A detailed study of the wall locked mode phenomenon is performed based on magnetic measurements from three RFP devices. The two possible mechanisms for wall locking are investigated. Locking as a result of tearing modes interacting with a static field error and locking due to the presence of a non-ideal boundary. The characteristics of the wall locked mode are qualitatively similar in a device with a conducting shell system (TPE-RX) compared to a device with a resistive shell (Extrap T2). A theoretical model is used for evaluating the threshold values for wall locking due to eddy currents in the vacuum vessel in these devices. A good correlation with experiment is observed for the conducting shell device. The possibility of successfully sustaining discharges in a resistive shell RFP is introduced in the recently rebuilt device Extrap T2R. Fast spontaneous mode rotation is observed, resulting in low magnetic fluctuations, low loop voltage and improved confinement. Wall locking is rarely observed. The low tearing mode amplitudes allow for the theoretically predicted internal non-resonant on-axis resistive wall modes to be observed. These modes have not previously been distinguished due to the formation of wall

  3. Stability of short wavelength tearing and twisting modes

    International Nuclear Information System (INIS)

    Waelbroeck, F.L.

    1998-01-01

    The stability and mutual interaction of tearing and twisting modes in a torus is governed by matrices that generalize the well-known Δ' stability index. The diagonal elements of these matrices determine the intrinsic stability of modes that reconnect the magnetic field at a single resonant surface. The off-diagonal elements indicate the strength of the coupling between the different modes. The author shows how the elements of these matrices can be evaluated, in the limit of short wavelength, from the free energy driving radially extended ballooning modes. The author applies the results by calculating the tearing and twisting Δ' for a model high-beta equilibrium with circular flux surfaces

  4. Observations on resistive wall modes

    International Nuclear Information System (INIS)

    Gerwin, R.A.; Finn, J.M.

    1996-01-01

    Several results on resistive wall modes and their application to tokamaks are presented. First, it is observed that in the presence of collisional parallel dynamics there is an exact cancellation to lowest order of the dissipative and sound wave effects for an ideal Ohm's law. This is easily traced to the fact that the parallel dynamics occurs along the perturbed magnetic field lines for such electromagnetic modes. Such a cancellation does not occur in the resistive layer of a tearing-like mode. The relevance to models for resistive wall modes using an electrostatic Hammett-Perkins type operator to model Landau damping will be discussed. Second, we observe that with an ideal Ohm's law, resistive wall modes can be destabilized by rotation in that part of parameter space in which the ideal MHD modes are stable with the wall at infinity. This effect can easily be explained by interpreting the resistive wall instability in terms of mode coupling between the backward stable MHD mode and a stable mode locked into the wall. Such an effect can occur for very small rotation for tearing-resistive wall modes in which inertia dominates viscosity in the layer, but the mode is stabilized by further rotation. For modes for which viscosity dominates in the layer, rotation is purely stabilizing. For both tearing models, a somewhat higher rotation frequency gives stability essentially whenever the tearing mode is stable with a perfectly conducting wall. These tearing/resistive wall results axe also simply explained in terms of mode coupling. It has been shown that resonant external ideal modes can be stabilized in the presence of resistive wall and resistive plasma with rotation of order the nominal tearing mode growth rate. We show that these modes behave as resistive wall tearing modes in the sense above. This strengthens the suggestion that rotational stabilization of the external kink with a resistive wall is due to the presence of resistive layers, even for ideal modes

  5. Locked modes and magnetic field errors in MST

    International Nuclear Information System (INIS)

    Almagri, A.F.; Assadi, S.; Prager, S.C.; Sarff, J.S.; Kerst, D.W.

    1992-06-01

    In the MST reversed field pinch magnetic oscillations become stationary (locked) in the lab frame as a result of a process involving interactions between the modes, sawteeth, and field errors. Several helical modes become phase locked to each other to form a rotating localized disturbance, the disturbance locks to an impulsive field error generated at a sawtooth crash, the error fields grow monotonically after locking (perhaps due to an unstable interaction between the modes and field error), and over the tens of milliseconds of growth confinement degrades and the discharge eventually terminates. Field error control has been partially successful in eliminating locking

  6. Boosting Majorana Zero Modes

    Directory of Open Access Journals (Sweden)

    Torsten Karzig

    2013-11-01

    Full Text Available One-dimensional topological superconductors are known to host Majorana zero modes at domain walls terminating the topological phase. Their non-Abelian nature allows for processing quantum information by braiding operations that are insensitive to local perturbations, making Majorana zero modes a promising platform for topological quantum computation. Motivated by the ultimate goal of executing quantum-information processing on a finite time scale, we study domain walls moving at a constant velocity. We exploit an effective Lorentz invariance of the Hamiltonian to obtain an exact solution of the associated quasiparticle spectrum and wave functions for arbitrary velocities. Essential features of the solution have a natural interpretation in terms of the familiar relativistic effects of Lorentz contraction and time dilation. We find that the Majorana zero modes remain stable as long as the domain wall moves at subluminal velocities with respect to the effective speed of light of the system. However, the Majorana bound state dissolves into a continuous quasiparticle spectrum after the domain wall propagates at luminal or even superluminal velocities. This relativistic catastrophe implies that there is an upper limit for possible braiding frequencies even in a perfectly clean system with an arbitrarily large topological gap. We also exploit our exact solution to consider domain walls moving past static impurities present in the system.

  7. Expression of Cry1Ac toxin-binding region in Plutella xyllostella cadherin-like receptor and studying their interaction mode by molecular docking and site-directed mutagenesis.

    Science.gov (United States)

    Hu, Xiaodan; Zhang, Xiao; Zhong, Jianfeng; Liu, Yuan; Zhang, Cunzheng; Xie, Yajing; Lin, Manman; Xu, Chongxin; Lu, Lina; Zhu, Qing; Liu, Xianjin

    2018-05-01

    Cadherin-like protein has been identified as the primary Bacillus thuringiensis (Bt) Cry toxin receptor in Lepidoptera pests and plays a key role in Cry toxin insecticidal. In this study, we successfully expressed the putative Cry1Ac toxin-binding region (CR7-CR11) of Plutella xylostella cadherin-like in Escherichia coli BL21 (DE3). The expressed CR7-CR11 fragment showed binding ability to Cry1Ac toxin under denaturing (Ligand blot) and non-denaturing (ELISA) conditions. The three-dimensional structure of CR7-CR11 was constructed by homology modeling. Molecular docking results of CR7-CR11 and Cry1Ac showed that domain II and domain III of Cry1Ac were taking part in binding to CR7-CR11, while CR7-CR8 was the region of CR7-CR11 in interacting with Cry1Ac. The interaction of toxin-receptor complex was found to arise from hydrogen bond and hydrophobic interaction. Through the computer-aided alanine mutation scanning, amino acid residues of Cry1Ac (Met341, Asn442 and Ser486) and CR7-CR11 (Asp32, Arg101 and Arg127) were predicted as the hot spot residues involved in the interaction of the toxin-receptor complex. At last, we verified the importance role of these key amino acid residues by binding assay. These results will lay a foundation for further elucidating the insecticidal mechanism of Cry toxin and enhancing Cry toxin insecticidal activity by molecular modification. Copyright © 2018 Elsevier B.V. All rights reserved.

  8. Magnon dark modes and gradient memory.

    Science.gov (United States)

    Zhang, Xufeng; Zou, Chang-Ling; Zhu, Na; Marquardt, Florian; Jiang, Liang; Tang, Hong X

    2015-11-16

    Extensive efforts have been expended in developing hybrid quantum systems to overcome the short coherence time of superconducting circuits by introducing the naturally long-lived spin degree of freedom. Among all the possible materials, single-crystal yttrium iron garnet has shown up recently as a promising candidate for hybrid systems, and various highly coherent interactions, including strong and even ultrastrong coupling, have been demonstrated. One distinct advantage in these systems is that spins form well-defined magnon modes, which allows flexible and precise tuning. Here we demonstrate that by dissipation engineering, a non-Markovian interaction dynamics between the magnon and the microwave cavity photon can be achieved. Such a process enables us to build a magnon gradient memory to store information in the magnon dark modes, which decouple from the microwave cavity and thus preserve a long lifetime. Our findings provide a promising approach for developing long-lifetime, multimode quantum memories.

  9. Default mode network connectivity during task execution.

    Science.gov (United States)

    Vatansever, D; Menon, D K; Manktelow, A E; Sahakian, B J; Stamatakis, E A

    2015-11-15

    Initially described as task-induced deactivations during goal-directed paradigms of high attentional load, the unresolved functionality of default mode regions has long been assumed to interfere with task performance. However, recent evidence suggests a potential default mode network involvement in fulfilling cognitive demands. We tested this hypothesis in a finger opposition paradigm with task and fixation periods which we compared with an independent resting state scan using functional magnetic resonance imaging and a comprehensive analysis pipeline including activation, functional connectivity, behavioural and graph theoretical assessments. The results indicate task specific changes in the default mode network topography. Behaviourally, we show that increased connectivity of the posterior cingulate cortex with the left superior frontal gyrus predicts faster reaction times. Moreover, interactive and dynamic reconfiguration of the default mode network regions' functional connections illustrates their involvement with the task at hand with higher-level global parallel processing power, yet preserved small-world architecture in comparison with rest. These findings demonstrate that the default mode network does not disengage during this paradigm, but instead may be involved in task relevant processing. Copyright © 2015 Elsevier Inc. All rights reserved.

  10. Multi modal child-to-child interaction

    DEFF Research Database (Denmark)

    Fisker, Tine Basse

    In this presentation the interaction and relation of three boys is analyzed using multi modal analysis. The analysis clearly, and surprisingly demonstrates that the boys interact via different modes and that they are able to handle several interaction partners at the same time. They co......-construct interaction in rather complex and unexpected ways using verbal as well as non-verbal modes in interaction....

  11. Guaranteed performance in reaching mode of sliding mode ...

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    addresses the design of constant plus proportional rate reaching law-based SMC for second-order ... Reaching mode; sliding mode controlled systems; output tracking ... The uncertainty in the input distribution function g is expressed as.

  12. The Ndc80 internal loop is required for recruitment of the Ska complex to establish end-on microtubule attachment to kinetochores

    DEFF Research Database (Denmark)

    Zhang, Gang; Kelstrup, Christian D; Hu, Xiao-Wen

    2012-01-01

    The Ndc80 complex establishes end-on attachment of kinetochores to microtubules essential for chromosome segregation. The Ndc80 subunit is characterized by an N-terminal region, that binds directly to microtubules, and a long coiled-coil region that interacts with Nuf2. A loop region in Ndc80 tha...... chromosome segregation through the recruitment of specific proteins to the kinetochore....

  13. Mode-to-mode energy transfers in convective patterns

    Indian Academy of Sciences (India)

    Abstract. We investigate the energy transfer between various Fourier modes in a low- dimensional model for thermal convection. We have used the formalism of mode-to-mode energy transfer rate in our calculation. The evolution equations derived using this scheme is the same as those derived using the hydrodynamical ...

  14. Azimuthal decomposition of optical modes

    CSIR Research Space (South Africa)

    Dudley, Angela L

    2012-07-01

    Full Text Available This presentation analyses the azimuthal decomposition of optical modes. Decomposition of azimuthal modes need two steps, namely generation and decomposition. An azimuthally-varying phase (bounded by a ring-slit) placed in the spatial frequency...

  15. Localized Acoustic Surface Modes

    KAUST Repository

    Farhat, Mohamed

    2015-08-04

    We introduce the concept of localized acoustic surface modes (ASMs). We demonstrate that they are induced on a two-dimensional cylindrical rigid surface with subwavelength corrugations under excitation by an incident acoustic plane wave. Our results show that the corrugated rigid surface is acoustically equivalent to a cylindrical scatterer with uniform mass density that can be represented using a Drude-like model. This, indeed, suggests that plasmonic-like acoustic materials can be engineered with potential applications in various areas including sensing, imaging, and cloaking.

  16. 互动式手机多媒体广告的优势和应用模式分析%Analysis of the Advantages and Application Mode of Interactive Mobile Phone Multimedia Advertising

    Institute of Scientific and Technical Information of China (English)

    罗星

    2014-01-01

    This article is mainly to carry out a full range analysis on the present situation and characteristics of multimedia technology in the main mobile phone advertising time, and study the status of advertising development, the application status of interactive multimedia technology in mobile phone advertising based on the characteristics of multimedia technology, the characteristics of interactive advertising and diversified patterns.%本篇文章主要是对多媒体技术在主打手机广告时候的现状和特点进行全方位分析,进行对广告发展的现状进行研究和在多媒体技术特点的基础上,对现今互动式多媒体技术在手机广告上的应用现状,及互动式广告的特点和多样化的模式进行详细的研究。

  17. Identification of a New Interaction Mode between the Src Homology 2 Domain of C-terminal Src Kinase (Csk) and Csk-binding Protein/Phosphoprotein Associated with Glycosphingolipid Microdomains♦

    Science.gov (United States)

    Tanaka, Hiroaki; Akagi, Ken-ichi; Oneyama, Chitose; Tanaka, Masakazu; Sasaki, Yuichi; Kanou, Takashi; Lee, Young-Ho; Yokogawa, Daisuke; Dobenecker, Marc-Werner; Nakagawa, Atsushi; Okada, Masato; Ikegami, Takahisa

    2013-01-01

    Proteins with Src homology 2 (SH2) domains play major roles in tyrosine kinase signaling. Structures of many SH2 domains have been studied, and the regions involved in their interactions with ligands have been elucidated. However, these analyses have been performed using short peptides consisting of phosphotyrosine followed by a few amino acids, which are described as the canonical recognition sites. Here, we report the solution structure of the SH2 domain of C-terminal Src kinase (Csk) in complex with a longer phosphopeptide from the Csk-binding protein (Cbp). This structure, together with biochemical experiments, revealed the existence of a novel binding region in addition to the canonical phosphotyrosine 314-binding site of Cbp. Mutational analysis of this second region in cells showed that both canonical and novel binding sites are required for tumor suppression through the Cbp-Csk interaction. Furthermore, the data indicate an allosteric connection between Cbp binding and Csk activation that arises from residues in the βB/βC loop of the SH2 domain. PMID:23548896

  18. Raman amplification of OAM modes

    DEFF Research Database (Denmark)

    Ingerslev, Kasper; Gregg, Patrick; Galili, Michael

    2017-01-01

    The set of fibre modes carrying orbital angular momentum (OAM) is a possible basis for mode division multiplexing. In this regard, fibres supporting OAM modes have been fabricated [1], and optical communication using these fibres, has been demonstrated [2]. A vital part of any long range...

  19. ACCA College English Teaching Mode

    Science.gov (United States)

    Ding, Renlun

    2008-01-01

    This paper elucidates a new college English teaching mode--"ACCA" (Autonomous Cooperative Class-teaching All-round College English Teaching Mode). Integrated theories such as autonomous learning and cooperative learning into one teaching mode, "ACCA", which is being developed and advanced in practice as well, is the achievement…

  20. Fluxon modes in superconducting multilayers

    DEFF Research Database (Denmark)

    Pedersen, Niels Falsig; Madsen, Søren Peder

    2004-01-01

    We show how to construct fluxon modes from plasma modes in the inductively coupled stacked Josephson junctions, and consider some special cases of these fluxon modes analytically. In some cases we can find exact analytical solutions when we choose the bias current in a special way. We also consid...

  1. Standardization of Keyword Search Mode

    Science.gov (United States)

    Su, Di

    2010-01-01

    In spite of its popularity, keyword search mode has not been standardized. Though information professionals are quick to adapt to various presentations of keyword search mode, novice end-users may find keyword search confusing. This article compares keyword search mode in some major reference databases and calls for standardization. (Contains 3…

  2. Modes of fossil preservation

    Science.gov (United States)

    Schopf, J.M.

    1975-01-01

    The processes of geologic preservation are important for understanding the organisms represented by fossils. Some fossil differences are due to basic differences in organization of animals and plants, but the interpretation of fossils has also tended to be influenced by modes of preservation. Four modes of preservation generally can be distinguished: (1) Cellular permineralization ("petrifaction") preserves anatomical detail, and, occasionally, even cytologic structures. (2) Coalified compression, best illustrated by structures from coal but characteristic of many plant fossils in shale, preserves anatomical details in distorted form and produces surface replicas (impressions) on enclosing matrix. (3) Authigenic preservation replicates surface form or outline (molds and casts) prior to distortion by compression and, depending on cementation and timing, may intergrade with fossils that have been subject to compression. (4) Duripartic (hard part) preservation is characteristic of fossil skeletal remains, predominantly animal. Molds, pseudomorphs, or casts may form as bulk replacements following dissolution of the original fossil material, usually by leaching. Classification of the kinds of preservation in fossils will aid in identifying the processes responsible for modifying the fossil remains of both animals and plants. ?? 1975.

  3. Resonant count diagram and solar g mode oscillations

    International Nuclear Information System (INIS)

    Guenther, D.B.; Demarque, P.

    1984-01-01

    Evidence is provided to support the hypothesis that, because of the particular frequency separations of the solar g modes, resonant three-wave interactions stimulate only a selected few g modes. A resonant count diagram was obtained by plotting the total number of possible resonant three-wave interactions or a given beat frequency against the inverse of the beat frequency (the beat period), within a given frequency tolerance. The 1 = 1, 2, 3, 4 g modes calculated by Christensen-Dalsgaard, Gough and Morgan (1979) for a standard model of the Sun were used. The diagram has a significant peak at 160 minutes as well as other peaks at longer periods. The g modes that Delache and Scherrer (1983) tentatively identified from the Crimea-Stanford data were also plotted. These modes were found to correspond with the other peaks in the diagram. This coincidence between the observed g modes and the peaks in the resonant count diagram suggest that the observed g modes do owe their observability to resonant three-wave interactions

  4. Surface tearing modes in tokamaks

    International Nuclear Information System (INIS)

    Takizuka, Tomonori; Kurita, Gen-ichi; Azumi, Masafumi; Takeda, Tatsuoki

    1985-10-01

    Surface tearing modes in tokamaks are studied numerically and analytically. The eigenvalue problem is solved to obtain the growth rate and the mode structure. We investigate in detail dependences of the growth rate of the m/n = 2/1 resistive MHD modes on the safety factor at the plasma surface, current profile, wall position, and resistivity. The surface tearing mode moves the plasma surface even when the wall is close to the surface. The stability diagram for these modes is presented. (author)

  5. U(SMes*)n, (n=3, 4) and Ln(SMes*)3 (Ln = La, Ce, Pr, Nd): Lanthanide(III)/actinide(III) differentiation in agostic interactions and an unprecedented eta(3) Ligation mode of the aryl-thiolate ligand, from X-ray diffraction and DFT analysis

    International Nuclear Information System (INIS)

    Roger, Mathieu; Barros, Noemi; Arliguie, Therese; Thuery, Pierre; Maron, Laurent; Ephritikhine, Michel

    2006-01-01

    Reaction of U(NEt 2 ) 4 with HS-2,4,6- t Bu 3 C 6 H 2 (HSMes*) gave U(SMes*) 3 (NEt 2 )(py) (1), whereas similar treatment of U[N(SiMe 3 )SiMe 2 CH 2 ][N(SiMe 3 ) 2 ] 2 afforded U(SMes*)[N(SiMe 3 ) 2 ] 3 (2) and U(SMes*) 3 [N(SiMe 3 ) 2 ]. The first neutral homoleptic uranium(IV) thiolate to have been crystallographically characterized, U(SMes*) 4 (4), was isolated from the reaction of U(BH 4 ) 4 and KSMes*. The first homoleptic thiolate complex of uranium(III), U(SMes*) 3 (5), was synthesized by proton-lysis of U[N(SiMe 3 ) 2 ] 3 with HSMes* in cyclohexane. The crystal structure of 5 exhibits the novel η 3 ligation mode for the aryl-thiolate ligand. Comparison of the crystal structure of 5 with those of the isomorphous lanthanide congeners Ln(SMes*) 3 (Ln) La, Ce, Pr, and Nd) indicates that the U-S, U-C ipso , and U-C ortho bond lengths are shorter than the corresponding ones in the 4f-element analogues, when taking into account the variation in the ionic radii of the metals. The distance between the uranium and the carbon atoms involved in the U center dot center dot center dot H-C ε agostic interaction of each thiolate ligand is shorter, by ∼ 0.05 angstrom, than that expected from a purely ionic bonding model. The lanthanide( III)/actinide(III) differentiation was analyzed by density functional theory (DFT). The nature of the M-S bond is shown to be ionic strongly polarized at the sulfur for M) U and ion-covalent (i.e. strongly ionic with low orbital interaction), for M) Ln. The strength of the U center dot center dot center dot H-C ε agostic interaction is proposed to be controlled by the maximization of the interaction between U + and S - under steric constraints. The η 3 ligation mode of the aryl-thiolate ligand is also obtained from DFT. (authors)

  6. U(SMes*)n, (n = 3, 4) and Ln(SMes*)3 (Ln = La, Ce, Pr, Nd): lanthanide(III)/actinide(III) differentiation in agostic interactions and an unprecedented eta3 ligation mode of the arylthiolate ligand, from X-ray diffraction and DFT analysis.

    Science.gov (United States)

    Roger, Mathieu; Barros, Noémi; Arliguie, Thérèse; Thuéry, Pierre; Maron, Laurent; Ephritikhine, Michel

    2006-07-12

    Reaction of U(NEt(2))(4) with HS-2,4,6-(t)Bu(3)C(6)H(2) (HSMes) gave U(SMes)(3)(NEt(2))(py) (1), whereas similar treatment of U[N(SiMe(3))SiMe(2)CH(2)][N(SiMe(3))(2)](2) afforded U(SMes)[N(SiMe(3))(2)](3) (2) and U(SMes)(3)[N(SiMe(3))(2)]. The first neutral homoleptic uranium(IV) thiolate to have been crystallographically characterized, U(SMes)(4) (4), was isolated from the reaction of U(BH(4))(4) and KSMes. The first homoleptic thiolate complex of uranium(III), U(SMes)(3) (5), was synthesized by protonolysis of U[N(SiMe(3))(2)](3) with HSMes in cyclohexane. The crystal structure of 5 exhibits the novel eta(3) ligation mode for the arylthiolate ligand. Comparison of the crystal structure of 5 with those of the isomorphous lanthanide congeners Ln(SMes)(3) (Ln = La, Ce, Pr, and Nd) indicates that the U-S, U-C(ipso)(), and U-C(ortho)() bond lengths are shorter than the corresponding ones in the 4f-element analogues, when taking into account the variation in the ionic radii of the metals. The distance between the uranium and the carbon atoms involved in the U...H-C epsilon agostic interaction of each thiolate ligand is shorter, by approximately 0.05 A, than that expected from a purely ionic bonding model. The lanthanide(III)/actinide(III) differentiation was analyzed by density functional theory (DFT). The nature of the M-S bond is shown to be ionic strongly polarized at the sulfur for M = U and iono-covalent (i.e. strongly ionic with low orbital interaction), for M = Ln. The strength of the U...H-C epsilon agostic interaction is proposed to be controlled by the maximization of the interaction between U(+) and S(-) under steric constraints. The eta(3) ligation mode of the arylthiolate ligand is also obtained from DFT.

  7. The intrinsically disordered structural platform of the plant defence hub protein RPM1-interacting protein 4 provides insights into its mode of action in the host-pathogen interface and evolution of the nitrate-induced domain protein family.

    Science.gov (United States)

    Sun, Xiaolin; Greenwood, David R; Templeton, Matthew D; Libich, David S; McGhie, Tony K; Xue, Bin; Yoon, Minsoo; Cui, Wei; Kirk, Christopher A; Jones, William T; Uversky, Vladimir N; Rikkerink, Erik H A

    2014-09-01

    Arabidopsis thaliana (At) RPM1-interacting protein 4 (RIN4), targeted by many defence-suppressing bacterial type III effectors and monitored by several resistance proteins, regulates plant immune responses to pathogen-associated molecular patterns and type III effectors. Little is known about the overall protein structure of AtRIN4, especially in its unbound form, and the relevance of structure to its diverse biological functions. AtRIN4 contains two nitrate-induced (NOI) domains and is a member of the NOI family. Using experimental and bioinformatic approaches, we demonstrate that the unbound AtRIN4 is intrinsically disordered under physiological conditions. The intrinsically disordered polypeptide chain of AtRIN4 is interspersed with molecular recognition features (MoRFs) and anchor-identified long-binding regions, potentially allowing it to undergo disorder-to-order transitions upon binding to partner(s). A poly-l-proline II structure, often responsible for protein recognition, is also identified in AtRIN4. By performing bioinformatics analyses on RIN4 homologues from different plant species and the NOI proteins from Arabidopsis, we infer the conservation of intrinsic disorder, MoRFs and long-binding regions of AtRIN4 in other plant species and the NOI family. Intrinsic disorder and MoRFs could provide RIN4 proteins with the binding promiscuity and plasticity required to act as hubs in a pivotal position within plant defence signalling cascades. © 2014 FEBS.

  8. Majorana Zero Modes in Graphene

    Directory of Open Access Journals (Sweden)

    P. San-Jose

    2015-12-01

    Full Text Available A clear demonstration of topological superconductivity (TS and Majorana zero modes remains one of the major pending goals in the field of topological materials. One common strategy to generate TS is through the coupling of an s-wave superconductor to a helical half-metallic system. Numerous proposals for the latter have been put forward in the literature, most of them based on semiconductors or topological insulators with strong spin-orbit coupling. Here, we demonstrate an alternative approach for the creation of TS in graphene-superconductor junctions without the need for spin-orbit coupling. Our prediction stems from the helicity of graphene’s zero-Landau-level edge states in the presence of interactions and from the possibility, experimentally demonstrated, of tuning their magnetic properties with in-plane magnetic fields. We show how canted antiferromagnetic ordering in the graphene bulk close to neutrality induces TS along the junction and gives rise to isolated, topologically protected Majorana bound states at either end. We also discuss possible strategies to detect their presence in graphene Josephson junctions through Fraunhofer pattern anomalies and Andreev spectroscopy. The latter, in particular, exhibits strong unambiguous signatures of the presence of the Majorana states in the form of universal zero-bias anomalies. Remarkable progress has recently been reported in the fabrication of the proposed type of junctions, which offers a promising outlook for Majorana physics in graphene systems.

  9. Action Research and Interactive Research

    DEFF Research Database (Denmark)

    Svensson, lennart; Nielsen, Kurt Aagaard

    2006-01-01

    The authors present trends in Nordic action research. They ask critical questions in the development towards mode 2 and points out alternative roads for a scientific consolidation of action research and interactive research.......The authors present trends in Nordic action research. They ask critical questions in the development towards mode 2 and points out alternative roads for a scientific consolidation of action research and interactive research....

  10. The Integrated Mode Management Interface

    Science.gov (United States)

    Hutchins, Edwin

    1996-01-01

    Mode management is the processes of understanding the character and consequences of autoflight modes, planning and selecting the engagement, disengagement and transitions between modes, and anticipating automatic mode transitions made by the autoflight system itself. The state of the art is represented by the latest designs produced by each of the major airframe manufacturers, the Boeing 747-400, the Boeing 777, the McDonnell Douglas MD-11, and the Airbus A320/A340 family of airplanes. In these airplanes autoflight modes are selected by manipulating switches on the control panel. The state of the autoflight system is displayed on the flight mode annunciators. The integrated mode management interface (IMMI) is a graphical interface to autoflight mode management systems for aircraft equipped with flight management computer systems (FMCS). The interface consists of a vertical mode manager and a lateral mode manager. Autoflight modes are depicted by icons on a graphical display. Mode selection is accomplished by touching (or mousing) the appropriate icon. The IMMI provides flight crews with an integrated interface to autoflight systems for aircraft equipped with flight management computer systems (FMCS). The current version is modeled on the Boeing glass-cockpit airplanes (747-400, 757/767). It runs on the SGI Indigo workstation. A working prototype of this graphics-based crew interface to the autoflight mode management tasks of glass cockpit airplanes has been installed in the Advanced Concepts Flight Simulator of the CSSRF of NASA Ames Research Center. This IMMI replaces the devices in FMCS equipped airplanes currently known as mode control panel (Boeing), flight guidance control panel (McDonnell Douglas), and flight control unit (Airbus). It also augments the functions of the flight mode annunciators. All glass cockpit airplanes are sufficiently similar that the IMMI could be tailored to the mode management system of any modern cockpit. The IMMI does not replace the

  11. Electron spin-lattice relaxation mechanisms of radiation produced trapped electrons and hydrogen atoms in aqueous and organic glassy matrices. Modulation of electron nuclear dipolar interaction by tunnelling modes in a glassy matrix. [. gamma. rays

    Energy Technology Data Exchange (ETDEWEB)

    Bowman, M K; Kevan, L [Wayne State Univ., Detroit, Mich. (USA). Dept. of Chemistry

    1977-01-01

    The spin lattice relaxation of trapped electrons in aqueous and organic glasses and trapped hydrogen atoms in phosphoric acid glass has been directly studied as a function of temperature by the saturation recovery method. Below 50 to 100 K, the major spin lattice relaxation mechanism involves modulation of the electron nuclear dipolar (END) interaction with nuclei in the radical's environment by tunnelling of those nuclei between two or more positions. This relaxation mechanism occurs with high efficiency and has a characteristic linear temperature dependence. The tunnelling nuclei around trapped electrons do not seem to involve the nearest neighbor nuclei which are oriented by the electron in the process of solvation. Instead the tunnelling nuclei typically appear to be next nearest neighbors to the trapped electron. The identities of the tunnelling nuclei have been deduced by isotopic substitution and are attributed to: Na in 10 mol dm/sup -3/ NaOH aqueous glass, ethyl protons in ethanol glass, methyl protons in methanol glass and methyl protons in MTHF glass. For trapped hydrogen atoms in phosphoric acid, the phosphorus nuclei appear to be the effective tunnelling nuclei. Below approximately 10 K the spin lattice relaxation is dominated by a temperature independent cross relaxation term for H atoms in phosphoric acid glass and for electrons in 10 mol dm/sup -3/ NaOH aqueous glass, but not for electrons in organic glasses. This is compared with recent electron-electron double resonance studies of cross relaxation in these glasses. The spin lattice relaxation of O/sup -/ formed in 10 mol dm/sup -3/ NaOH aqueous glass was also studied and found to be mainly dominated by a Raman process with an effective Debye temperature of about 100 K.

  12. Impact of magnetic fields on the R-mode instability

    International Nuclear Information System (INIS)

    Rezzolla, L.

    2001-01-01

    The instability of r-mode oscillations in rapidly rotating neutron stars has attracted attention as a potential mechanism for producing high frequency, almost periodic gravitational waves. The analyses carried out so far have shown the existence of the instability and have considered damping by shear and bulk viscosity, as well as the interaction with a solid star crust. However, the magnetohydrodynamic coupling of the modes with a stellar magnetic field, which is likely to be present, has not been fully investigated yet. Here we discuss the relevance of a magnetic field, its modifications under the action of the r-mode instability, and how the interaction between r-mode oscillations and a magnetic field might limit the onset and duration of the instability. (author)

  13. Unconventional geometric quantum computation in a two-mode cavity

    International Nuclear Information System (INIS)

    Wu Chunfeng; Wang Zisheng; Feng Xunli; Lai, C. H.; Oh, C. H.; Goan, H.-S.; Kwek, L. C.

    2007-01-01

    We propose a scheme for implementing unconventional geometric quantum computation by using the interaction of two atoms with a two-mode cavity field. The evolution of the system results in a nontrivial two-qubit phase gate. The operation of the proposed gate involves only metastable states of the atom and hence is not affected by spontaneous emission. The effect of cavity decay on the gate is investigated. It is shown that the evolution time of the gate in the two-mode case is less than that in the single-mode case proposed by Feng et al. [Phys. Rev. A 75, 052312 (2007)]. Thus the gate can be more decay tolerant than the previous one. The scheme can also be generalized to a system consisting of two atoms interacting with an N-mode cavity field

  14. Cladding modes of optical fibers: properties and applications

    International Nuclear Information System (INIS)

    Ivanov, Oleg V; Nikitov, Sergei A; Gulyaev, Yurii V

    2006-01-01

    One of the new methods of fiber optics uses cladding modes for controlling propagation of radiation in optical fibers. This paper reviews the results of studies on the propagation, excitation, and interaction of cladding modes in optical fibers. The resonance between core and cladding modes excited by means of fiber Bragg gratings, including tilted ones, is analyzed. Propagation of cladding modes in microstructured fibers is considered. The most frequently used method of exciting cladding modes is described, based on the application of long-period fiber gratings. Examples are presented of long-period gratings used as sensors and gain equalizers for fiber amplifiers, as well as devices for coupling light into and out of optical fibers. (instruments and methods of investigation)

  15. Nondestructive evaluation of helicopter rotor blades using guided Lamb modes.

    Science.gov (United States)

    Chakrapani, Sunil Kishore; Barnard, Daniel; Dayal, Vinay

    2014-03-01

    This paper presents an application for turning and direct modes in a complex composite laminate structure. The propagation and interaction of turning modes and fundamental Lamb modes are investigated in the skin, spar and web sections of a helicopter rotor blade. Finite element models were used to understand the various mode conversions at geometric discontinuities such as web-spar joints. Experimental investigation was carried out with the help of air coupled ultrasonic transducers. The turning and direct modes were confirmed with the help of particle displacements and velocities. Experimental B-Scans were performed on damaged and undamaged samples for qualitative and quantitative assessment of the structure. A strong correlation between the numerical and experimental results was observed and reported. Copyright © 2013 Elsevier B.V. All rights reserved.

  16. Separate Poles Mode for Large-Capacity HVDC System

    Science.gov (United States)

    Zhu, Lin; Gao, Qin

    2017-05-01

    This paper proposes a novel connection mode, separate poles mode (SPM), for large-capacity HVDC systems. The proposed mode focuses on the core issues of HVDC connection in interconnected power grids and principally aims at increasing effective electric distance between poles, which helps to mitigate the interaction problems between AC system and DC system. Receiving end of bipolar HVDC has been divided into different inverter stations under the mode, and thus significantly alleviates difficulties in power transmission and consumption of receiving-end AC grids. By investigating the changes of multi-feed short-circuit ratio (MISCR), finding that HVDC with SPM shows critical impacts upon itself and other HVDC systems with conventional connection mode, which demonstrates that SPM can make balance between MISCR increase and short-circuit current limit.

  17. Modes of Governance in the Dutch Social Housing Sector

    OpenAIRE

    Ruys, P.H.M.; Bruil, J.; Dix, H.G.

    2007-01-01

    Abstract: We describe and analyze five consecutive modes of governance in the Dutch social housing sector. We compare these institutional forms with the five policy values that the sector was assumed to realize. For that purpose we propose and use a new, analytical framework based on a separation principle that is applied to the coercion domain (the governance of transactions) as well as to the interaction domain (the welfare values). The consecutive modes of governance were introduced to cop...

  18. Review of tearing mode stabilization by RF power in tokamaks

    International Nuclear Information System (INIS)

    Giruzzi, G.; Zabiego, M.; Zohm, H.

    1999-01-01

    Control of tearing modes by means of heating and current drive inside the magnetic islands is one of the most important applications of RF power in tokamak reactors. The theoretical basis of this concept is reviewed, focusing on aspects related to RF-plasma interaction. Applications to the stabilization of neoclassical tearing modes in ITER by Electron Cyclotron Current Drive are presented to illustrate the basic physical dependences. The most significant experimental results and prospects for future applications are also discussed

  19. Linear stability of tearing modes

    International Nuclear Information System (INIS)

    Cowley, S.C.; Kulsrud, R.M.; Hahm, T.S.

    1986-05-01

    This paper examines the stability of tearing modes in a sheared slab when the width of the tearing layer is much smaller than the ion Larmor radius. The ion response is nonlocal, and the quasineutrality retains its full integal form. An expansion procedure is introduced to solve the quasineutrality equation in powers of the width of the tearing layer over the ion Larmor radius. The expansion procedure is applied to the collisionless and semi-collisional tearing modes. The first order terms in the expansion we find to be strongly stabilizing. The physics of the mode and of the stabilization is discussed. Tearing modes are observed in experiments even though the slab theory predicts stability. It is proposed that these modes grow from an equilibrium with islands at the rational surfaces. If the equilibrium islands are wider than the ion Larmor radius, the mode is unstable when Δ' is positive

  20. Audit mode change, corporate governance

    OpenAIRE

    Limei Cao; Wanfu Li; Limin Zhang

    2015-01-01

    This study investigates changes in audit strategy in China following the introduction of risk-based auditing standards rather than an internal control-based audit mode. Specifically, we examine whether auditors are implementing the risk-based audit mode to evaluate corporate governance before distributing audit resources. The results show that under the internal control-based audit mode, the relationship between audit effort and corporate governance was weak. However, implementation of the ri...

  1. Amplification of magnetic modes in laser-created plasmas

    International Nuclear Information System (INIS)

    Matte, J.P.; Bendib, A.; Luciani, J.F.

    1987-01-01

    The amplification of magnetic (Weibel) modes in laser-plasma interaction is investigated by use of unperturbed distribution functions given by Fokker-Planck simulations and a dispersion relation valid for all collisionality regimes. In the five cases studied, a strongly growing mode is found in the underdense plasma, where v-bar/sub x/ 2 2 , and the usual slowly growing one in the overdense plasma. The first mode grows convectively outwards by more than 10 4 . The convection velocities are found to be very different from Nernst values

  2. Hyper-resistivity produced by tearing mode turbulence

    International Nuclear Information System (INIS)

    Strauss, H.R.

    1986-01-01

    Tearing mode turbulence produces a hyper-resistivity or effective anomalous electron viscosity. The hyper-resistivity is calculated for the mean magnetic field quasilinearly, and for long-wavelength modes using the direct interaction approximation. The hyper-resistivity accounts for current relaxation in reversed-field pinch experiments, and gives a magnetic fluctuation sealing of S -1 /sup // 3 . It causes enhanced tearing mode growth rates in the turbulent phase of tokamak disruptions. In astrophysics, it limits magnetic energy growth due to the dynamo effect, and may explain rapid reconnection phenomena such as solar flares

  3. Observation and explanation of the JET n=0 chirping mode

    Energy Technology Data Exchange (ETDEWEB)

    Boswell, C.J. [Plasma Science and Fusion Center, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States)]. E-mail: christopher.boswell@navy.mil; Berk, H.L. [Institute for Fusion Studies, University of Texas at Austin, Austin, TX 78712-1060 (United States); Borba, D.N. [Centro de Fusao Nuclear Associacao Euratom-IST, Instituto Superior Tecnico, 1049001 Lisbon (Portugal); EFDA Close Support Unit, Culham Science Centre, OX14 3DB (United Kingdom); Johnson, T. [Alfven Laboratory, KTH, Euratom-VR Association (Sweden); Pinches, S.D. [Max-Planck Institute for Plasma Physics, EURATOM Association, D-85748 Garching (Germany); Sharapov, S.E. [Euratom-UKAEA Fusion Association, Culham Science Centre, Abingdon OX14 3DB (United Kingdom)

    2006-10-09

    Persistent rapid up and down frequency chirping modes with a toroidal mode number of zero (n=0) have been observed in the JET tokamak when energetic ions, with a mean energy {approx}500keV, were created by high field side ion cyclotron resonance frequency heating. This heating method enables the formation of an energetically inverted ion distribution function that allows ions to spontaneously excite the observed instability, identified as a global geodesic acoustic mode. The interpretation is that phase space structures form and interact with the fluid zonal flow to produce the pronounced frequency chirping.

  4. A Systematic Assessment of Empirical Research on Foreign Entry Mode

    DEFF Research Database (Denmark)

    Wulff, Jesper

    2016-01-01

    of dimensions. Findings Findings question the frequent use of commonly used measures (e.g. advertising intensity) and control variables (e.g. firm size) and suggest that statements about the importance of mode choice for subsidiary performance may be premature. Methodologically, this study identifies critical...... issues with regard to interpretation of interactions and the entry mode choice set. Research limitations/implications This study limits itself to study the direction of relationships and does not analyze effect sizes. Further, future research may benefit from broadening the entry mode choice by extending...

  5. Monoclonal antibody fragment removal mediated by mixed mode resins.

    Science.gov (United States)

    O'Connor, Ellen; Aspelund, Matthew; Bartnik, Frank; Berge, Mark; Coughlin, Kelly; Kambarami, Mutsa; Spencer, David; Yan, Huiming; Wang, William

    2017-05-26

    Efforts to increase monoclonal antibody expression in cell culture can result in the presence of fragmented species requiring removal in downstream processing. Capto adhere, HEA Hypercel, and PPA Hypercel anion exchange/hydrophobic interaction mixed mode resins were evaluated for their fragment removal capabilities and found to separate large hinge IgG1 antibody fragment (LHF) from monomer. Removal of greater than 75% of LHF population occurred at pH 8 and low conductivity. The mechanism of fragment removal was investigated in two series of experiments. The first experimental series consisted of comparison to chromatographic behavior on corresponding single mode resins. Both single mode anion exchange and hydrophobic interaction resins failed to separate LHF. The second experimental series studied the impact of phase modifiers, ethylene glycol, urea, and arginine on the mixed mode mediated removal. The addition of ethylene glycol decreased LHF removal by half. Further decreases in LHF separation were seen upon incubation with urea and arginine. Therefore, it was discovered that the purification is the result of a mixed mode phenomena dominated by hydrophobic interaction and hydrogen bonding effects. The site of interaction between the LHF and mixed mode resin was determined by chemical labeling of lysine residues with sulfo-NHS acetate. The labeling identified the antibody hinge and light chain regions as mediating the fragment separation. Sequence analysis showed that under separation conditions, a hydrophobic proline patch and hydrogen bonding serine and threonine residues mediate the hinge interaction with the Capto adhere ligand. Additionally, a case study is presented detailing the optimization of fragment removal using Capto adhere resin to achieve purity and yield targets in a manufacturing facility. This study demonstrated that mixed mode resins can be readily integrated into commercial antibody platform processes when additional chromatographic abilities

  6. Zero modes and entanglement entropy

    Energy Technology Data Exchange (ETDEWEB)

    Yazdi, Yasaman K. [Perimeter Institute for Theoretical Physics,31 Caroline St. N., Waterloo, ON, N2L 2Y5 (Canada); Department of Physics and Astronomy, University of Waterloo,200 University Avenue West, Waterloo, ON, N2L 3G1 (Canada)

    2017-04-26

    Ultraviolet divergences are widely discussed in studies of entanglement entropy. Also present, but much less understood, are infrared divergences due to zero modes in the field theory. In this note, we discuss the importance of carefully handling zero modes in entanglement entropy. We give an explicit example for a chain of harmonic oscillators in 1D, where a mass regulator is necessary to avoid an infrared divergence due to a zero mode. We also comment on a surprising contribution of the zero mode to the UV-scaling of the entanglement entropy.

  7. Normal modes of Bardeen discs

    International Nuclear Information System (INIS)

    Verdaguer, E.

    1983-01-01

    The short wavelength normal modes of self-gravitating rotating polytropic discs in the Bardeen approximation are studied. The discs' oscillations can be seen in terms of two types of modes: the p-modes whose driving forces are pressure forces and the r-modes driven by Coriolis forces. As a consequence of differential rotation coupling between the two takes place and some mixed modes appear, their properties can be studied under the assumption of weak coupling and it is seen that they avoid the crossing of the p- and r-modes. The short wavelength analysis provides a basis for the classification of the modes, which can be made by using the properties of their phase diagrams. The classification is applied to the large wavelength modes of differentially rotating discs with strong coupling and to a uniformly rotating sequence with no coupling, which have been calculated in previous papers. Many of the physical properties and qualitative features of these modes are revealed by the analysis. (author)

  8. Magnetorheological dampers in shear mode

    International Nuclear Information System (INIS)

    Wereley, N M; Cho, J U; Choi, Y T; Choi, S B

    2008-01-01

    In this study, three types of shear mode damper using magnetorheological (MR) fluids are theoretically analyzed: linear, rotary drum, and rotary disk dampers. The damping performance of these shear mode MR dampers is characterized in terms of the damping coefficient, which is the ratio of the equivalent viscous damping at field-on status to the damping at field-off status. For these three types of shear mode MR damper, the damping coefficient or dynamic range is derived using three different constitutive models: the Bingham–plastic, biviscous, and Herschel–Bulkley models. The impact of constitutive behavior on shear mode MR dampers is theoretically presented and compared

  9. Mode Combinations and International Operations

    DEFF Research Database (Denmark)

    Benito, Gabriel R. G.; Petersen, Bent; Welch, Lawrence S.

    2011-01-01

    reveals that companies tend to combine modes of operation; thereby producing unique foreign operation mode “packages” for given activities and/or countries, and that the packages are liable to be modified over time – providing a potentially important optional path for international expansion. Our data...... key markets (China, UK and USA) as the basis for an exploration of the extent to which, and how and why, companies combine clearly different foreign operation modes. We examine their use of foreign operation mode combinations within given value activities as well as within given countries. The study...

  10. Mode Combinations and International Operations

    DEFF Research Database (Denmark)

    Benito, Gabriel R. G.; Petersen, Bent; Welch, Lawrence S.

    2011-01-01

    reveals that companies tend to combine modes of operation; thereby producing unique foreign operation mode “packages” for given activities and/or countries, and that the packages are liable to be modified over time—providing a potentially important optional path for international expansion. The data show...... markets (China, UK and USA) is used as the basis for an exploration of the extent to which, and how and why, companies combine clearly different foreign operation modes. We examine their use of foreign operation mode combinations within given value activities as well as within given countries. The study...

  11. Scissors Mode of Dipolar Quantum Droplets of Dysprosium Atoms

    Science.gov (United States)

    Ferrier-Barbut, Igor; Wenzel, Matthias; Böttcher, Fabian; Langen, Tim; Isoard, Mathieu; Stringari, Sandro; Pfau, Tilman

    2018-04-01

    We report on the observation of the scissors mode of a single dipolar quantum droplet. The existence of this mode is due to the breaking of the rotational symmetry by the dipole-dipole interaction, which is fixed along an external homogeneous magnetic field. By modulating the orientation of this magnetic field, we introduce a new spectroscopic technique for studying dipolar quantum droplets. This provides a precise probe for interactions in the system, allowing us to extract a background scattering length for 164Dy of 69 (4 )a0 . Our results establish an analogy between quantum droplets and atomic nuclei, where the existence of the scissors mode is also only due to internal interactions. They further open the possibility to explore physics beyond the available theoretical models for strongly dipolar quantum gases.

  12. Ballooning modes or Fourier modes in a toroidal plasma?

    International Nuclear Information System (INIS)

    Connor, J.W.; Taylor, J.B.

    1987-01-01

    The relationship between two different descriptions of eigenmodes in a torus is investigated. In one the eigenmodes are similar to Fourier modes in a cylinder and are highly localized near a particular rational surface. In the other they are the so-called ballooning modes that extend over many rational surfaces. Using a model that represents both drift waves and resistive interchanges the transition from one of these structures to the other is investigated. In this simplified model the transition depends on a single parameter which embodies the competition between toroidal coupling of Fourier modes (which enhances ballooning) and variation in frequency of Fourier modes from one rational surface to another (which diminishes ballooning). As the coupling is increased each Fourier mode acquires a sideband on an adjacent rational surface and these sidebands then expand across the radius to form the extended mode described by the conventional ballooning mode approximation. This analysis shows that the ballooning approximation is appropriate for drift waves in a tokamak but not for resistive interchanges in a pinch. In the latter the conventional ballooning effect is negligible but they may nevertheless show a ballooning feature. This is localized near the same rational surface as the primary Fourier mode and so does not lead to a radially extended structure

  13. Development of the Modes of Collaboration framework

    Science.gov (United States)

    Pawlak, Alanna; Irving, Paul W.; Caballero, Marcos D.

    2018-01-01

    Group work is becoming increasingly common in introductory physics classrooms. Understanding how students engage in these group learning environments is important for designing and facilitating productive learning opportunities for students. We conducted a study in which we collected video of groups of students working on conceptual electricity and magnetism problems in an introductory physics course. In this setting, students needed to negotiate a common understanding and coordinate group decisions in order to complete the activity successfully. We observed students interacting in several distinct ways while solving these problems. Analysis of these observations focused on identifying the different ways students interacted and articulating what defines and distinguishes them, resulting in the development of the modes of collaboration framework. The modes of collaboration framework defines student interactions along three dimensions: social, discursive, and disciplinary content. This multidimensional approach offers a unique lens through which to consider group work and provides a flexibility that could allow the framework to be adapted for a variety of contexts. We present the framework and several examples of its application here.

  14. Spatial-mode switchable ring fiber laser based on low mode-crosstalk all-fiber mode MUX/DEMUX

    Science.gov (United States)

    Ren, Fang; Yu, Jinyi; Wang, Jianping

    2018-05-01

    We report an all-fiber ring laser that emits linearly polarized (LP) modes based on the intracavity all-fiber mode multiplexer/demultiplexer (MUX/DEMUX). Multiple LP modes in ring fiber laser are generated by taking advantage of mode MUX/DEMUX. The all-fiber mode MUX/DEMUX are composed of cascaded mode-selective couplers (MSCs). The output lasing mode of the ring fiber laser can be switched among the three lowest-order LP modes by employing combination of a mode MUX and a simple N × 1 optical switch. The slope efficiencies, optical spectra and mode profiles are measured.

  15. Interactive Environment Design in Smart City

    Science.gov (United States)

    Deng, DeXiang; Chen, LanSha; Zhou, Xi

    2017-08-01

    The interactive environment design of smart city is not just an interactive progress or interactive mode design, rather than generate an environment such as the “organic” life entity as human beings through interactive design, forming a smart environment with perception, memory, thinking, and reaction.

  16. Remark on the computation of mode sums

    International Nuclear Information System (INIS)

    Allen, Theodore J.; Olsson, M. G.; Schmidt, Jeffrey R.

    2000-01-01

    The computation of mode sums of the types encountered in basic quantum field theoretic applications is addressed with an emphasis on their expansions into functions of distance that can be interpreted as potentials. We show how to regularize and calculate the Casimir energy for the continuum Nambu-Goto string with massive ends as well as for the discrete Isgur-Paton non-relativistic string with massive ends. As an additional example, we examine the effect on the interquark potential of a constant Kalb-Ramond field strength interacting with a QCD string. (c) 2000 The American Physical Society

  17. Mixed Mode cohesive law with interface dilatation

    DEFF Research Database (Denmark)

    Sørensen, Bent F.; Goutianos, Stergios

    2014-01-01

    displacements. As the crack faces displace relatively to each other, the roughness asperities ride on top of each other and result in an opening (dilatation) in the normal direction. Furthermore, the interaction of the crack surfaces in the contact zone gives rise to compressive normal stresses and frictional...... shear stresses opposing the crack face displacements. A phenomenological Mixed Mode cohesive zone law, derived from a potential function, is developed to describe the above mentioned fracture behaviour under monotonic opening. The interface dilatation introduces two new lengths. The cohesive law...

  18. Cavity enhanced interference of orthogonal modes in a birefringent medium

    Science.gov (United States)

    Kolluru, Kiran; Saha, Sudipta; Gupta, S. Dutta

    2018-03-01

    Interference of orthogonal modes in a birefringent crystal mediated by a rotator is known to lead to interesting physical effects (Solli et al., 2003). In this paper we show that additional feedback offered by a Fabry-Perot cavity (containing the birefringent crystal and the rotator) can lead to a novel strong interaction regime. Usual signatures of the strong interaction regime like the normal mode splitting and avoided crossings, sensitive to the rotator orientation, are reported. A high finesse cavity is shown to offer an optical setup for measuring small angles. The results are based on direct calculations of the cavity transmissions along with an analysis of its dispersion relation.

  19. Generation of high order modes

    CSIR Research Space (South Africa)

    Ngcobo, S

    2012-07-01

    Full Text Available with the location of the Laguerre polynomial zeros. The Diffractive optical element is used to shape the TEM00 Gassian beam and force the laser to operate on a higher order TEMp0 Laguerre-Gaussian modes or high order superposition of Laguerre-Gaussian modes...

  20. Homogeneous modes of cosmological instantons

    Energy Technology Data Exchange (ETDEWEB)

    Gratton, Steven; Turok, Neil

    2001-06-15

    We discuss the O(4) invariant perturbation modes of cosmological instantons. These modes are spatially homogeneous in Lorentzian spacetime and thus not relevant to density perturbations. But their properties are important in establishing the meaning of the Euclidean path integral. If negative modes are present, the Euclidean path integral is not well defined, but may nevertheless be useful in an approximate description of the decay of an unstable state. When gravitational dynamics is included, counting negative modes requires a careful treatment of the conformal factor problem. We demonstrate that for an appropriate choice of coordinate on phase space, the second order Euclidean action is bounded below for normalized perturbations and has a finite number of negative modes. We prove that there is a negative mode for many gravitational instantons of the Hawking-Moss or Coleman{endash}De Luccia type, and discuss the associated spectral flow. We also investigate Hawking-Turok constrained instantons, which occur in a generic inflationary model. Implementing the regularization and constraint proposed by Kirklin, Turok and Wiseman, we find that those instantons leading to substantial inflation do not possess negative modes. Using an alternate regularization and constraint motivated by reduction from five dimensions, we find a negative mode is present. These investigations shed new light on the suitability of Euclidean quantum gravity as a potential description of our universe.

  1. Homogeneous modes of cosmological instantons

    International Nuclear Information System (INIS)

    Gratton, Steven; Turok, Neil

    2001-01-01

    We discuss the O(4) invariant perturbation modes of cosmological instantons. These modes are spatially homogeneous in Lorentzian spacetime and thus not relevant to density perturbations. But their properties are important in establishing the meaning of the Euclidean path integral. If negative modes are present, the Euclidean path integral is not well defined, but may nevertheless be useful in an approximate description of the decay of an unstable state. When gravitational dynamics is included, counting negative modes requires a careful treatment of the conformal factor problem. We demonstrate that for an appropriate choice of coordinate on phase space, the second order Euclidean action is bounded below for normalized perturbations and has a finite number of negative modes. We prove that there is a negative mode for many gravitational instantons of the Hawking-Moss or ColemanendashDe Luccia type, and discuss the associated spectral flow. We also investigate Hawking-Turok constrained instantons, which occur in a generic inflationary model. Implementing the regularization and constraint proposed by Kirklin, Turok and Wiseman, we find that those instantons leading to substantial inflation do not possess negative modes. Using an alternate regularization and constraint motivated by reduction from five dimensions, we find a negative mode is present. These investigations shed new light on the suitability of Euclidean quantum gravity as a potential description of our universe

  2. Intelligence and musical mode preference

    DEFF Research Database (Denmark)

    Bonetti, Leonardo; Costa, Marco

    2016-01-01

    The relationship between fluid intelligence and preference for major–minor musical mode was investigated in a sample of 80 university students. Intelligence was assessed by the Raven’s Advanced Progressive Matrices. Musical mode preference was assessed by presenting 14 pairs of musical stimuli...... differences at the cognitive and personality level related to the enjoyment of sad music....

  3. Mode coupling trigger of neoclassical magnetohydrodynamic tearing modes in tokamaks

    International Nuclear Information System (INIS)

    Gianakon, T.A.; Hegna, C.C.; Callen, J.D.

    1997-05-01

    Numerical studies of the nonlinear evolution of coupled magnetohydrodynamic - type tearing modes in three-dimensional toroidal geometry with neoclassical effects are presented. The inclusion of neoclassical physics introduces an additional free-energy source for the nonlinear formation of magnetic islands through the effects of a bootstrap current in Ohm's law. The neoclassical tearing mode is demonstrated to be destabilized in plasmas which are otherwise Δ' stable, albeit once a threshold island width is exceeded. A possible mechanism for exceeding or eliminating this threshold condition is demonstrated based on mode coupling due to toroidicity with a pre-existing instability at the q = 1 surface

  4. Inter-comb synchronization by mode-to-mode locking

    Science.gov (United States)

    Chun, Byung Jae; Kim, Young-Jin; Kim, Seung-Woo

    2016-08-01

    Two combs of fiber femtosecond lasers are synchronized through the optical frequency reference created by injection-locking of a diode laser to a single comb mode. Maintaining a mHz-level narrow linewidth, the optical frequency reference permits two combs to be stabilized by mode-to-mode locking with a relative stability of 1.52  ×  10-16 at 10 s with a frequency slip of 2.46 mHz. This inter-comb synchronization can be utilized for applications such as dual-comb spectroscopy or ultra-short pulse synthesis without extra narrow-linewidth lasers.

  5. Mode coupling of electron plasma waves

    International Nuclear Information System (INIS)

    Harte, J.A.

    1975-01-01

    The driven coupled mode equations are derived for a two fluid, unequal temperature (T/sub e/ much greater than T/sub i/) plasma in the one-dimensional, electrostatic model and applied to the coupling of electron plasma waves. It is assumed that the electron to ion mass ratio identical with m/sub e/M/sub i// much less than 1 and eta 2 /sub ko/k lambda/sub De/ less than 1 where eta 2 /sub ko/ is the pump wave's power normalized to the plasma thermal energy, k the mode wave number and lambda/sub De/ the electron Debye length. Terms up to quadratic in pump power are retained. The equations describe the linear plasma modes oscillating at the wave number k and at ω/sub ek/, the Bohn Gross frequency, and at Ω/sub k/, the ion acoustic frequency, subject to the damping rates ν/sub ek/ and ν/sub ik/ for electrons and ions and their interactions due to intense high frequency waves E/sub k//sup l/. n/sub o/ is the background density, n/sub ik/ the fluctuating ion density, ω/sub pe/ the plasma frequency

  6. Radiation-induced ηe-modes

    International Nuclear Information System (INIS)

    Shukla, P.K.; Yu, M.Y.

    1990-01-01

    Impurity radiation in a plasma can cause not only static instabilities, but also dynamic instabilities related to the drift and acoustic waves. Radiative instabilities are of much interest because they are associated with relatively high frequency and short wavelength fluctuations, which have been suspected to be responsible for anomalous electron energy transport in tokamak edge plasmas. In this paper, we consider radiation-induced η e instabilities, taking into account electrostatic effects as well as density and temperature inhomogeneities. Also included are the effects of finite gyroradius and dissipation. It is found that the latter can cause strong linear coupling between the modes of interest. The resulting instabilities can have larger growth rates than the static radiative instability. Analytical expressions for the growth rates and instability regimes are given for the limiting cases of practical interest. In particular, it is shown that the η e -mode can couple to both radiation and dissipation to cause resistive instabilities. The parameter regimes of the original radiative as well as the dissipative modes are thereby broadened and shifted because of the interaction. (author) 3 refs

  7. Toroidal mode-conversion in the ICRF

    International Nuclear Information System (INIS)

    Jaun, A.; Hellsten, T.; Chiu, S.C.

    1997-08-01

    Mode-conversion is studied in the ion-cyclotron range of frequencies (ICRF) taking into account the toroidal geometry relevant for tokamaks. The global wavefields obtained using the gyrokinetic toroidal PENN code illustrate how the fast wave propagates to the neighborhood of the ion-ion hybrid resonance, where it is converted to a slow wave which deposits the wave energy through resonant interactions with the particles. The power deposition profiles obtained are dramatically different from the toroidal resonance absorption, showing that Budden's model is not a good approximation in the torus. Radially and poloidally localized wavefield structures characteristic of slow wave eigenmodes are predicted and could in experiments be driven to large amplitudes so as to interact efficiently with fast particles. (author) 5 figs., 1 tab., 48 refs

  8. Damping Measurements of Plasma Modes

    Science.gov (United States)

    Anderegg, F.; Affolter, M.; Driscoll, C. F.

    2010-11-01

    For azimuthally symmetric plasma modes in a magnesium ion plasma, confined in a 3 Tesla Penning-Malmberg trap with a density of n ˜10^7cm-3, we measure a damping rate of 2s-1plasma column, alters the frequency of the mode from 16 KHz to 192 KHz. The oscillatory fluid displacement is small compared to the wavelength of the mode; in contrast, the fluid velocity, δvf, can be large compared to v. The real part of the frequency satisfies a linear dispersion relation. In long thin plasmas (α> 10) these modes are Trivelpiece-Gould (TG) modes, and for smaller values of α they are Dubin spheroidal modes. However the damping appears to be non-linear; initially large waves have weaker exponential damping, which is not yet understood. Recent theoryootnotetextM.W. Anderson and T.M. O'Neil, Phys. Plasmas 14, 112110 (2007). calculates the damping of TG modes expected from viscosity due to ion-ion collisions; but the measured damping, while having a similar temperature and density dependence, is about 40 times larger than calculated. This discrepancy might be due to an external damping mechanism.

  9. Galactic Center Minispiral: Interaction Modes of Neutron Stars

    Czech Academy of Sciences Publication Activity Database

    Zajaček, Michal; Karas, Vladimír; Kunneriath, Devaky

    2015-01-01

    Roč. 55, č. 3 (2015), s. 203-214 ISSN 1210-2709 R&D Projects: GA ČR GB14-37086G Institutional support: RVO:67985815 Keywords : galaxy center * individual objects * Sagittarius A Subject RIV: BN - Astronomy, Celestial Mechanics, Astrophysics

  10. Interaction of solitary pulses in single mode optical fibres | Usman ...

    African Journals Online (AJOL)

    Two solitary waves launched, by way of incidence, into an optical fibre from a single pulse if the pulses are in-phase as understood from results of inverse scattering transform method applied to the cubic nonlinear Schrödinger equations, (CNLSE\\'s). The single CNLSE is then understood to describe evolution of coupled ...

  11. INTERACTION MODE BETWEEN METHYLENE BLUE-Sm(III ...

    African Journals Online (AJOL)

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    between methylene blue (MB)-Sm(III) complex and herring sperm DNA by using acridine orange .... the complex was recorded as KBr pellets on Spectrum One FTIR system (PE Company, USA), ..... mechanism of drugs and drug design.

  12. Mode synthesizing atomic force microscopy and mode-synthesizing sensing

    Science.gov (United States)

    Passian, Ali; Thundat, Thomas George; Tetard, Laurene

    2013-05-17

    A method of analyzing a sample that includes applying a first set of energies at a first set of frequencies to a sample and applying, simultaneously with the applying the first set of energies, a second set of energies at a second set of frequencies, wherein the first set of energies and the second set of energies form a multi-mode coupling. The method further includes detecting an effect of the multi-mode coupling.

  13. Dual-cavity mode converter for a fundamental mode output in an over-moded relativistic backward-wave oscillator

    International Nuclear Information System (INIS)

    Li, Jiawei; Huang, Wenhua; Xiao, Renzhen; Bai, Xianchen; Zhang, Yuchuan; Zhang, Xiaowei; Shao, Hao; Chen, Changhua; Zhu, Qi

    2015-01-01

    A dual-cavity TM 02 –TM 01 mode converter is designed for a dual-mode operation over-moded relativistic backward-wave oscillator. With the converter, the fundamental mode output is achieved. Particle-in-cell simulation shows that the efficiency of beam-wave conversion was over 46% and a pureTM 01 mode output was obtained. Effects of end reflection provided by the mode converter were studied. Adequate TM 01 mode feedback provided by the converter enhances conversion efficiency. The distance between the mode converter and extraction cavity critically affect the generation of microwaves depending on the reflection phase of TM 01 mode feedback

  14. Secondary Instability of Second Modes in Hypersonic Boundary Layers

    Science.gov (United States)

    Li, Fei; Choudhari, Meelan M.; Chang, Chau-Lyan; White, Jeffery A.

    2012-01-01

    Second mode disturbances dominate the primary instability stage of transition in a number of hypersonic flow configurations. The highest amplification rates of second mode disturbances are usually associated with 2D (or axisymmetric) perturbations and, therefore, a likely scenario for the onset of the three-dimensionality required for laminar-turbulent transition corresponds to the parametric amplification of 3D secondary instabilities in the presence of 2D, finite amplitude second mode disturbances. The secondary instability of second mode disturbances is studied for selected canonical flow configurations. The basic state for the secondary instability analysis is obtained by tracking the linear and nonlinear evolution of 2D, second mode disturbances using nonlinear parabolized stability equations. Unlike in previous studies, the selection of primary disturbances used for the secondary instability analysis was based on their potential relevance to transition in a low disturbance environment and the effects of nonlinearity on the evolution of primary disturbances was accounted for. Strongly nonlinear effects related to the self-interaction of second mode disturbances lead to an upstream shift in the upper branch neutral location. Secondary instability computations confirm the previously known dominance of subharmonic modes at relatively small primary amplitudes. However, for the Purdue Mach 6 compression cone configuration, it was shown that a strong fundamental secondary instability can exist for a range of initial amplitudes of the most amplified second mode disturbance, indicating that the exclusive focus on subharmonic modes in the previous applications of secondary instability theory to second mode primary instability may not have been fully justified.

  15. Isoscalar compression modes in relativistic random phase approximation

    International Nuclear Information System (INIS)

    Ma, Zhong-yu; Van Giai, Nguyen.; Wandelt, A.; Vretenar, D.; Ring, P.

    2001-01-01

    Monopole and dipole compression modes in nuclei are analyzed in the framework of a fully consistent relativistic random phase approximation (RRPA), based on effective mean-field Lagrangians with nonlinear meson self-interaction terms. The large effect of Dirac sea states on isoscalar strength distribution functions is illustrated for the monopole mode. The main contribution of Fermi and Dirac sea pair states arises through the exchange of the scalar meson. The effect of vector meson exchange is much smaller. For the monopole mode, RRPA results are compared with constrained relativistic mean-field calculations. A comparison between experimental and calculated energies of isoscalar giant monopole resonances points to a value of 250-270 MeV for the nuclear matter incompressibility. A large discrepancy remains between theoretical predictions and experimental data for the dipole compression mode

  16. Building the Cooperative Teaching Mode of “Team Teaching”

    Directory of Open Access Journals (Sweden)

    Guan Huisheng

    2013-12-01

    Full Text Available Considering the limitation of higher education teaching mode of “only the teacher’s words count”, we build the cooperative teaching mode of “ team teaching” which is humanism-based, student-based and learning-centered. It emphasizes “challenge and cooperation” between teachers and students as well as promotes communication and interaction during the teaching process to ensure open teaching and students’ participation. Compared with the traditional teaching mode, the cooperative teaching mode of “team teaching” highlights its innovative value of teaching and provides a feasible framework during the process of pre-class preparation, teaching guidance, student-teacher debate and conclusion and further study.

  17. Equilibrium calculations and mode analysis

    International Nuclear Information System (INIS)

    Herrnegger, F.

    1987-01-01

    The STEP asymptotic stellarator expansion procedure was used to study the MHD equilibrium and stability properties of stellarator configurations without longitudinal net-current, which also apply to advanced stellarators. The effects of toroidal curvature and magnetic well, and the Shafranov shift were investigated. A classification of unstable modes in toroidal stellarators is given. For WVII-A coil-field configurations having a β value of 1% and a parabolic pressure profile, no free-boundary modes are found. This agrees with the experimental fact that unstable behavior of the plasma column is not observed for this parameter range. So a theoretical β-limit for stability against ideal MHD modes can be estimated by mode analysis for the WVII-A device

  18. Common mode and coupled failure

    International Nuclear Information System (INIS)

    Taylor, J.R.

    1975-10-01

    Based on examples and data from Abnormal Occurence Reports for nuclear reactors, a classification of common mode or coupled failures is given, and some simple statistical models are investigated. (author)

  19. Amplitude damping of vortex modes

    CSIR Research Space (South Africa)

    Dudley, Angela L

    2010-09-01

    Full Text Available An interferometer, mimicking an amplitude damping channel for vortex modes, is presented. Experimentally the action of the channel is in good agreement with that predicted theoretically. Since we can characterize the action of the channel on orbital...

  20. Peeling mode relaxation ELM model

    International Nuclear Information System (INIS)

    Gimblett, C. G.

    2006-01-01

    This paper discusses an approach to modelling Edge Localised Modes (ELMs) in which toroidal peeling modes are envisaged to initiate a constrained relaxation of the tokamak outer region plasma. Relaxation produces both a flattened edge current profile (which tends to further destabilise a peeling mode), and a plasma-vacuum negative current sheet which has a counteracting stabilising influence; the balance that is struck between these two effects determines the radial extent (rE) of the ELM relaxed region. The model is sensitive to the precise position of the mode rational surfaces to the plasma surface and hence there is a 'deterministic scatter' in the results that has an accord with experimental data. The toroidal peeling stability criterion involves the edge pressure, and using this in conjunction with predictions of rE allows us to evaluate the ELM energy losses and compare with experiment. Predictions of trends with the edge safety factor and collisionality are also made