Tungsten and Molybdenum Regulation of Formate Dehydrogenase Expression in Desulfovibrio vulgaris Hildenborough ▿

PubMed Central

da Silva, Sofia M.; Pimentel, Catarina; Valente, Filipa M. A.; Rodrigues-Pousada, Claudina; Pereira, Inês A. C.

2011-01-01

Formate is an important energy substrate for sulfate-reducing bacteria in natural environments, and both molybdenum- and tungsten-containing formate dehydrogenases have been reported in these organisms. In this work, we studied the effect of both metals on the levels of the three formate dehydrogenases encoded in the genome of Desulfovibrio vulgaris Hildenborough, with lactate, formate, or hydrogen as electron donors. Using Western blot analysis, quantitative real-time PCR, activity-stained gels, and protein purification, we show that a metal-dependent regulatory mechanism is present, resulting in the dimeric FdhAB protein being the main enzyme present in cells grown in the presence of tungsten and the trimeric FdhABC3 protein being the main enzyme in cells grown in the presence of molybdenum. The putatively membrane-associated formate dehydrogenase is detected only at low levels after growth with tungsten. Purification of the three enzymes and metal analysis shows that FdhABC3 specifically incorporates Mo, whereas FdhAB can incorporate both metals. The FdhAB enzyme has a much higher catalytic efficiency than the other two. Since sulfate reducers are likely to experience high sulfide concentrations that may result in low Mo bioavailability, the ability to use W is likely to constitute a selective advantage. PMID:21498650

Localizing transcripts to single cells suggests an important role of uncultured deltaproteobacteria in the termite gut hydrogen economy.

PubMed

Rosenthal, Adam Z; Zhang, Xinning; Lucey, Kaitlyn S; Ottesen, Elizabeth A; Trivedi, Vikas; Choi, Harry M T; Pierce, Niles A; Leadbetter, Jared R

2013-10-01

Identifying microbes responsible for particular environmental functions is challenging, given that most environments contain an uncultivated microbial diversity. Here we combined approaches to identify bacteria expressing genes relevant to catabolite flow and to locate these genes within their environment, in this case the gut of a "lower," wood-feeding termite. First, environmental transcriptomics revealed that 2 of the 23 formate dehydrogenase (FDH) genes known in the system accounted for slightly more than one-half of environmental transcripts. FDH is an essential enzyme of H2 metabolism that is ultimately important for the assimilation of lignocellulose-derived energy by the insect. Second, single-cell PCR analysis revealed that two different bacterial types expressed these two transcripts. The most commonly transcribed FDH in situ is encoded by a previously unappreciated deltaproteobacterium, whereas the other FDH is spirochetal. Third, PCR analysis of fractionated gut contents demonstrated that these bacteria reside in different spatial niches; the spirochete is free-swimming, whereas the deltaproteobacterium associates with particulates. Fourth, the deltaproteobacteria expressing FDH were localized to protozoa via hybridization chain reaction-FISH, an approach for multiplexed, spatial mapping of mRNA and rRNA targets. These results underscore the importance of making direct vs. inference-based gene-species associations, and have implications in higher termites, the most successful termite lineage, in which protozoa have been lost from the gut community. Contrary to expectations, in higher termites, FDH genes related to those from the protozoan symbiont dominate, whereas most others were absent, suggesting that a successful gene variant can persist and flourish after a gut perturbation alters a major environmental niche.

Reduction of Carbon Dioxide by a Molybdenum-Containing Formate Dehydrogenase: A Kinetic and Mechanistic Study.

PubMed

Maia, Luisa B; Fonseca, Luis; Moura, Isabel; Moura, José J G

2016-07-20

Carbon dioxide accumulation is a major concern for the ecosystems, but its abundance and low cost make it an interesting source for the production of chemical feedstocks and fuels. However, the thermodynamic and kinetic stability of the carbon dioxide molecule makes its activation a challenging task. Studying the chemistry used by nature to functionalize carbon dioxide should be helpful for the development of new efficient (bio)catalysts for atmospheric carbon dioxide utilization. In this work, the ability of Desulfovibrio desulfuricans formate dehydrogenase (Dd FDH) to reduce carbon dioxide was kinetically and mechanistically characterized. The Dd FDH is suggested to be purified in an inactive form that has to be activated through a reduction-dependent mechanism. A kinetic model of a hysteretic enzyme is proposed to interpret and predict the progress curves of the Dd FDH-catalyzed reactions (initial lag phase and subsequent faster phase). Once activated, Dd FDH is able to efficiently catalyze, not only the formate oxidation (kcat of 543 s(-1), Km of 57.1 μM), but also the carbon dioxide reduction (kcat of 46.6 s(-1), Km of 15.7 μM), in an overall reaction that is thermodynamically and kinetically reversible. Noteworthy, both Dd FDH-catalyzed formate oxidation and carbon dioxide reduction are completely inactivated by cyanide. Current FDH reaction mechanistic proposals are discussed and a different mechanism is here suggested: formate oxidation and carbon dioxide reduction are proposed to proceed through hydride transfer and the sulfo group of the oxidized and reduced molybdenum center, Mo(6+)═S and Mo(4+)-SH, are suggested to be the direct hydride acceptor and donor, respectively.

Physiological and biochemical characterization of the soluble formate dehydrogenase, a molybdoenzyme from Alcaligenes eutrophus.

PubMed Central

Friedebold, J; Bowien, B

1993-01-01

Organoautotrophic growth of Alcaligenes eutrophus on formate was dependent on the presence of molybdate in the medium. Supplementation of the medium with tungstate lead to growth cessation. Corresponding effects of these anions were observed for the activity of the soluble, NAD(+)-linked formate dehydrogenase (S-FDH; EC 1.2.1.2) of the organism. Lack of molybdate or presence of tungstate resulted in an almost complete loss of S-FDH activity. S-FDH was purified to near homogeneity in the presence of nitrate as a stabilizing agent. The native enzyme exhibited an M(r) of 197,000 and a heterotetrameric quaternary structure with nonidentical subunits of M(r) 110,000 (alpha), 57,000 (beta), 19,400 (gamma), and 11,600 (delta). It contained 0.64 g-atom of molybdenum, 25 g-atom of nonheme iron, 20 g-atom of acid-labile sulfur, and 0.9 mol of flavin mononucleotide per mol. The fluorescence spectrum of iodine-oxidized S-FDH was nearly identical to the form A spectrum of milk xanthine oxidase, proving the presence of a pterin cofactor. The molybdenum-complexing cofactor was identified as molybdopterin guanine dinucleotide in an amount of 0.71 mol/mol of S-FDH. Apparent Km values of 3.3 mM for formate and 0.09 mM for NAD+ were determined. The enzyme coupled the oxidation of formate to a number of artificial electron acceptors and was strongly inactivated by formate in the absence of NAD+. It was inhibited by cyanide, azide, nitrate, and Hg2+ ions. Thus, the enzyme belongs to a new group of complex molybdo-flavo Fe-S FDH that so far has been detected in only one other aerobic bacterium. Images PMID:8335630

A-Type Carrier Protein ErpA Is Essential for Formation of an Active Formate-Nitrate Respiratory Pathway in Escherichia coli K-12

PubMed Central

Pinske, Constanze

2012-01-01

A-type carrier (ATC) proteins of the Isc (iron-sulfur cluster) and Suf (sulfur mobilization) iron-sulfur ([Fe-S]) cluster biogenesis pathways are proposed to traffic preformed [Fe-S] clusters to apoprotein targets. In this study, we analyzed the roles of the ATC proteins ErpA, IscA, and SufA in the maturation of the nitrate-inducible, multisubunit anaerobic respiratory enzymes formate dehydrogenase N (Fdh-N) and nitrate reductase (Nar). Mutants lacking SufA had enhanced activities of both enzymes. While both Fdh-N and Nar activities were strongly reduced in an iscA mutant, both enzymes were inactive in an erpA mutant and in a mutant unable to synthesize the [Fe-S] cluster scaffold protein IscU. It could be shown for both Fdh-N and Nar that loss of enzyme activity correlated with absence of the [Fe-S] cluster-containing small subunit. Moreover, a slowly migrating form of the catalytic subunit FdnG of Fdh-N was observed, consistent with impeded twin arginine translocation (TAT)-dependent transport. The highly related Fdh-O enzyme was also inactive in the erpA mutant. Although the Nar enzyme has its catalytic subunit NarG localized in the cytoplasm, it also exhibited aberrant migration in an erpA iscA mutant, suggesting that these modular enzymes lack catalytic integrity due to impaired cofactor biosynthesis. Cross-complementation experiments demonstrated that multicopy IscA could partially compensate for lack of ErpA with respect to Fdh-N activity but not Nar activity. These findings suggest that ErpA and IscA have overlapping roles in assembly of these anaerobic respiratory enzymes but demonstrate that ErpA is essential for the production of active enzymes. PMID:22081393

Understanding and Improving the Activity of Flavin Dependent Halogenases via Random and Targeted Mutagenesis

PubMed Central

Andorfer, Mary C.

2018-01-01

Flavin dependent halogenases (FDHs) catalyze the halogenation of organic substrates by coordinating reactions of reduced flavin, molecular oxygen, and chloride. Targeted and random mutagenesis of these enzymes has been used to both understand and alter their reactivity. These studies have led to insights into residues essential for catalysis and FDH variants with improved stability, expanded substrate scope, and altered site selectivity. Mutations throughout FDH structures have contributed to all of these advances. More recent studies have sought to rationalize the impact of these mutations on FDH function and to identify new FDHs to deepen our understanding of this enzyme class and to expand their utility for biocatalytic applications. PMID:29589959

Discovery of an acidic, thermostable and highly NADP+ dependent formate dehydrogenase from Lactobacillus buchneri NRRL B-30929

USDA-ARS?s Scientific Manuscript database

Objectives: To identify a robust NADP+ dependent formate dehydrogenase from Lactobacillus buchneri NRRL B-30929 (LbFDH) with unique biochemical properties. Results: A new NADP+ dependent formate dehydrogenase gene (fdh) was cloned from genomic DNA of L. buchneri NRRL B-30929. The recombinant constru...

Growth- and substrate-dependent transcription of formate dehydrogenase and hydrogenase coding genes in Syntrophobacter fumaroxidans and Methanospirillum hungatei.

PubMed

Worm, Petra; Stams, Alfons J M; Cheng, Xu; Plugge, Caroline M

2011-01-01

Transcription of genes coding for formate dehydrogenases (fdh genes) and hydrogenases (hyd genes) in Syntrophobacter fumaroxidans and Methanospirillum hungatei was studied following growth under different conditions. Under all conditions tested, all fdh and hyd genes were transcribed. However, transcription levels of the individual genes varied depending on the substrate and growth conditions. Our results strongly suggest that in syntrophically grown S. fumaroxidans cells, the [FeFe]-hydrogenase (encoded by Sfum_844-46), FDH1 (Sfum_2703-06) and Hox (Sfum_2713-16) may confurcate electrons from NADH and ferredoxin to protons and carbon dioxide to produce hydrogen and formate, respectively. Based on bioinformatic analysis, a membrane-integrated energy-converting [NiFe]-hydrogenase (Mhun_1741-46) of M. hungatei might be involved in the energy-dependent reduction of CO(2) to formylmethanofuran. The best candidates for F(420)-dependent N(5),N(10)-methyl-H(4) MPT and N(5),N(10),-methylene-H(4)MPT reduction are the cytoplasmic [NiFe]-hydrogenase and FDH1. 16S rRNA ratios indicate that in one of the triplicate co-cultures of S. fumaroxidans and M. hungatei, less energy was available for S. fumaroxidans. This led to enhanced transcription of genes coding for the Rnf-complex (Sfum_2694-99) and of several fdh and hyd genes. The Rnf-complex probably reoxidized NADH with ferredoxin reduction, followed by ferredoxin oxidation by the induced formate dehydrogenases and hydrogenases.

Focal dermal hypoplasia (Goltz-Gorlin syndrome): a new case with a novel variant in the PORCN gene (c.1250T>C:p.F417S) and unusual spinal anomaly.

PubMed

Garavelli, Livia; Simonte, Graziella; Rosato, Simonetta; Wischmeijer, Anita; Albertini, Enrico; Guareschi, Elisa; Longo, Caterina; Albertini, Giuseppe; Gelmini, Chiara; Greco, Chiara; Errico, Stefania; Savino, Gustavo; Pavanello, Marco; Happle, Rudolf; Unger, Sheila; Superti-Furga, Andrea; Grzeschik, Karl-Heinz

2013-07-01

Focal dermal hypoplasia (FDH; Goltz-Gorlin syndrome; OMIM 305600) is a disorder that features involvement of the skin, skeletal system, and eyes. It is caused by loss-of-function mutations in the PORCN gene. We report a young girl with FDH, microphthalmos associated with colobomatous orbital cyst, dural ectasia and cystic malformation of the spinal cord, and a de novo variant in PORCN. This association has not been previously reported, and based on these observations the phenotypic spectrum of FDH might be broader than previously appreciated. It would be prudent to alter the suggested surveillance for this rare disorder. Copyright © 2013 Wiley Periodicals, Inc.

Helicity moduli of three-dimensional dilute XY models

NASA Astrophysics Data System (ADS)

Garg, Anupam; Pandit, Rahul; Solla, Sara A.; Ebner, C.

1984-07-01

The helicity moduli of various dilute, classical XY models on three-dimensional lattices are studied with a view to understanding some aspects of the superfluidity of 4He in Vycor glass. A spinwave calculation is used to obtain the low-temperature helicity modulus of a regularly-diluted XY model. A similar calculation is performed for the randomly bond-diluted and site-diluted XY models in the limit of low dilution. A Monte Carlo simulation is used to obtain the helicity modulus of the randomly bond-diluted XY model over a wide range of temperature and dilution. It is found that the randomly diluted models do agree and the regularly diluted model does not agree with certain experimentally found features of the variation in superfluid fraction with coverage of 4He in Vycor glass.

Improving the direct electron transfer in monolithic bioelectrodes prepared by immobilization of FDH enzyme on carbon-coated anodic aluminum oxide films

NASA Astrophysics Data System (ADS)

Castro-Muñiz, Alberto; Hoshikawa, Yasuto; Komiyama, Hiroshi; Nakayama, Wataru; Itoh, Tetsuji; Kyotani, Takashi

2016-02-01

The present work reports the preparation of binderless carbon-coated porous films and the study of their performance as monolithic bioanodes. The films were prepared by coating anodic aluminum oxide (AAO) films with a thin layer of nitrogen-doped carbon by chemical vapor deposition. The films have cylindrical straight pores with controllable diameter and length. These monolithic films were used directly as bioelectrodes by loading the films with D-fructose dehydrogenase (FDH), an oxidoreductase enzyme that catalyzes the oxidation of D-fructose to 5-keto-D-fructose. The immobilization of the enzymes was carried out by physical adsorption in liquid phase and with an electrostatic attraction method. The latter method takes advantage of the fact that FDH is negatively charged during the catalytic oxidation of fructose. Thus the immobilization was performed under the application of a positive voltage to the CAAO film in a FDH-fructose solution in McIlvaine buffer (pH 5) at 25 ºC. As a result, the FDH modified electrodes with the latter method show much better electrochemical response than that with the conventional physical adsorption method. Due to the singular porous structure of the monolithic films, which consists of an array of straight and parallel nanochannels, it is possible to rule out the effect of the diffusion of the D-fructose into the pores. Thus the improvement in the performance upon using the electrostatic attraction method can be ascribed not only to a higher uptake, but also to a more appropriate molecule orientation of the enzyme units on the surface of the electrodes.

POZ domain transcription factor, FBI-1, represses transcription of ADH5/FDH by interacting with the zinc finger and interfering with DNA binding activity of Sp1.

PubMed

Lee, Dong-Kee; Suh, Dongchul; Edenberg, Howard J; Hur, Man-Wook

2002-07-26

The POZ domain is a protein-protein interaction motif that is found in many transcription factors, which are important for development, oncogenesis, apoptosis, and transcription repression. We cloned the POZ domain transcription factor, FBI-1, that recognizes the cis-element (bp -38 to -22) located just upstream of the core Sp1 binding sites (bp -22 to +22) of the ADH5/FDH minimal promoter (bp -38 to +61) in vitro and in vivo, as revealed by electrophoretic mobility shift assay and chromatin immunoprecipitation assay. The ADH5/FDH minimal promoter is potently repressed by the FBI-1. Glutathione S-transferase fusion protein pull-down showed that the POZ domains of FBI-1, Plzf, and Bcl-6 directly interact with the zinc finger DNA binding domain of Sp1. DNase I footprinting assays showed that the interaction prevents binding of Sp1 to the GC boxes of the ADH5/FDH promoter. Gal4-POZ domain fusions targeted proximal to the GC boxes repress transcription of the Gal4 upstream activator sequence-Sp1-adenovirus major late promoter. Our data suggest that POZ domain represses transcription by interacting with Sp1 zinc fingers and by interfering with the DNA binding activity of Sp1.

Efficient biosynthesis of L-phenylglycine by an engineered Escherichia coli with a tunable multi-enzyme-coordinate expression system.

PubMed

Liu, Qiaoli; Zhou, Junping; Yang, Taowei; Zhang, Xian; Xu, Meijuan; Rao, Zhiming

2018-03-01

Whole-cell catalysis with co-expression of two or more enzymes in a single host as a simple low-cost biosynthesis method has been widely studied and applied but hardly with regulation of multi-enzyme expression. Here we developed an efficient whole-cell catalyst for biosynthesis of L-phenylglycine (L-Phg) from benzoylformic acid through co-expression of leucine dehydrogenase from Bacillus cereus (BcLeuDH) and NAD + -dependent mutant formate dehydrogenase from Candida boidinii (CbFDH A10C ) in Escherichia coli with tunable multi-enzyme-coordinate expression system. By co-expressing one to four copies of CbFDH A10C and optimization of the RBS sequence of BcLeuDH in the expression system, the ratio of BcLeuDH to CbFDH in E. coli BL21/pETDuet-rbs 4 leudh-3fdh A10C was finally regulated to 2:1, which was the optimal one determined by enzyme-catalyzed synthesis. The catalyst activity of E. coli BL21/pETDuet-rbs 4 leudh-3fdh A10C was 28.4 mg L -1  min -1  g -1 dry cell weight for L-Phg production using whole-cell transformation, it's was 3.7 times higher than that of engineered E. coli without enzyme expression regulation. Under optimum conditions (pH 8.0 and 35 °C), 60 g L -1 benzoylformic acid was completely converted to pure chiral L-Phg in 4.5 h with 10 g L -1 dry cells and 50.4 g L -1 ammonium formate, and with enantiomeric excess > 99.9%. This multi-enzyme-coordinate expression system strategy significantly improved L-Phg productivity and demonstrated a novel low-cost method for enantiopure L-Phg production.

Discovery of a new metal and NAD+-dependent formate dehydrogenase from Clostridium ljungdahlii.

PubMed

Çakar, M Mervan; Mangas-Sanchez, Juan; Birmingham, William R; Turner, Nicholas J; Binay, Barış

2018-04-21

Over the next decades, with the growing concern of rising atmospheric carbon dioxide (CO 2 ) levels, the importance of investigating new approaches for its reduction becomes crucial. Reclamation of CO 2 for conversion into biofuels represents an alternative and attractive production method that has been studied in recent years, now with enzymatic methods gaining more attention. Formate dehydrogenases (FDHs) are NAD(P)H-dependent oxidoreductases that catalyze the conversion of formate into CO 2 and have been extensively used for cofactor recycling in chemoenzymatic processes. A new FDH from Clostridium ljungdahlii (ClFDH) has been recently shown to possess activity in the reverse reaction: the mineralization of CO 2 into formate. In this study, we show the successful homologous expression of ClFDH in Escherichia coli. Biochemical and kinetic characterization of the enzyme revealed that this homologue also demonstrates activity toward CO 2 reduction. Structural analysis of the enzyme through homology modeling is also presented.

Light Driven CO2 Fixation by Using Cyanobacterial Photosystem I and NADPH-Dependent Formate Dehydrogenase

PubMed Central

Ihara, Masaki; Kawano, Yusuke; Urano, Miho; Okabe, Ayako

2013-01-01

The ultimate goal of this research is to construct a new direct CO2 fixation system using photosystems in living algae. Here, we report light-driven formate production from CO2 by using cyanobacterial photosystem I (PS I). Formate, a chemical hydrogen carrier and important industrial material, can be produced from CO2 by using the reducing power and the catalytic function of formate dehydrogenase (FDH). We created a bacterial FDH mutant that experimentally switched the cofactor specificity from NADH to NADPH, and combined it with an in vitro-reconstituted cyanobacterial light-driven NADPH production system consisting of PS I, ferredoxin (Fd), and ferredoxin-NADP+-reductase (FNR). Consequently, light-dependent formate production under a CO2 atmosphere was successfully achieved. In addition, we introduced the NADPH-dependent FDH mutant into heterocysts of the cyanobacterium Anabaena sp. PCC 7120 and demonstrated an increased formate concentration in the cells. These results provide a new possibility for photo-biological CO2 fixation. PMID:23936519

Light driven CO2 fixation by using cyanobacterial photosystem I and NADPH-dependent formate dehydrogenase.

PubMed

Ihara, Masaki; Kawano, Yusuke; Urano, Miho; Okabe, Ayako

2013-01-01

The ultimate goal of this research is to construct a new direct CO2 fixation system using photosystems in living algae. Here, we report light-driven formate production from CO2 by using cyanobacterial photosystem I (PS I). Formate, a chemical hydrogen carrier and important industrial material, can be produced from CO2 by using the reducing power and the catalytic function of formate dehydrogenase (FDH). We created a bacterial FDH mutant that experimentally switched the cofactor specificity from NADH to NADPH, and combined it with an in vitro-reconstituted cyanobacterial light-driven NADPH production system consisting of PS I, ferredoxin (Fd), and ferredoxin-NADP(+)-reductase (FNR). Consequently, light-dependent formate production under a CO2 atmosphere was successfully achieved. In addition, we introduced the NADPH-dependent FDH mutant into heterocysts of the cyanobacterium Anabaena sp. PCC 7120 and demonstrated an increased formate concentration in the cells. These results provide a new possibility for photo-biological CO2 fixation.

Sulphur shuttling across a chaperone during molybdenum cofactor maturation.

PubMed

Arnoux, Pascal; Ruppelt, Christian; Oudouhou, Flore; Lavergne, Jérôme; Siponen, Marina I; Toci, René; Mendel, Ralf R; Bittner, Florian; Pignol, David; Magalon, Axel; Walburger, Anne

2015-02-04

Formate dehydrogenases (FDHs) are of interest as they are natural catalysts that sequester atmospheric CO2, generating reduced carbon compounds with possible uses as fuel. FDHs activity in Escherichia coli strictly requires the sulphurtransferase EcFdhD, which likely transfers sulphur from IscS to the molybdenum cofactor (Mo-bisPGD) of FDHs. Here we show that EcFdhD binds Mo-bisPGD in vivo and has submicromolar affinity for GDP-used as a surrogate of the molybdenum cofactor's nucleotide moieties. The crystal structure of EcFdhD in complex with GDP shows two symmetrical binding sites located on the same face of the dimer. These binding sites are connected via a tunnel-like cavity to the opposite face of the dimer where two dynamic loops, each harbouring two functionally important cysteine residues, are present. On the basis of structure-guided mutagenesis, we propose a model for the sulphuration mechanism of Mo-bisPGD where the sulphur atom shuttles across the chaperone dimer.

Sulphur shuttling across a chaperone during molybdenum cofactor maturation

NASA Astrophysics Data System (ADS)

Arnoux, Pascal; Ruppelt, Christian; Oudouhou, Flore; Lavergne, Jérôme; Siponen, Marina I.; Toci, René; Mendel, Ralf R.; Bittner, Florian; Pignol, David; Magalon, Axel; Walburger, Anne

2015-02-01

Formate dehydrogenases (FDHs) are of interest as they are natural catalysts that sequester atmospheric CO2, generating reduced carbon compounds with possible uses as fuel. FDHs activity in Escherichia coli strictly requires the sulphurtransferase EcFdhD, which likely transfers sulphur from IscS to the molybdenum cofactor (Mo-bisPGD) of FDHs. Here we show that EcFdhD binds Mo-bisPGD in vivo and has submicromolar affinity for GDP—used as a surrogate of the molybdenum cofactor’s nucleotide moieties. The crystal structure of EcFdhD in complex with GDP shows two symmetrical binding sites located on the same face of the dimer. These binding sites are connected via a tunnel-like cavity to the opposite face of the dimer where two dynamic loops, each harbouring two functionally important cysteine residues, are present. On the basis of structure-guided mutagenesis, we propose a model for the sulphuration mechanism of Mo-bisPGD where the sulphur atom shuttles across the chaperone dimer.

Helicity is the only integral invariant of volume-preserving transformations

PubMed Central

Enciso, Alberto; Peralta-Salas, Daniel; de Lizaur, Francisco Torres

2016-01-01

We prove that any regular integral invariant of volume-preserving transformations is equivalent to the helicity. Specifically, given a functional ℐ defined on exact divergence-free vector fields of class C1 on a compact 3-manifold that is associated with a well-behaved integral kernel, we prove that ℐ is invariant under arbitrary volume-preserving diffeomorphisms if and only if it is a function of the helicity. PMID:26864201

One-loop corrections to light cone wave functions: The dipole picture DIS cross section

NASA Astrophysics Data System (ADS)

Hänninen, H.; Lappi, T.; Paatelainen, R.

2018-06-01

We develop methods to perform loop calculations in light cone perturbation theory using a helicity basis, refining the method introduced in our earlier work. In particular this includes implementing a consistent way to contract the four-dimensional tensor structures from the helicity vectors with d-dimensional tensors arising from loop integrals, in a way that can be fully automatized. We demonstrate this explicitly by calculating the one-loop correction to the virtual photon to quark-antiquark dipole light cone wave function. This allows us to calculate the deep inelastic scattering cross section in the dipole formalism to next-to-leading order accuracy. Our results, obtained using the four dimensional helicity scheme, agree with the recent calculation by Beuf using conventional dimensional regularization, confirming the regularization scheme independence of this cross section.

Reversible interconversion of carbon dioxide and formate by an electroactive enzyme

PubMed Central

Reda, Torsten; Plugge, Caroline M.; Abram, Nerilie J.; Hirst, Judy

2008-01-01

Carbon dioxide (CO2) is a kinetically and thermodynamically stable molecule. It is easily formed by the oxidation of organic molecules, during combustion or respiration, but is difficult to reduce. The production of reduced carbon compounds from CO2 is an attractive proposition, because carbon-neutral energy sources could be used to generate fuel resources and sequester CO2 from the atmosphere. However, available methods for the electrochemical reduction of CO2 require excessive overpotentials (are energetically wasteful) and produce mixtures of products. Here, we show that a tungsten-containing formate dehydrogenase enzyme (FDH1) adsorbed to an electrode surface catalyzes the efficient electrochemical reduction of CO2 to formate. Electrocatalysis by FDH1 is thermodynamically reversible—only small overpotentials are required, and the point of zero net catalytic current defines the reduction potential. It occurs under thoroughly mild conditions, and formate is the only product. Both as a homogeneous catalyst and on the electrode, FDH1 catalyzes CO2 reduction with a rate more than two orders of magnitude faster than that of any known catalyst for the same reaction. Formate oxidation is more than five times faster than CO2 reduction. Thermodynamically, formate and hydrogen are oxidized at similar potentials, so formate is a viable energy source in its own right as well as an industrially important feedstock and a stable intermediate in the conversion of CO2 to methanol and methane. FDH1 demonstrates the feasibility of interconverting CO2 and formate electrochemically, and it is a template for the development of robust synthetic catalysts suitable for practical applications. PMID:18667702

An integrated bienzyme glucose oxidase-fructose dehydrogenase-tetrathiafulvalene-3-mercaptopropionic acid-gold electrode for the simultaneous determination of glucose and fructose.

PubMed

Campuzano, Susana; Loaiza, Oscar A; Pedrero, María; de Villena, F Javier Manuel; Pingarrón, José M

2004-06-01

A bienzyme biosensor for the simultaneous determination of glucose and fructose was developed by coimmobilising glucose oxidase (GOD), fructose dehydrogenase (FDH), and the mediator, tetrathiafulvalene (TTF), by cross-linking with glutaraldehyde atop a 3-mercaptopropionic acid (MPA) self-assembled monolayer (SAM) on a gold disk electrode (AuE). The performance of this bienzyme electrode under batch and flow injection (FI) conditions, as well as an amperometric detection in high-performance liquid chromatography (HPLC), are reported. The order of enzyme immobilisation atop the MPA-SAM affected the biosensor amperometric response in terms of sensitivity, with the immobilisation order GOD, FDH, TTF being selected. Similar analytical characteristics to those obtained with single GOD or FDH SAM-based biosensors for glucose and fructose were achieved with the bienzyme electrode, indicating that no noticeable changes in the biosensor responses to the analytes occurred as a consequence of the coimmobilisation of both enzymes on the same MPA-AuE. The suitability of the bienzyme biosensor for the analysis of real samples under flow injection conditions was tested by determining glucose in two certified serum samples. The simultaneous determination of glucose and fructose in the same sample cannot be performed without a separation step because at the detection potential used (+0.10 V), both sugars show amperometric response. Consequently, HPLC with amperometric detection at the TTF-FDH-GOD-MPA-AuE was accomplished. Glucose and fructose were simultaneously determined in honey, cola softdrink, and commercial apple juice, and the results were compared with those obtained by using other reference methods.

Goltz-Gorlin Syndrome: Revisiting the Clinical Spectrum.

PubMed

Yesodharan, Dhanya; Büschenfelde, Uta Meyer Zum; Kutsche, Kerstin; Mohandas Nair, K; Nampoothiri, Sheela

2018-01-31

To describe the varying phenotypic spectrum of Focal Dermal Hypoplasia (FDH) and to emphasize the need for identifying the condition in mildly affected females which is crucial for offering a prenatal diagnosis in subsequent pregnancy owing to the risk of having a severely affected baby. The phenotype-genotype correlation of 4 patients with FDH, over a period of 11 y from the genetic clinic in a tertiary care centre from Kerala, India was done. All four mutation proven patients were females (2 adults and 2 children). One of the adult female subjects were mildly affected, though she had a history of having a severely affected female child who expired on day six. Among the 2 affected children, one of them had an unaffected mother and the other had an affected mother. FDH has a wide clinical spectrum from very subtle findings to severe manifestations. The lethality of the condition in males and the disfigurement and multisystem involvement in females highlights the importance of confirmation of diagnosis by molecular analysis so that the family can be offered prenatal diagnosis in subsequent pregnancy.

Artificial leaf device for solar fuel production.

PubMed

Amao, Yutaka; Shuto, Naho; Furuno, Kana; Obata, Asami; Fuchino, Yoshiko; Uemura, Keiko; Kajino, Tsutomu; Sekito, Takeshi; Iwai, Satoshi; Miyamoto, Yasushi; Matsuda, Masatoshi

2012-01-01

Solar fuels, such as hydrogen gas produced from water and methanol produced from carbon dioxide reduction by artificial photosynthesis, have received considerable attention. In natural leaves the photosynthetic proteins are well-organized in the thylakoid membrane. To develop an artificial leaf device for solar low-carbon fuel production from CO2, a chlorophyll derivative chlorin-e6 (Chl-e6; photosensitizer), 1-carboxylundecanoyl-1'-methyl-4,4'-bipyrizinium bromide, iodide (CH3V(CH2)9COOH; the electron carrier) and formate dehydrogenase (FDH) (the catalyst) immobilised onto a silica-gel-based thin layer chromatography plate (the Chl-V-FDH device) was investigated. From luminescence spectroscopy measurements, the photoexcited triplet state of Chl-e6 was quenched by the CH3V(CH2)9COOH moiety on the device, indicating the photoinduced electron transfer from the photoexcited triplet state of Chl-e6 to the CH3V(CH2)9COOH moiety. When the CO2-saturated sample solution containing NADPH (the electron donor) was flowed onto the Chl-V-FDH device under visible light irradiation, the formic acid concentration increased with increasing irradiation time.

Nitrate reductase-formate dehydrogenase couple involved in the fungal denitrification by Fusarium oxysporum.

PubMed

Uchimura, Hiromasa; Enjoji, Hitoshi; Seki, Takafumi; Taguchi, Ayako; Takaya, Naoki; Shoun, Hirofumi

2002-04-01

Dissimilatory nitrate reductase (Nar) was solubilized and partially purified from the large particle (mitochondrial) fraction of the denitrifying fungus Fusarium oxysporum and characterized. Many lines of evidence showed that the membrane-bound Nar is distinct from the soluble, assimilatory nitrate reductase. Further, the spectral and other properties of the fungal Nar were similar to those of dissimilatory Nars of Escherichia coli and denitrifying bacteria, which are comprised of a molybdoprotein, a cytochrome b, and an iron-sulfur protein. Formate-nitrate oxidoreductase activity was also detected in the mitochondrial fraction, which was shown to arise from the coupling of formate dehydrogenase (Fdh), Nar, and a ubiquinone/ubiquinol pool. This is the first report of the occurrence in a eukaryote of Fdh that is associated with the respiratory chain. The coupling with Fdh showed that the fungal Nar system is more similar to that involved in the nitrate respiration by Escherichia coli than that in the bacterial denitrifying system. Analyses of the mutant species of F. oxysporum that were defective in Nar and/or assimilatory nitrate reductase conclusively showed that Nar is essential for the fungal denitrification.

Isotopic effects in the collinear reactive FHH system

NASA Technical Reports Server (NTRS)

Lepetit, B.; Launay, J. M.; Le Dourneuf, M.

1986-01-01

Exact quantum reaction probabilities for a collinear model of the F + HH, HD, DD and DH reactions on the MV potential energy surface have been computed using hyperspherical coordinates. The results, obtained up to a total energy of 1.8 eV, show three main features: (1) resonances, whose positions and widths are analyzed simply in the hyperspherical formalism; (2) a slowly varying background increasing for FHD, decreasing for FDH, and oscillating for FHH and FDD, whose variations are interpreted by classical dynamics; and (3) partial reaction probabilities revealing decreasing vibrational adiabaticity in the order FHH-FDD-FHD-FDH.

Genetically Engineered Escherichia coli Nissle 1917 Synbiotics Reduce Metabolic Effects Induced by Chronic Consumption of Dietary Fructose

PubMed Central

Somabhai, Chaudhari Archana; Raghuvanshi, Ruma; Nareshkumar, G.

2016-01-01

Aims To assess protective efficacy of genetically modified Escherichia coli Nissle 1917 (EcN) on metabolic effects induced by chronic consumption of dietary fructose. Materials and Methods EcN was genetically modified with fructose dehydrogenase (fdh) gene for conversion of fructose to 5-keto-D-fructose and mannitol-2-dehydrogenase (mtlK) gene for conversion to mannitol, a prebiotic. Charles foster rats weighing 150–200 g were fed with 20% fructose in drinking water for two months. Probiotic treatment of EcN (pqq), EcN (pqq-glf-mtlK), EcN (pqq-fdh) was given once per week 109 cells for two months. Furthermore, blood and liver parameters for oxidative stress, dyslipidemia and hyperglycemia were estimated. Fecal samples were collected to determine the production of short chain fatty acids and pyrroloquinoline quinone (PQQ) production. Results EcN (pqq-glf-mtlK), EcN (pqq-fdh) transformants were confirmed by restriction digestion and functionality was checked by PQQ estimation and HPLC analysis. There was significant increase in body weight, serum glucose, liver injury markers, lipid profile in serum and liver, and decrease in antioxidant enzyme activity in high-fructose-fed rats. However the rats treated with EcN (pqq-glf-mtlK) and EcN (pqq-fdh) showed significant reduction in lipid peroxidation along with increase in serum and hepatic antioxidant enzyme activities. Restoration of liver injury marker enzymes was also seen. Increase in short chain fatty acids (SCFA) demonstrated the prebiotic effects of mannitol and gluconic acid. Conclusions Our study demonstrated the effectiveness of probiotic EcN producing PQQ and fructose metabolizing enzymes against the fructose induced hepatic steatosis suggesting that its potential for use in treating fructose induced metabolic syndrome. PMID:27760187

Genetic polymorphisms in the formaldehyde dehydrogenase gene and their biological significance.

PubMed

Just, Walter; Zeller, Jasmin; Riegert, Clarissa; Speit, Günter

2011-11-30

The GSH-dependent formaldehyde dehydrogenase (FDH) is the most important enzyme for the metabolic inactivation of formaldehyde. We studied three polymorphisms of this gene with the intention to elucidate their relevance for inter-individual differences in the protection against the (geno-)toxicity of FA. The first polymorphism (rs11568816) was investigated using real-time PCR and restriction fragment analysis in 150 subjects. However, we did not find the polymorphic sequence in any of the subjects. We studied a second polymorphism (rs17028487), representing a base exchange (c.*114A>G) in exon 9 of the FDH gene. We analyzed 70 subjects with the SNaPshot Primer Extension method and subsequent analysis in a ABI PRISM 3100, but no variant allele was identified. A third polymorphism, rs13832 in exon 9 (c.*493G>T), was studied in a group of 105 subjects by the SNaPshot Primer Extension method. 43 of the subjects were heterozygous for the polymorphism (G/T), 46 homozygous for the T allele, and 16 were homozygous for the G-allele. Real-time RT-PCR measurements of FDH mRNA did not indicate a significant difference in transcript levels between the heterozygous and the homozygous groups. The in vitro comet assay after FA exposure of blood samples obtained from 5 homozygous GG and 3 homozygous TT subjects did not lead to a significant difference between these two groups. Altogether, our study did not identify biologically relevant polymorphisms in transcribed regions of the FDH gene, which may lead to inter-individual differences in the metabolic inactivation of FA. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Comparison of magnetic helicity close to the sun and in magnetic clouds

NASA Astrophysics Data System (ADS)

Rust, D.

Magnetic helicity is present in the solar atmosphere - as inferred from vector magnetograph measurements, solar filaments, S-shaped coronal structures known as sigmoids, and sunspot whorls. I will survey the possible solar sources of this magnetic helicity. Included are fieldline footpoint motions, effects of Coriolis forces, effects of convection, shear associated with differential rotation, and, of course, the internal dynamo. Besides the survey of possible local mechanisms for helicity generation, I will consider the global view of the flow of helicity from the sun into interplanetary space. The principal agents by which the sun sheds helicity are coronal mass ejections (CMEs). They are often associated with interplanetary magnetic clouds (MCs), whose fields are regularly probed with sensitive spacecraft magnetometers. MCs yield more direct measurements of helicity. They show that each MC carries helicity away from the sun. A major issue in solar-heliospheric research is whether the amount of helicity that MCs carry away in a solar cycle can be accounted for by the helicity generation mechanisms proposed so far. The NASA Solar and Heliospheric Physics Program supports this work under grants NAG5- 7921 and NAG 5-11584.

Improvement of ethanol productivity and energy efficiency by degradation of inhibitors using recombinant Zymomonas mobilis (pHW20a-fdh).

PubMed

Dong, Hong-Wei; Fan, Li-Qiang; Luo, Zichen; Zhong, Jian-Jiang; Ryu, Dewey D Y; Bao, Jie

2013-09-01

Toxic compounds, such as formic acid, furfural, and hydroxymethylfurfural (HMF) generated during pretreatment of corn stover (CS) at high temperature and low pH, inhibit growth of Zymomonas mobilis and lower the conversion efficiency of CS to biofuel and other products. The inhibition of toxic compounds is considered as one of the major technical barriers in the lignocellulose bioconversion. In order to detoxify and/or degrade these toxic compounds by the model ethanologenic strain Z. mobilis itself in situ the fermentation medium, we constructed a recombinant Z. mobilis ZM4 (pHW20a-fdh) strain that is capable of degrading toxic inhibitor, formate. This is accomplished by cloning heterologous formate dehydrogenase gene (fdh) from Saccharomyces cerevisiae and by coupling this reaction of NADH regeneration reaction system with furfural and HMF degradation in the recombinant Z. mobilis strain. The NADH regeneration reaction also improved both the energy efficiency and cell physiological activity of the recombinant organism, which were definitely confirmed by the improved cell growth, ethanol yield, and ethanol productivity during fermentation with CS hydrolysate. Copyright © 2013 Wiley Periodicals, Inc.

Respiratory proteins contribute differentially to Campylobacter jejuni’s survival and in vitro interaction with hosts’ intestinal cells

PubMed Central

2012-01-01

Background The genetic features that facilitate Campylobacter jejuni’s adaptation to a wide range of environments are not completely defined. However, whole genome expression studies showed that respiratory proteins (RPs) were differentially expressed under varying conditions and stresses, suggesting further unidentified roles for RPs in C. jejuni’s adaptation. Therefore, our objectives were to characterize the contributions of selected RPs to C. jejuni’s i- key survival phenotypes under different temperature (37°C vs. 42°C) and oxygen (microaerobic, ambient, and oxygen-limited/anaerobic) conditions and ii- its interactions with intestinal epithelial cells from disparate hosts (human vs. chickens). Results C. jejuni mutant strains with individual deletions that targeted five RPs; nitrate reductase (ΔnapA), nitrite reductase (ΔnrfA), formate dehydrogenase (ΔfdhA), hydrogenase (ΔhydB), and methylmenaquinol:fumarate reductase (ΔmfrA) were used in this study. We show that only the ΔfdhA exhibited a decrease in motility; however, incubation at 42°C significantly reduced the deficiency in the ΔfdhA’s motility as compared to 37°C. Under all tested conditions, the ΔmfrA showed a decreased susceptibility to hydrogen peroxide (H2O2), while the ΔnapA and the ΔfdhA showed significantly increased susceptibility to the oxidant as compared to the wildtype. Further, the susceptibility of the ΔnapA to H2O2 was significantly more pronounced at 37°C. The biofilm formation capability of individual RP mutants varied as compared to the wildtype. However, the impact of the deletion of certain RPs affected biofilm formation in a manner that was dependent on temperature and/or oxygen concentration. For example, the ΔmfrA displayed significantly deficient and increased biofilm formation under microaerobic conditions at 37°C and 42°C, respectively. However, under anaerobic conditions, the ΔmfrA was only significantly impaired in biofilm formation at 42°C. Additionally, the RPs mutants showed differential ability for infecting and surviving in human intestinal cell lines (INT-407) and primary chicken intestinal epithelial cells, respectively. Notably, the ΔfdhA and the ΔhydB were deficient in interacting with both cell types, while the ΔmfrA displayed impairments only in adherence to and invasion of INT-407. Scanning electron microscopy showed that the ΔhydB and the ΔfdhA exhibited filamentous and bulging (almost spherical) cell shapes, respectively, which might be indicative of defects in cell division. Conclusions We conclude that the RPs contribute to C. jejuni’s motility, H2O2 resistance, biofilm formation, and in vitro interactions with hosts’ intestinal cells. Further, the impact of certain RPs varied in response to incubation temperature and/or oxygen concentration. Therefore, RPs may facilitate the prevalence of C. jejuni in a variety of niches, contributing to the pathogen’s remarkable potential for adaptation. PMID:23148765

Helical vortices: linear stability analysis and nonlinear dynamics

NASA Astrophysics Data System (ADS)

Selçuk, C.; Delbende, I.; Rossi, M.

2018-02-01

We numerically investigate, within the context of helical symmetry, the dynamics of a regular array of two or three helical vortices with or without a straight central hub vortex. The Navier-Stokes equations are linearised to study the instabilities of such basic states. For vortices with low pitches, an unstable mode is extracted which corresponds to a displacement mode and growth rates are found to compare well with results valid for an infinite row of point vortices or an infinite alley of vortex rings. For larger pitches, the system is stable with respect to helically symmetric perturbations. In the nonlinear regime, we follow the time-evolution of the above basic states when initially perturbed by the dominant instability mode. For two vortices, sequences of overtaking events, leapfrogging and eventually merging are observed. The transition between such behaviours occurs at a critical ratio involving the core size and the vortex-separation distance. Cases with three helical vortices are also presented.

Fluor Daniel Hanford Inc. integrated safety management system phase 1 verification final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

PARSONS, J.E.

1999-10-28

The purpose of this review is to verify the adequacy of documentation as submitted to the Approval Authority by Fluor Daniel Hanford, Inc. (FDH). This review is not only a review of the Integrated Safety Management System (ISMS) System Description documentation, but is also a review of the procedures, policies, and manuals of practice used to implement safety management in an environment of organizational restructuring. The FDH ISMS should support the Hanford Strategic Plan (DOE-RL 1996) to safely clean up and manage the site's legacy waste; deploy science and technology while incorporating the ISMS theme to ''Do work safely''; andmore » protect human health and the environment.« less

An Algorithm for Protein Helix Assignment Using Helix Geometry

PubMed Central

Cao, Chen; Xu, Shutan; Wang, Lincong

2015-01-01

Helices are one of the most common and were among the earliest recognized secondary structure elements in proteins. The assignment of helices in a protein underlies the analysis of its structure and function. Though the mathematical expression for a helical curve is simple, no previous assignment programs have used a genuine helical curve as a model for helix assignment. In this paper we present a two-step assignment algorithm. The first step searches for a series of bona fide helical curves each one best fits the coordinates of four successive backbone Cα atoms. The second step uses the best fit helical curves as input to make helix assignment. The application to the protein structures in the PDB (protein data bank) proves that the algorithm is able to assign accurately not only regular α-helix but also 310 and π helices as well as their left-handed versions. One salient feature of the algorithm is that the assigned helices are structurally more uniform than those by the previous programs. The structural uniformity should be useful for protein structure classification and prediction while the accurate assignment of a helix to a particular type underlies structure-function relationship in proteins. PMID:26132394

Helical and rod-shaped bacteria swim in helical trajectories with little additional propulsion from helical shape

NASA Astrophysics Data System (ADS)

Fu, Henry; Constantino, Maira; Jabbarzadeh, Mehdi; Bansil, Rama

2017-11-01

It has frequently been hypothesized that the helical body shapes of flagellated bacteria may yield some advantage in swimming ability. The helical-shaped pathogen Helicobacter pylori allows us to test these claims. Using fast time-resolution and high-magnification phase-contrast microscopy to simultaneously image and track individual bacteria we determine cell body shape as well as rotational and translational speeds. Using the method of regularized Stokeslets, we directly compare observed speeds and trajectories to numerical calculations to validate the numerical model. Although experimental observations are limited to select cases, the model allows quantification of the effects of body helicity, length, and diameter. We find that due to relatively slow body rotation rates, the helical shape makes at most a 15% contribution to propulsive thrust. The effect of body shape on swimming speeds is instead dominated by variations in translational drag required to move the cell body. Because helical cells are one of the strongest candidates for propulsion arising from the cell body, our results imply that quite generally, swimming speeds of flagellated bacteria can only be increased a little by by body propulsion.

Methanol toxicity and formate oxidation in NEUT2 mice.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cook, R. J.; Champion, K. M.; Giometti, C. S.

2001-09-15

NEUT2 mice are deficient in cytosolic 10-formyltetrahydrofolate dehydrogenase (FDH; EC 1.5.1.6) which catalyzes the oxidation of excess folate-linked one-carbon units in the form of 10-formyltetrahydrofolate to CO{sub 2} and tetrahydrofolate. The absence of FDH should impair the oxidation of formate via the folate-dependent pathway and as a consequence render homozygous NEUT2 mice more susceptible to methanol toxicity. Normal (CB6-F1) and NEUT2 heterozygous and homozygous mice had essentially identical LD50 values for methanol, 6.08, 6.00, and 6.03 g/kg, respectively. Normal mice oxidized low doses of [{sup 14}C]sodium formate (ip 5 mg/kg) to {sup 14}CO{sub 2} at approximately twice the rate ofmore » homozygous NEUT2 mice, indicating the presence of another formate-oxidizing system in addition to FDH. Treatment of mice with the catalase inhibitor, 3-aminotriazole (1 g/kg ip) had no effect on the rate of formate oxidation, indicating that at low concentrations formate was not oxidized peroxidatively by catalase. High doses of [{sup 14}C]sodium formate (ip 100 mg/kg) were oxidized to {sup 14}CO{sub 2} at identical rates in normal and NEUT2 homozygous mice. Pretreatment with 3-aminotriazole (1 g/kg ip) in this instance resulted in a 40 and 50% decrease in formate oxidation to CO2 in both normal and homozygous NEUT2 mice, respectively. These results indicate that mice are able to oxidize formate to CO{sub 2} by at least three different routes: (1) folate-dependent via FDH at low levels of formate; (2) peroxidation by catalase at high levels of formate; and (3) by an unknown route(s) which appears to function at both low and high levels of formate. The implications of these observations are discussed in terms of the current hypotheses concerning methanol and formate toxicity in rodents and primates.« less

Oxalate-Metabolising Genes of the White-Rot Fungus Dichomitus squalens Are Differentially Induced on Wood and at High Proton Concentration

PubMed Central

de Vries, Ronald P.; Timonen, Sari; Hildén, Kristiina

2014-01-01

Oxalic acid is a prevalent fungal metabolite with versatile roles in growth and nutrition, including degradation of plant biomass. However, the toxicity of oxalic acid makes regulation of its intra- and extracellular concentration crucial. To increase the knowledge of fungal oxalate metabolism, a transcriptional level study on oxalate-catabolising genes was performed with an effective lignin-degrading white-rot fungus Dichomitus squalens, which has demonstrated particular abilities in production and degradation of oxalic acid. The expression of oxalic-acid decomposing oxalate decarboxylase (ODC) and formic-acid decomposing formate dehydrogenase (FDH) encoding genes was followed during the growth of D. squalens on its natural spruce wood substrate. The effect of high proton concentration on the regulation of the oxalate-catabolising genes was determined after addition of organic acid (oxalic acid) and inorganic acid (hydrochloric acid) to the liquid cultures of D. squalens. In order to evaluate the co-expression of oxalate-catabolising and manganese peroxidase (MnP) encoding genes, the expression of one MnP encoding gene, mnp1, of D. squalens was also surveyed in the solid state and liquid cultures. Sequential action of ODC and FDH encoding genes was detected in the studied cultivations. The odc1, fdh2 and fdh3 genes of D. squalens showed constitutive expression, whereas ODC2 and FHD1 most likely are the main responsible enzymes for detoxification of high concentrations of oxalic and formic acids. The results also confirmed the central role of ODC1 when D. squalens grows on coniferous wood. Phylogenetic analysis revealed that fungal ODCs have evolved from at least two gene copies whereas FDHs have a single ancestral gene. As a conclusion, the multiplicity of oxalate-catabolising genes and their differential regulation on wood and in acid-amended cultures of D. squalens point to divergent physiological roles for the corresponding enzymes. PMID:24505339

The Alcohol Dehydrogenase Gene Family in Melon (Cucumis melo L.): Bioinformatic Analysis and Expression Patterns

PubMed Central

Jin, Yazhong; Zhang, Chong; Liu, Wei; Tang, Yufan; Qi, Hongyan; Chen, Hao; Cao, Songxiao

2016-01-01

Alcohol dehydrogenases (ADH), encoded by multigene family in plants, play a critical role in plant growth, development, adaptation, fruit ripening and aroma production. Thirteen ADH genes were identified in melon genome, including 12 ADHs and one formaldehyde dehydrogenease (FDH), designated CmADH1-12 and CmFDH1, in which CmADH1 and CmADH2 have been isolated in Cantaloupe. ADH genes shared a lower identity with each other at the protein level and had different intron-exon structure at nucleotide level. No typical signal peptides were found in all CmADHs, and CmADH proteins might locate in the cytoplasm. The phylogenetic tree revealed that 13 ADH genes were divided into three groups respectively, namely long-, medium-, and short-chain ADH subfamily, and CmADH1,3-11, which belongs to the medium-chain ADH subfamily, fell into six medium-chain ADH subgroups. CmADH12 may belong to the long-chain ADH subfamily, while CmFDH1 may be a Class III ADH and serve as an ancestral ADH in melon. Expression profiling revealed that CmADH1, CmADH2, CmADH10 and CmFDH1 were moderately or strongly expressed in different vegetative tissues and fruit at medium and late developmental stages, while CmADH8 and CmADH12 were highly expressed in fruit after 20 days. CmADH3 showed preferential expression in young tissues. CmADH4 only had slight expression in root. Promoter analysis revealed several motifs of CmADH genes involved in the gene expression modulated by various hormones, and the response pattern of CmADH genes to ABA, IAA and ethylene were different. These CmADHs were divided into ethylene-sensitive and –insensitive groups, and the functions of CmADHs were discussed. PMID:27242871

DOE Office of Scientific and Technical Information (OSTI.GOV)

L. Delgado-Aparicio, et. al.

New observations of the formation and dynamics of long-lived impurity-induced helical "snake" modes in tokamak plasmas have recently been carried-out on Alcator C-Mod. The snakes form as an asymmetry in the impurity ion density that undergoes a seamless transition from a small helically displaced density to a large crescent-shaped helical structure inside q < 1, with a regularly sawtoothing core. The observations show that the conditions for the formation and persistence of a snake cannot be explained by plasma pressure alone. Instead, many features arise naturally from nonlinear interactions in a 3D MHD model that separately evolves the plasma densitymore » and temperature« less

Formation and stability of impurity "snakes" in tokamak plasmas.

PubMed

Delgado-Aparicio, L; Sugiyama, L; Granetz, R; Gates, D A; Rice, J E; Reinke, M L; Bitter, M; Fredrickson, E; Gao, C; Greenwald, M; Hill, K; Hubbard, A; Hughes, J W; Marmar, E; Pablant, N; Podpaly, Y; Scott, S; Wilson, R; Wolfe, S; Wukitch, S

2013-02-08

New observations of the formation and dynamics of long-lived impurity-induced helical "snake" modes in tokamak plasmas have recently been carried out on Alcator C-Mod. The snakes form as an asymmetry in the impurity ion density that undergoes a seamless transition from a small helically displaced density to a large crescent-shaped helical structure inside q<1, with a regularly sawtoothing core. The observations show that the conditions for the formation and persistence of a snake cannot be explained by plasma pressure alone. Instead, many features arise naturally from nonlinear interactions in a 3D MHD model that separately evolves the plasma density and temperature.

Chaotic and regular instantons in helical shell models of turbulence

NASA Astrophysics Data System (ADS)

De Pietro, Massimo; Mailybaev, Alexei A.; Biferale, Luca

2017-03-01

Shell models of turbulence have a finite-time blowup in the inviscid limit, i.e., the enstrophy diverges while the single-shell velocities stay finite. The signature of this blowup is represented by self-similar instantonic structures traveling coherently through the inertial range. These solutions might influence the energy transfer and the anomalous scaling properties empirically observed for the forced and viscous models. In this paper we present a study of the instantonic solutions for a set of four shell models of turbulence based on the exact decomposition of the Navier-Stokes equations in helical eigenstates. We find that depending on the helical structure of each model, instantons are chaotic or regular. Some instantonic solutions tend to recover mirror symmetry for scales small enough. Models that have anomalous scaling develop regular nonchaotic instantons. Conversely, models that have nonanomalous scaling in the stationary regime are those that have chaotic instantons. The direction of the energy carried by each single instanton tends to coincide with the direction of the energy cascade in the stationary regime. Finally, we find that whenever the small-scale stationary statistics is intermittent, the instanton is less steep than the dimensional Kolmogorov scaling, independently of whether or not it is chaotic. Our findings further support the idea that instantons might be crucial to describe some aspects of the multiscale anomalous statistics of shell models.

Conductance and amantadine binding of a pore formed by a lysine-flanked transmembrane domain of SARS coronavirus envelope protein

PubMed Central

Torres, Jaume; Maheswari, Uma; Parthasarathy, Krupakar; Ng, Lifang; Liu, Ding Xiang; Gong, Xiandi

2007-01-01

The coronavirus responsible for the severe acute respiratory syndrome (SARS-CoV) contains a small envelope protein, E, with putative involvement in host cell apoptosis and virus morphogenesis. It has been suggested that E protein can form a membrane destabilizing transmembrane (TM) hairpin, or homooligomerize to form a regular TM α-helical bundle. We have shown previously that the topology of the α-helical putative TM domain of E protein (ETM), flanked by two lysine residues at C and N termini to improve solubility, is consistent with a regular TM α-helix, with orientational parameters in lipid bilayers that are consistent with a homopentameric model. Herein, we show that this peptide, reconstituted in lipid bilayers, shows sodium conductance. Channel activity is inhibited by the anti-influenza drug amantadine, which was found to bind our preparation with moderate affinity. Results obtained from single or double mutants indicate that the organization of the transmembrane pore is consistent with our previously reported pentameric α-helical bundle model. PMID:17766393

VhuD Facilitates Electron Flow from H2 or Formate to Heterodisulfide Reductase in Methanococcus maripaludis

PubMed Central

Costa, Kyle C.; Lie, Thomas J.; Xia, Qin

2013-01-01

Flavin-based electron bifurcation has recently been characterized as an essential energy conservation mechanism that is utilized by hydrogenotrophic methanogenic Archaea to generate low-potential electrons in an ATP-independent manner. Electron bifurcation likely takes place at the flavin associated with the α subunit of heterodisulfide reductase (HdrA). In Methanococcus maripaludis the electrons for this reaction come from either formate or H2 via formate dehydrogenase (Fdh) or Hdr-associated hydrogenase (Vhu). However, how these enzymes bind to HdrA to deliver electrons is unknown. Here, we present evidence that the δ subunit of hydrogenase (VhuD) is central to the interaction of both enzymes with HdrA. When M. maripaludis is grown under conditions where both Fdh and Vhu are expressed, these enzymes compete for binding to VhuD, which in turn binds to HdrA. Under these conditions, both enzymes are fully functional and are bound to VhuD in substoichiometric quantities. We also show that Fdh copurifies specifically with VhuD in the absence of other hydrogenase subunits. Surprisingly, in the absence of Vhu, growth on hydrogen still occurs; we show that this involves F420-reducing hydrogenase. The data presented here represent an initial characterization of specific protein interactions centered on Hdr in a hydrogenotrophic methanogen that utilizes multiple electron donors for growth. PMID:24039260

Helical and rod-shaped bacteria swim in helical trajectories with little additional propulsion from helical shape

PubMed Central

Constantino, Maira A.; Jabbarzadeh, Mehdi; Fu, Henry C.; Bansil, Rama

2016-01-01

It has frequently been hypothesized that the helical body shapes of flagellated bacteria may yield some advantage in swimming ability. In particular, the helical-shaped pathogen Helicobacter pylori is often claimed to swim like a corkscrew through its harsh gastric habitat, but there has been no direct confirmation or quantification of such claims. Using fast time-resolution and high-magnification two-dimensional (2D) phase-contrast microscopy to simultaneously image and track individual bacteria in bacterial broth as well as mucin solutions, we show that both helical and rod-shaped H. pylori rotated as they swam, producing a helical trajectory. Cell shape analysis enabled us to determine shape as well as the rotational and translational speed for both forward and reverse motions, thereby inferring flagellar kinematics. Using the method of regularized Stokeslets, we directly compare observed speeds and trajectories to numerical calculations for both helical and rod-shaped bacteria in mucin and broth to validate the numerical model. Although experimental observations are limited to select cases, the model allows quantification of the effects of body helicity, length, and diameter. We find that due to relatively slow body rotation rates, the helical shape makes at most a 15% contribution to propulsive thrust. The effect of body shape on swimming speeds is instead dominated by variations in translational drag required to move the cell body. Because helical cells are one of the strongest candidates for propulsion arising from the cell body, our results imply that quite generally, swimming speeds of flagellated bacteria can only be increased a little by body propulsion. PMID:28138539

Improved synthesis of chiral alcohols with Escherichia coli cells co-expressing pyridine nucleotide transhydrogenase, NADP+-dependent alcohol dehydrogenase and NAD+-dependent formate dehydrogenase.

PubMed

Weckbecker, Andrea; Hummel, Werner

2004-11-01

Recombinant pyridine nucleotide transhydrogenase (PNT) from Escherichia coli has been used to regenerate NAD+ and NADPH. The pnta and pntb genes encoding for the alpha- and beta-subunits were cloned and co-expressed with NADP+-dependent alcohol dehydrogenase (ADH) from Lactobacillus kefir and NAD+-dependent formate dehydrogenase (FDH) from Candida boidinii. Using this whole-cell biocatalyst, efficient conversion of prochiral ketones to chiral alcohols was achieved: 66% acetophenone was reduced to (R)-phenylethanol over 12 h, whereas only 19% (R)-phenylethanol was formed under the same conditions with cells containing ADH and FDH genes but without PNT genes. Cells that were permeabilized with toluene showed ketone reduction only if both cofactors were present.

Light scattering measurements supporting helical structures for chromatin in solution.

PubMed

Campbell, A M; Cotter, R I; Pardon, J F

1978-05-01

Laser light scattering measurements have been made on a series of polynucleosomes containing from 50 to 150 nucleosomes. Radii of gyration have been determined as a function of polynucleosome length for different ionic strength solutions. The results suggest that at low ionic strength the chromatin adopts a loosely helical structure rather than a random coil. The helix becomes more regular on increasing the ionic strength, the dimension resembling those proposed by Finch and Klug for their solenoid model.

Structural details (kinks and non-α conformations) in transmembrane helices are intrahelically determined and can be predicted by sequence pattern descriptors

PubMed Central

Rigoutsos, Isidore; Riek, Peter; Graham, Robert M.; Novotny, Jiri

2003-01-01

One of the promising methods of protein structure prediction involves the use of amino acid sequence-derived patterns. Here we report on the creation of non-degenerate motif descriptors derived through data mining of training sets of residues taken from the transmembrane-spanning segments of polytopic proteins. These residues correspond to short regions in which there is a deviation from the regular α-helical character (i.e. π-helices, 310-helices and kinks). A ‘search engine’ derived from these motif descriptors correctly identifies, and discriminates amongst instances of the above ‘non-canonical’ helical motifs contained in the SwissProt/TrEMBL database of protein primary structures. Our results suggest that deviations from α-helicity are encoded locally in sequence patterns only about 7–9 residues long and can be determined in silico directly from the amino acid sequence. Delineation of such variations in helical habit is critical to understanding the complex structure–function relationships of polytopic proteins and for drug discovery. The success of our current methodology foretells development of similar prediction tools capable of identifying other structural motifs from sequence alone. The method described here has been implemented and is available on the World Wide Web at http://cbcsrv.watson.ibm.com/Ttkw.html. PMID:12888523

Structural details (kinks and non-alpha conformations) in transmembrane helices are intrahelically determined and can be predicted by sequence pattern descriptors.

PubMed

Rigoutsos, Isidore; Riek, Peter; Graham, Robert M; Novotny, Jiri

2003-08-01

One of the promising methods of protein structure prediction involves the use of amino acid sequence-derived patterns. Here we report on the creation of non-degenerate motif descriptors derived through data mining of training sets of residues taken from the transmembrane-spanning segments of polytopic proteins. These residues correspond to short regions in which there is a deviation from the regular alpha-helical character (i.e. pi-helices, 3(10)-helices and kinks). A 'search engine' derived from these motif descriptors correctly identifies, and discriminates amongst instances of the above 'non-canonical' helical motifs contained in the SwissProt/TrEMBL database of protein primary structures. Our results suggest that deviations from alpha-helicity are encoded locally in sequence patterns only about 7-9 residues long and can be determined in silico directly from the amino acid sequence. Delineation of such variations in helical habit is critical to understanding the complex structure-function relationships of polytopic proteins and for drug discovery. The success of our current methodology foretells development of similar prediction tools capable of identifying other structural motifs from sequence alone. The method described here has been implemented and is available on the World Wide Web at http://cbcsrv.watson.ibm.com/Ttkw.html.

The Software Design for the Wide-Field Infrared Explorer Attitude Control System

NASA Technical Reports Server (NTRS)

Anderson, Mark O.; Barnes, Kenneth C.; Melhorn, Charles M.; Phillips, Tom

1998-01-01

The Wide-Field Infrared Explorer (WIRE), currently scheduled for launch in September 1998, is the fifth of five spacecraft in the NASA/Goddard Small Explorer (SMEX) series. This paper presents the design of WIRE's Attitude Control System flight software (ACS FSW). WIRE is a momentum-biased, three-axis stabilized stellar pointer which provides high-accuracy pointing and autonomous acquisition for eight to ten stellar targets per orbit. WIRE's short mission life and limited cryogen supply motivate requirements for Sun and Earth avoidance constraints which are designed to prevent catastrophic instrument damage and to minimize the heat load on the cryostat. The FSW implements autonomous fault detection and handling (FDH) to enforce these instrument constraints and to perform several other checks which insure the safety of the spacecraft. The ACS FSW implements modules for sensor data processing, attitude determination, attitude control, guide star acquisition, actuator command generation, command/telemetry processing, and FDH. These software components are integrated with a hierarchical control mode managing module that dictates which software components are currently active. The lowest mode in the hierarchy is the 'safest' one, in the sense that it utilizes a minimal complement of sensors and actuators to keep the spacecraft in a stable configuration (power and pointing constraints are maintained). As higher modes in the hierarchy are achieved, the various software functions are activated by the mode manager, and an increasing level of attitude control accuracy is provided. If FDH detects a constraint violation or other anomaly, it triggers a safing transition to a lower control mode. The WIRE ACS FSW satisfies all target acquisition and pointing accuracy requirements, enforces all pointing constraints, provides the ground with a simple means for reconfiguring the system via table load, and meets all the demands of its real-time embedded environment (16 MHz Intel 80386 processor with 80387 coprocessor running under the VRTX operating system). The mode manager organizes and controls all the software modules used to accomplish these goals, and in particular, the FDH module is tightly coupled with the mode manager.

Instabilities of a rotating helical rod

NASA Astrophysics Data System (ADS)

Park, Yunyoung; Ko, William; Kim, Yongsam; Lim, Sookkyung

2016-11-01

Bacteria such as Escherichia coli and Vibrio alginolyticus have helical flagellar filament. By rotating a motor, which is located at the bottom end of the flagellar filament embedded in the cell body, CCW or CW, they swim forward or backward. We model a left-handed helix by the Kirchhoff rod theory and use regularized Stokes formulation to study an interaction between the surrounding fluid and the flagellar filament. We perform numerical studies focusing on relations between physical parameters and critical angular frequency of the motor, which separates overwhiring from twirling. We are also interested in the buckling instability of the hook, which is very flexible elastic rod. By measuring buckling angle, which is an angle between rotational axis and helical axis, we observe the effects of physical parameters on buckling of the hook.

Dynamic positioning configuration and its first-order optimization

NASA Astrophysics Data System (ADS)

Xue, Shuqiang; Yang, Yuanxi; Dang, Yamin; Chen, Wu

2014-02-01

Traditional geodetic network optimization deals with static and discrete control points. The modern space geodetic network is, on the other hand, composed of moving control points in space (satellites) and on the Earth (ground stations). The network configuration composed of these facilities is essentially dynamic and continuous. Moreover, besides the position parameter which needs to be estimated, other geophysical information or signals can also be extracted from the continuous observations. The dynamic (continuous) configuration of the space network determines whether a particular frequency of signals can be identified by this system. In this paper, we employ the functional analysis and graph theory to study the dynamic configuration of space geodetic networks, and mainly focus on the optimal estimation of the position and clock-offset parameters. The principle of the D-optimization is introduced in the Hilbert space after the concept of the traditional discrete configuration is generalized from the finite space to the infinite space. It shows that the D-optimization developed in the discrete optimization is still valid in the dynamic configuration optimization, and this is attributed to the natural generalization of least squares from the Euclidean space to the Hilbert space. Then, we introduce the principle of D-optimality invariance under the combination operation and rotation operation, and propose some D-optimal simplex dynamic configurations: (1) (Semi) circular configuration in 2-dimensional space; (2) the D-optimal cone configuration and D-optimal helical configuration which is close to the GPS constellation in 3-dimensional space. The initial design of GPS constellation can be approximately treated as a combination of 24 D-optimal helixes by properly adjusting the ascending node of different satellites to realize a so-called Walker constellation. In the case of estimating the receiver clock-offset parameter, we show that the circular configuration, the symmetrical cone configuration and helical curve configuration are still D-optimal. It shows that the given total observation time determines the optimal frequency (repeatability) of moving known points and vice versa, and one way to improve the repeatability is to increase the rotational speed. Under the Newton's law of motion, the frequency of satellite motion determines the orbital altitude. Furthermore, we study three kinds of complex dynamic configurations, one of which is the combination of D-optimal cone configurations and a so-called Walker constellation composed of D-optimal helical configuration, the other is the nested cone configuration composed of n cones, and the last is the nested helical configuration composed of n orbital planes. It shows that an effective way to achieve high coverage is to employ the configuration composed of a certain number of moving known points instead of the simplex configuration (such as D-optimal helical configuration), and one can use the D-optimal simplex solutions or D-optimal complex configurations in any combination to achieve powerful configurations with flexile coverage and flexile repeatability. Alternately, how to optimally generate and assess the discrete configurations sampled from the continuous one is discussed. The proposed configuration optimization framework has taken the well-known regular polygons (such as equilateral triangle and quadrangular) in two-dimensional space and regular polyhedrons (regular tetrahedron, cube, regular octahedron, regular icosahedron, or regular dodecahedron) into account. It shows that the conclusions made by the proposed technique are more general and no longer limited by different sampling schemes. By the conditional equation of D-optimal nested helical configuration, the relevance issues of GNSS constellation optimization are solved and some examples are performed by GPS constellation to verify the validation of the newly proposed optimization technique. The proposed technique is potentially helpful in maintenance and quadratic optimization of single GNSS of which the orbital inclination and the orbital altitude change under the precession, as well as in optimally nesting GNSSs to perform global homogeneous coverage of the Earth.

Sustainment Study of Flipped Spherical Torus Plasmas on HIST

NASA Astrophysics Data System (ADS)

Takamiya, T.; Nagata, M.; Kawami, K.; Hasegawa, H.; Fukumoto, N.; Uyama, T.; Masamune, S.; Iida, M.; Katsurai, M.

2003-10-01

We have discovered that helicity-driven ST plasmas relax toward the flipped state by decreasing the external toroidal field and reversing its sign in time [1]. From the viewpoint of coaxial helicity injection (CHI) current drive, it is conceivable that the flipped ST (F-ST), which consists of only closed flux surfaces, compares favorably with the normal ST. We have investigated the sustainment mechanism of the F-ST plasma. The helicity-driven relaxed theory shows that there exist the mixed states of ST and F-ST in the flux conserver. Helicity is transferred to F-ST through the ST with coupling with gun electrodes. It has been found that magnetic reconnection between the toroidal magnetic field plays important role in the sustainment of the F-ST. The magnetic field in the outer edge region shows regular oscillations which have a large amplitude of the n=1 mode. The core region of the F-ST seems to be relatively stable. [1] M. Nagata, et al., Phys. Rev. Lett. 90, 225001 (2003)

The spatial configuration of ordered polynucleotide chains. II. The poly(rA) helix.

PubMed Central

Olson, W K

1975-01-01

Approximate details of the spatial configuration of the ordered single-stranded poly(rA) molecule in dilute solution have been obtained in a combined theoretical analysis of base stacking and chain flexibility. Only those regularly repeating structures which fulfill the criterion of conformational flexibility (based upon all available experimental and theoretical evidence of preferred bond rotations) and which also exhibit the right-handed base stacking pattern observed in nmr investigations of poly(rA) are deemed suitable single-stranded helices. In addition, the helical geometry of the stacked structures is required to be consistent with the experimentally observed dimensions of both completely ordered and partially ordered poly(rA) chains. Only a single category of poly(rA) helices (very similar in all conformational details to the individual chains of the poly(rA) double-stranded X-ray structure) is thus obtained. Other conformationally feasible polynucleotide helices characterized simply by a parallel and overlapping base stacking arrangement are also discussed. PMID:1052529

Generic patient-reported outcomes in child health research: a review of conceptual content using World Health Organization definitions.

PubMed

Fayed, Nora; de Camargo, Olaf Kraus; Kerr, Elizabeth; Rosenbaum, Peter; Dubey, Ankita; Bostan, Cristina; Faulhaber, Markus; Raina, Parminder; Cieza, Alarcos

2012-12-01

Our aims were to (1) describe the conceptual basis of popular generic instruments according to World Health Organization (WHO) definitions of functioning, disability, and health (FDH), and quality of life (QOL) with health-related quality of life (HRQOL) as a subcomponent of QOL; (2) map the instruments to the International Classification of Functioning, Disability and Health (ICF); and (3) provide information on how the analyzed instruments were used in the literature. This should enable users to make valid choices about which instruments have the desired content for a specific context or purpose. Child health-based literature over a 5-year period was reviewed to find research employing health status and QOL/HRQOL instruments. WHO definitions of FDH and QOL were applied to each item of the 15 most used instruments to differentiate measures of FDH and QOL/HRQOL. The ICF was used to describe the health and health-related content (if any) in those instruments. Additional aspects of instrument use were extracted from these articles. Many instruments that were used to measure QOL/HRQOL did not reflect WHO definitions of QOL. The ICF domains within instruments were highly variable with respect to whether body functions, activities and participation, or environment were emphasized. There is inconsistency among researchers about how to measure HRQOL and QOL. Moreover, when an ICF content analysis is applied, there is variability among instruments in the health components included and emphasized. Reviewing content is important for matching instruments to their intended purpose. © The Authors. Developmental Medicine & Child Neurology © 2012 Mac Keith Press.

Growth and recombinant protein expression with Escherichia coli in different batch cultivation media.

PubMed

Hortsch, Ralf; Weuster-Botz, Dirk

2011-04-01

Parallel operated milliliter-scale stirred tank bioreactors were applied for recombinant protein expression studies in simple batch experiments without pH titration. An enzymatic glucose release system (EnBase), a complex medium, and the frequently used LB and TB media were compared with regard to growth of Escherichia coli and recombinant protein expression (alcohol dehydrogenase (ADH) from Lactobacillus brevis and formate dehydrogenase (FDH) from Candida boidinii). Dissolved oxygen and pH were recorded online, optical densities were measured at-line, and the activities of ADH and FDH were analyzed offline. Best growth was observed in a complex medium with maximum dry cell weight concentrations of 14 g L(-1). EnBase cultivations enabled final dry cell weight concentrations between 6 and 8 g L(-1). The pH remained nearly constant in EnBase cultivations due to the continuous glucose release, showing the usefulness of this glucose release system especially for pH-sensitive bioprocesses. Cell-specific enzyme activities varied considerably depending on the different media used. Maximum specific ADH activities were measured with the complex medium, 6 h after induction with IPTG, whereas the highest specific FDH activities were achieved with the EnBase medium at low glucose release profiles 24 h after induction. Hence, depending on the recombinant protein, different medium compositions, times for induction, and times for cell harvest have to be evaluated to achieve efficient expression of recombinant proteins in E. coli. A rapid experimental evaluation can easily be performed with parallel batch operated small-scale stirred tank bioreactors.

Non-lignified helical cell wall thickenings in root cortical cells of Aspleniaceae (Polypodiales): histology and taxonomical significance

PubMed Central

Leroux, O.; Bagniewska-Zadworna, A.; Rambe, S. K.; Knox, J. P.; Marcus, S. E.; Bellefroid, E.; Stubbe, D.; Chabbert, B.; Habrant, A.; Claeys, M.; Viane, R. L. L.

2011-01-01

Background and Aims Extraxylary helical cell wall thickenings in vascular plants are not well documented, except for those in orchid velamen tissues which have been studied extensively. Reports on their occurrence in ferns exist, but detailed information is missing. The aim of this study is to focus on the broad patterns of structure and composition and to study the taxonomic occurrence of helical cell wall thickenings in the fern family Aspleniaceae. Methods Structural and compositional aspects of roots have been examined by means of light, electron, epifluorescence and laser scanning confocal microscopy. To assess the taxonomical distribution of helical cell wall thickenings a molecular phylogenetic analysis based on rbcL sequences of 64 taxa was performed. Key Results The helical cell wall thickenings of all examined species showed considerable uniformity of design. The pattern consists of helical, regularly bifurcating and anastomosing strands. Compositionally, the cell wall thickenings were found to be rich in homogalacturonan, cellulose, mannan and xyloglucan. Thioacidolysis confirmed our negative phloroglucinol staining tests, demonstrating the absence of lignins in the root cortex. All taxa with helical cell wall thickenings formed a monophyletic group supported by a 100 % bootstrap value and composed of mainly epiphytic species. Conclusions This is the first report of non-lignified pectin-rich secondary cell walls in ferns. Based on our molecular analysis, we reject the hypothesis of parallel evolution of helical cell wall thickenings in Aspleniaceae. Helical cell wall thickenings can mechanically stabilize the cortex tissue, allowing maximal uptake of water and nutrients during rainfall events. In addition, it can also act as a boundary layer increasing the diffusive pathway towards the atmosphere, preventing desiccation of the stele of epiphytic growing species. PMID:21118842

On the Global Regularity of a Helical-Decimated Version of the 3D Navier-Stokes Equations

NASA Astrophysics Data System (ADS)

Biferale, Luca; Titi, Edriss S.

2013-06-01

We study the global regularity, for all time and all initial data in H 1/2, of a recently introduced decimated version of the incompressible 3D Navier-Stokes (dNS) equations. The model is based on a projection of the dynamical evolution of Navier-Stokes (NS) equations into the subspace where helicity (the L 2-scalar product of velocity and vorticity) is sign-definite. The presence of a second (beside energy) sign-definite inviscid conserved quadratic quantity, which is equivalent to the H 1/2-Sobolev norm, allows us to demonstrate global existence and uniqueness, of space-periodic solutions, together with continuity with respect to the initial conditions, for this decimated 3D model. This is achieved thanks to the establishment of two new estimates, for this 3D model, which show that the H 1/2 and the time average of the square of the H 3/2 norms of the velocity field remain finite. Such two additional bounds are known, in the spirit of the work of H. Fujita and T. Kato (Arch. Ration. Mech. Anal. 16:269-315, 1964; Rend. Semin. Mat. Univ. Padova 32:243-260, 1962), to be sufficient for showing well-posedness for the 3D NS equations. Furthermore, they are directly linked to the helicity evolution for the dNS model, and therefore with a clear physical meaning and consequences.

Conformational properties of two exopolysaccharides produced by Inquilinus limosus, a cystic fibrosis lung pathogen.

PubMed

Kuttel, Michelle; Ravenscroft, Neil; Foschiatti, Michela; Cescutti, Paola; Rizzo, Roberto

2012-03-01

Inquilinus limosus is a multi-resistant bacterium found in the respiratory tract of patients with cystic fibrosis. This bacterium produces two unique fully pyruvylated exopolysaccharides in similar quantities: an α-(1→2)-linked mannan and a β-(1→3)-linked glucan. We employed molecular modelling methods to probe the characteristic conformations and dynamics of these polysaccharides, with corroboration from potentiometric titrations and circular dichroism experiments. Our calculations reveal different structural motifs for the mannan and glucan polysaccharides: the glucan forms primarily right-handed helices with a wide range of extensions, while the mannan forms only left-handed helices. This finding is supported by our circular dichroism experiments. Our calculations also show that the (1→3)-β-d-Glcp linkage is more dynamically flexible than the (1→2)-α-d-Manp: the glucan characteristically forms a range of wide helices with large central cavities. In contrast, the mannan forms rigid regular 'bottlebrush' helices with a minimal central cavity. The widely different character of these two polymers suggests a possible differentiation of biological roles. Copyright © 2012 Elsevier Ltd. All rights reserved.

In vivo mechanical study of helical cardiac pacing electrode interacting with canine myocardium

NASA Astrophysics Data System (ADS)

Zhang, Xiangming; Ma, Nianke; Fan, Hualin; Niu, Guodong; Yang, Wei

2007-06-01

Cardiac pacing is a medical device to help human to overcome arrhythmia and to recover the regular beats of heart. A helical configuration of electrode tip is a new type of cardiac pacing lead distal tip. The helical electrode attaches itself to the desired site of heart by screwing its helical tip into the myocardium. In vivo experiments on anesthetized dogs were carried out to measure the acute interactions between helical electrode and myocardium during screw-in and pull-out processes. These data would be helpful for electrode tip design and electrode/myocardium adherence safety evaluation. They also provide reliability data for clinical site choice of human heart to implant and to fix the pacing lead. A special design of the helical tip using strain gauges is instrumented for the measurement of the screw-in and pull-out forces. We obtained the data of screw-in torques and pull-out forces for five different types of helical electrodes at nine designed sites on ten canine hearts. The results indicate that the screw-in torques increased steplike while the torque time curves presente saw-tooth fashion. The maximum torque has a range of 0.3 1.9 N mm. Obvious differences are observed for different types of helical tips and for different test sites. Large pull-out forces are frequently obtained at epicardium of left ventricle and right ventricle lateral wall, and the forces obtained at right ventricle apex and outflow tract of right ventricle are normally small. The differences in pull-out forces are dictated by the geometrical configuration of helix and regional structures of heart muscle.

Illumination with 630-nm red light reduces oxidative stress and restores memory by photo-activating catalase and formaldehyde dehydrogenase in SAMP8 mice.

PubMed

Zhang, Jingnan; Yue, Xiangpei; Luo, Hongjun; Jiang, Wenjing; Mei, Yufei; Ai, Li; Gao, Ge; Wu, Yan; Yang, Hui; An, Jieran; Ding, Shumao; Yang, Xu; Sun, Bingui; Luo, Wenhong; He, Rongqiao; Jia, Jianping; Lyu, Jihui; Tong, Zhiqian

2018-06-05

Pharmacological treatments for Alzheimer's disease (AD) have not resulted in desirable clinical efficacy over 100 years. Hydrogen peroxide (H2O2), a reactive and the most stable compound of reactive oxygen species (ROS), contributes to oxidative stress in AD patients. Here, we designed a medical device to emit red light at 630±15 nm from a light-emitting diode (LED-RL) and investigated whether the LED-RL reduces brain H2O2 levels and improves memory in senescence-accelerated prone 8 mouse (SAMP8) model of age-related dementia. We found that age-associated H2O2 directly inhibited formaldehyde dehydrogenase (FDH). FDH inactivity and semicarbazide-sensitive amine oxidase (SSAO) disorder resulted in endogenous formaldehyde (FA) accumulation. Unexpectedly, excess FA, in turn, caused acetylcholine (Ach) deficiency by inhibiting choline acetyltransferase (ChAT) activity in vitro and in vivo. Interestingly, the 630-nm red light can penetrate the skull and abdomen with light penetration rates: ~49% and ~43%, respectively. Illumination with LED-RL markedly activated both catalase and FDH in the brains, cultured cells and purified protein solutions, all reduced brain H2O2 and FA levels and restored brain Ach contents. Consequently, LED-RL not only prevented early-stage memory decline but also rescued late-stage memory deficits in SAMP8 mice. We developed a phototherapeutic device with 630-nm red light, and this LED-RL reduced brain H2O2 levels and reversed age-related memory disorders. The phototherapy of LED-RL has low photo toxicity and high rate of tissue penetration, and non-invasively reverses aging-associated cognitive decline. This finding opens a promising opportunity to translate LED-RL into clinical treatment for patients with dementia.

Fresh from the Ornamental Garden: Hips of Selected Rose Cultivars Rich in Phytonutrients.

PubMed

Cunja, Vlasta; Mikulic-Petkovsek, Maja; Weber, Nika; Jakopic, Jerneja; Zupan, Anka; Veberic, Robert; Stampar, Franci; Schmitzer, Valentina

2016-02-01

Morphological parameters (size, weight, color), the content of sugars, organic acids, lycopene, β-carotene, and phenolics were determined in hips of Rosa canina (RCA), Rosa sweginzowii (RSW), Rosa rugosa (RUG), and selected ornamental Rosa cultivars Fru Dagmar Hastrup (FDH), Repandia (REP), Veilchenblau (RVB), Aloha (RAL), Bonica (BON), and Golden Gate (RGG). Although traditionally used RCA hips contained the highest amount of cyanidin-3-glucoside (83 μg/g DW) and were the reddest (h° = 17.5), they did not stand out in other analyzed parameters. RGG climber had the biggest hips (8.86 g), which also contained highest sugar levels (50.9 g/100 g DW). RAL stood out as the cultivar rich in organic acids (33.9 g/100 g DW), mainly because of high quinic acid content (17.6 g/100g DW). FDH and RSW hips were characterized by particularly high ascorbic acid levels (4325 mg/100 g DW and 4711 mg/100 g DW). Other ornamental cultivars contained low amounts of ascorbic acid compared to the analyzed species. The phenolic profile was species/cultivars-specific. The greatest diversity of phenolic compounds was detected in RUG and FDH hips (55 and 54 different tentatively identified compounds with HPLC/MS). Flavanols represented the main phenolic class in most of the investigated species/cultivars and RGG hips contained the highest amount of catechin and proanthocyandin derivatives (15855 μg/g DW). Altogether RAL hips contained the highest quantity of phenolics (44746 μg/g DW) mainly due to high levels of hydrolysable tannins compared to other species/cultivars. Although small, hips of BON and REP were most abundant regarding β-carotene and lycopene content, respectively. © 2016 Institute of Food Technologists®

Identification of formaldehyde as the metabolite responsible for the mutagenicity of methyl tertiary-butyl ether in the activated mouse lymphoma assay.

PubMed

Mackerer, C R; Angelosanto, F A; Blackburn, G R; Schreiner, C A

1996-09-01

Methyl tertiary-butyl ether (MTBE), which is added to gasoline as an octane enhancer and to reduce automotive emissions, has been evaluated in numerous toxicological tests, including those for genotoxicity. MTBE did not show any mutagenic potential in the Ames bacterial assay or any clastogenicity in cytogenetic tests. However, it has been shown to be mutagenic in an in vitro gene mutation assay using mouse lymphoma cells when tested in the presence, but not in the absence, of a rat liver-derived metabolic activation system (S-9). In the present study, MTBE was tested to determine if formaldehyde, in the presence of the S-9, was responsible for the observed mutagenicity. A modification of the mouse lymphoma assay was employed which permits determination of whether a suspect material is mutagenic because it contains or is metabolized to formaldehyde. In the modified assay, the enzyme formaldehyde dehydrogenase (FDH) and its co-factor, NAD+ are added in large excess during the exposure period so that any formaldehyde produced in the system is rapidly converted to formic acid which is not genotoxic. An MTBE dose-responsive increase in the frequency of mutants and in cytotoxicity occurred without FDH present, and this effect was greatly reduced in the presence of FDH NAD+. The findings clearly demonstrate that formaldehyde derived from MTBE is responsible for mutagenicity of MTBE in the activated mouse lymphoma assay. Furthermore, the results suggest that the lack of mutagenicity/clastogenicity seen with MTBE in other in vitro assays might have resulted from inadequacies in the test systems employed for those assays.

Magnetic stripes and skyrmions with helicity reversals.

PubMed

Yu, Xiuzhen; Mostovoy, Maxim; Tokunaga, Yusuke; Zhang, Weizhu; Kimoto, Koji; Matsui, Yoshio; Kaneko, Yoshio; Nagaosa, Naoto; Tokura, Yoshinori

2012-06-05

It was recently realized that topological spin textures do not merely have mathematical beauty but can also give rise to unique functionalities of magnetic materials. An example is the skyrmion--a nano-sized bundle of noncoplanar spins--that by virtue of its nontrivial topology acts as a flux of magnetic field on spin-polarized electrons. Lorentz transmission electron microscopy recently emerged as a powerful tool for direct visualization of skyrmions in noncentrosymmetric helimagnets. Topologically, skyrmions are equivalent to magnetic bubbles (cylindrical domains) in ferromagnetic thin films, which were extensively explored in the 1970s for data storage applications. In this study we use Lorentz microscopy to image magnetic domain patterns in the prototypical magnetic oxide-M-type hexaferrite with a hint of scandium. Surprisingly, we find that the magnetic bubbles and stripes in the hexaferrite have a much more complex structure than the skyrmions and spirals in helimagnets, which we associate with the new degree of freedom--helicity (or vector spin chirality) describing the direction of spin rotation across the domain walls. We observe numerous random reversals of helicity in the stripe domain state. Random helicity of cylindrical domain walls coexists with the positional order of magnetic bubbles in a triangular lattice. Most unexpectedly, we observe regular helicity reversals inside skyrmions with an unusual multiple-ring structure.

Topology of modified helical gears and Tooth Contact Analysis (TCA) program

NASA Technical Reports Server (NTRS)

Litvin, Faydor L.; Zhang, Jiao

1989-01-01

The contents of this report covers: (1) development of optimal geometries for crowned helical gears; (2) a method for their generation; (3) tooth contact analysis (TCA) computer programs for the analysis of meshing and bearing contact of the crowned helical gears; and (4) modelling and simulation of gear shaft deflection. The developed method for synthesis was used to determine the optimal geometry for a crowned helical pinion surface and was directed to localize the bearing contact and guarantee favorable shape and a low level of transmission errors. Two new methods for generation of the crowned helical pinion surface are proposed. One is based on the application of a tool with a surface of revolution that slightly deviates from a regular cone surface. The tool can be used as a grinding wheel or as a shaver. The other is based on a crowning pinion tooth surface with predesigned transmission errors. The pinion tooth surface can be generated by a computer-controlled automatic grinding machine. The TCA program simulates the meshing and bearing contact of the misaligned gears. The transmission errors are also determined. The gear shaft deformation was modelled and investigated. It was found that the deflection of gear shafts has the same effect as gear misalignment.

In situ calibration of an infrared imaging video bolometer in the Large Helical Device

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mukai, K., E-mail: mukai.kiyofumi@LHD.nifs.ac.jp; Peterson, B. J.; Pandya, S. N.

The InfraRed imaging Video Bolometer (IRVB) is a powerful diagnostic to measure multi-dimensional radiation profiles in plasma fusion devices. In the Large Helical Device (LHD), four IRVBs have been installed with different fields of view to reconstruct three-dimensional profiles using a tomography technique. For the application of the measurement to plasma experiments using deuterium gas in LHD in the near future, the long-term effect of the neutron irradiation on the heat characteristics of an IRVB foil should be taken into account by regular in situ calibration measurements. Therefore, in this study, an in situ calibration system was designed.

A rare human syndrome provides genetic evidence that WNT signaling is required for reprogramming of fibroblasts to induced pluripotent stem cells

PubMed Central

Ross, Jason; Busch, Julia; Mintz, Ellen; Ng, Damian; Stanley, Alexandra; Brafman, David; Sutton, V. Reid; Van den Veyver, Ignatia; Willert, Karl

2015-01-01

SUMMARY WNT signaling promotes the reprogramming of somatic cells to an induced pluripotent state. We provide genetic evidence that WNT signaling is a requisite step during the induction of pluripotency. Fibroblasts from individuals with Focal Dermal Hypoplasia (FDH), a rare genetic syndrome caused by mutations in the essential WNT processing enzyme PORCN, fail to reprogram using standard methods. This blockade in reprogramming is overcome by ectopic WNT signaling and by PORCN overexpression, thus demonstrating that WNT signaling is essential for reprogramming. The rescue of reprogramming is critically dependent on the level of WNT signaling: steady baseline activation of the WNT pathway yields karyotypically normal iPS cells, whereas daily stimulation with Wnt3a produces FDH-iPS cells with severely abnormal karyotypes. Therefore, although WNT signaling is required for cellular reprogramming, inappropriate activation of WNT signaling induces chromosomal instability, highlighting the precarious nature of ectopic WNT activation, and its tight relationship with oncogenic transformation. PMID:25464842

Self assembling proteins

DOEpatents

Yeates, Todd O.; Padilla, Jennifer; Colovos, Chris

2004-06-29

Novel fusion proteins capable of self-assembling into regular structures, as well as nucleic acids encoding the same, are provided. The subject fusion proteins comprise at least two oligomerization domains rigidly linked together, e.g. through an alpha helical linking group. Also provided are regular structures comprising a plurality of self-assembled fusion proteins of the subject invention, and methods for producing the same. The subject fusion proteins find use in the preparation of a variety of nanostructures, where such structures include: cages, shells, double-layer rings, two-dimensional layers, three-dimensional crystals, filaments, and tubes.

Helical 1:1 α/Sulfono-γ-AA Heterogeneous Peptides with Antibacterial Activity

DOE Office of Scientific and Technical Information (OSTI.GOV)

She, Fengyu; Nimmagadda, Alekhya; Teng, Peng

As one of the greatest threats facing in 21st century, antibiotic resistance is now a major public health concern. Host-defense peptides (HDPs) offer an alternative approach to combat emerging multidrug-resistant bacteria. It is known that helical HDPs such as magainin 2 and its analogs adopt cationic amphipathic conformations upon interaction with bacterial membranes, leading to membrane disruption and subsequent bacterial cell death. We have previously shown that amphipathic sulfono-γ-AApeptides could mimic magainin 2 and exhibit bactericidal activity. In this article, we demonstrate for the first time that amphipathic helical 1:1 α/sulfono-γ-AA heterogeneous peptides, in which regular amino acids and sulfono-γ-AApeptidemore » building blocks are alternatively present in a 1:1 pattern, display potent antibacterial activity against both Gram-positive and Gram-negative bacterial pathogens. Small Angle X-ray Scattering (SAXS) suggests that the lead sequences adopt defined helical structures. The subsequent studies including 2 fluorescence microscopy and time-kill experiments indicate that these hybrid peptides exert antimicrobial activity by mimicking the mechanism of HDPs. Our findings may lead to the development of HDP-mimicking antimicrobial peptidomimetics that combat drug-resistant bacterial pathogens. In addition, our results also demonstrate the effective design of a new class of helical foldamer, which could be employed to interrogate other important biological targets such as protein-protein interactions in the future.« less

Hydration-induced crystalline transformation of starch polymer under ambient conditions.

PubMed

Qiao, Dongling; Zhang, Binjia; Huang, Jing; Xie, Fengwei; Wang, David K; Jiang, Fatang; Zhao, Siming; Zhu, Jie

2017-10-01

With synchrotron small/wide-angle X-ray scattering (SAXS/WAXS), we revealed that post-harvest hydration at ambient conditions can further alter the starch crystalline structure. The hydration process induced the alignment of starch helices into crystalline lamellae, irrespective of the starch type (A- or B-). In this process, non-crystalline helices were probably packed with water molecules to form new crystal units, thereby enhancing the overall concentration of starch crystallinity. In particular, a fraction of the monoclinic crystal units of the A-type starches encapsulated water molecules during hydration, leading to the outward movement of starch helices. Such movement resulted in the transformation of monoclinic units into hexagonal units, which was associated with the B-type crystallites. Hence, the hydration under ambient conditions could enhance the B-polymorphic features for both A-type and B-type starches. The new knowledge obtained here may guide the design of biopolymer-based liquid crystal materials with controlled lattice regularity and demanded features. Copyright © 2017 Elsevier B.V. All rights reserved.

Clostridium acidurici electron-bifurcating formate dehydrogenase.

PubMed

Wang, Shuning; Huang, Haiyan; Kahnt, Jörg; Thauer, Rudolf K

2013-10-01

Cell extracts of uric acid-grown Clostridium acidurici catalyzed the coupled reduction of NAD(+) and ferredoxin with formate at a specific activity of 1.3 U/mg. The enzyme complex catalyzing the electron-bifurcating reaction was purified 130-fold and found to be composed of four subunits encoded by the gene cluster hylCBA-fdhF2.

Growth, nutritional, and gastrointestinal aspects of focal dermal hypoplasia (Goltz-Gorlin syndrome)

USDA-ARS?s Scientific Manuscript database

Focal dermal hypoplasia (FDH) is a rare genetic disorder caused by mutations in the PORCN gene located on the X-chromosome. In the present study, we characterized the pattern of growth, body composition, and the nutritional and gastrointestinal aspects of children and adults (n'='19) affected with t...

Frequency-Domain Tomography for Single-shot, Ultrafast Imaging of Evolving Laser-Plasma Accelerators

NASA Astrophysics Data System (ADS)

Li, Zhengyan; Zgadzaj, Rafal; Wang, Xiaoming; Downer, Michael

2011-10-01

Intense laser pulses propagating through plasma create plasma wakefields that often evolve significantly, e.g. by expanding and contracting. However, such dynamics are known in detail only through intensive simulations. Laboratory visualization of evolving plasma wakes in the ``bubble'' regime is important for optimizing and scaling laser-plasma accelerators. Recently snap-shots of quasi-static wakes were recorded using frequency-domain holography (FDH). To visualize the wake's evolution, we have generalized FDH to frequency-domain tomography (FDT), which uses multiple probes propagating at different angles with respect to the pump pulse. Each probe records a phase streak, imprinting a partial record of the evolution of pump-created structures. We then topographically reconstruct the full evolution from all phase streaks. To prove the concept, a prototype experiment visualizing nonlinear index evolution in glass is demonstrated. Four probes propagating at 0, 0.6, 2, 14 degrees to the index ``bubble'' are angularly and temporally multiplexed to a single spectrometer to achieve cost-effective FDT. From these four phase streaks, an FDT algorithm analogous to conventional CT yields a single-shot movie of the pump's self-focusing dynamics.

Clostridium acidurici Electron-Bifurcating Formate Dehydrogenase

PubMed Central

Wang, Shuning; Huang, Haiyan; Kahnt, Jörg

2013-01-01

Cell extracts of uric acid-grown Clostridium acidurici catalyzed the coupled reduction of NAD+ and ferredoxin with formate at a specific activity of 1.3 U/mg. The enzyme complex catalyzing the electron-bifurcating reaction was purified 130-fold and found to be composed of four subunits encoded by the gene cluster hylCBA-fdhF2. PMID:23872566

Finance and supply management project execution plan

DOE Office of Scientific and Technical Information (OSTI.GOV)

BENNION, S.I.

As a subproject of the HANDI 2000 project, the Finance and Supply Management system is intended to serve FDH and Project Hanford major subcontractor with financial processes including general ledger, project costing, budgeting, and accounts payable, and supply management process including purchasing, inventory and contracts management. Currently these functions are performed with numerous legacy information systems and suboptimized processes.

Thermodynamic analysis of the disorder-to-α-helical transition of 18.5-kDa myelin basic protein reveals an equilibrium intermediate representing the most compact conformation.

PubMed

Vassall, Kenrick A; Jenkins, Andrew D; Bamm, Vladimir V; Harauz, George

2015-05-22

The intrinsically disordered, 18.5-kDa isoform of myelin basic protein (MBP) is a peripheral membrane protein that is essential to proper myelin formation in the central nervous system. MBP acts in oligodendrocytes both to adjoin membrane leaflets to each other in forming myelin and as a hub in numerous protein-protein and protein-membrane interaction networks. Like many intrinsically disordered proteins (IDPs), MBP multifunctionality arises from its high conformational plasticity and its ability to undergo reversible disorder-to-order transitions. One such transition is the disorder-to-α-helical conformational change that is induced upon MBP-membrane binding. Here, we have investigated the disorder-to-α-helical transition of MBP-derived α-peptides and the full-length 18.5-kDa protein. This transition was induced through titration of the membrane-mimetic solvent trifluoroethanol into both protein and peptide solutions, and conformational change was monitored using circular dichroism spectroscopy, 1-anilinonaphthalene-8-sulfonic acid binding, tryptophan fluorescence quenching, and Förster (fluorescence) resonance energy transfer measurements. The data suggest that the disorder-to-α-helical transition of MBP follows a 3-state model: disordered↔intermediate↔α-helical, with each of the identified equilibrium states likely representing a conformational ensemble. The disordered state is characterized by slight compaction with little regular secondary structure, whereas the intermediate is also disordered but globally more compact. Surprisingly, the α-helical conformation is less compact than the intermediate. This study suggests that multifunctionality in MBP could arise from differences in the population of energetically distinct ensembles under different conditions and also provides an example of an IDP that undergoes cooperative global conformation change. Copyright © 2015 Elsevier Ltd. All rights reserved.

Amylopectin molecular structure reflected in macromolecular organization of granular starch.

PubMed

Vermeylen, Rudi; Goderis, Bart; Reynaers, Harry; Delcour, Jan A

2004-01-01

For lintners with negligible amylose retrogradation, crystallinity related inversely to starch amylose content and, irrespective of starch source, incomplete removal of amorphous material was shown. The latter was more pronounced for B-type than for A-type starches. The two predominant lintner populations, with modal degrees of polymerization (DP) of 13-15 and 23-27, were best resolved for amylose-deficient and A-type starches. Results indicate a more specific hydrolysis of amorphous lamellae in such starches. Small-angle X-ray scattering showed a more intense 9-nm scattering peak for native amylose-deficient A-type starches than for their regular or B-type analogues. The experimental evidence indicates a lower contrasting density within the "crystalline" shells of the latter starches. A higher density in the amorphous lamellae, envisaged by the lamellar helical model, explains the relative acid resistance of linear amylopectin chains with DP > 20, observed in lintners of B-type starches. Because amylopectin chain length distributions were similar for regular and amylose-deficient starches of the same crystal type, we deduce that the more dense (and ordered) packing of double helices into lamellar structures in amylose-deficient starches is due to a different amylopectin branching pattern.

Regular Mechanical Transformation of Rotations Into Translations: Part 1. Kinematic Analysis and Definition of the Basic Characteristics

NASA Astrophysics Data System (ADS)

Abadjieva, Emilia; Abadjiev, Valentin

2017-06-01

The science that study the processes of motions transformation upon a preliminary defined law between non-coplanar axes (in general case) axes of rotations or axis of rotation and direction of rectilinear translation by three-link mechanisms, equipped with high kinematic joints, can be treated as an independent branch of Applied Mechanics. It deals with mechanical behaviour of these multibody systems in relation to the kinematic and geometric characteristics of the elements of the high kinematic joints, which form them. The object of study here is the process of regular transformation of rotation into translation. The developed mathematical model is subjected to the defined task for studying the sliding velocity vector function at the contact point from the surfaces elements of arbitrary high kinematic joints. The main kinematic characteristics of the studied type motions transformation (kinematic cylinders on level, kinematic relative helices (helical conoids) and kinematic pitch configurations) are defined on the bases of the realized analysis. These features expand the theoretical knowledge, which is the objective of the gearing theory. They also complement the system of kinematic and geometric primitives, that form the mathematical model for synthesis of spatial rack mechanisms.

Volumetric CT with sparse detector arrays (and application to Si-strip photon counters).

PubMed

Sisniega, A; Zbijewski, W; Stayman, J W; Xu, J; Taguchi, K; Fredenberg, E; Lundqvist, Mats; Siewerdsen, J H

2016-01-07

Novel x-ray medical imaging sensors, such as photon counting detectors (PCDs) and large area CCD and CMOS cameras can involve irregular and/or sparse sampling of the detector plane. Application of such detectors to CT involves undersampling that is markedly different from the commonly considered case of sparse angular sampling. This work investigates volumetric sampling in CT systems incorporating sparsely sampled detectors with axial and helical scan orbits and evaluates performance of model-based image reconstruction (MBIR) with spatially varying regularization in mitigating artifacts due to sparse detector sampling. Volumetric metrics of sampling density and uniformity were introduced. Penalized-likelihood MBIR with a spatially varying penalty that homogenized resolution by accounting for variations in local sampling density (i.e. detector gaps) was evaluated. The proposed methodology was tested in simulations and on an imaging bench based on a Si-strip PCD (total area 5 cm  ×  25 cm) consisting of an arrangement of line sensors separated by gaps of up to 2.5 mm. The bench was equipped with translation/rotation stages allowing a variety of scanning trajectories, ranging from a simple axial acquisition to helical scans with variable pitch. Statistical (spherical clutter) and anthropomorphic (hand) phantoms were considered. Image quality was compared to that obtained with a conventional uniform penalty in terms of structural similarity index (SSIM), image uniformity, spatial resolution, contrast, and noise. Scan trajectories with intermediate helical width (~10 mm longitudinal distance per 360° rotation) demonstrated optimal tradeoff between the average sampling density and the homogeneity of sampling throughout the volume. For a scan trajectory with 10.8 mm helical width, the spatially varying penalty resulted in significant visual reduction of sampling artifacts, confirmed by a 10% reduction in minimum SSIM (from 0.88 to 0.8) and a 40% reduction in the dispersion of SSIM in the volume compared to the constant penalty (both penalties applied at optimal regularization strength). Images of the spherical clutter and wrist phantoms confirmed the advantages of the spatially varying penalty, showing a 25% improvement in image uniformity and 1.8  ×  higher CNR (at matched spatial resolution) compared to the constant penalty. The studies elucidate the relationship between sampling in the detector plane, acquisition orbit, sampling of the reconstructed volume, and the resulting image quality. They also demonstrate the benefit of spatially varying regularization in MBIR for scenarios with irregular sampling patterns. Such findings are important and integral to the incorporation of a sparsely sampled Si-strip PCD in CT imaging.

Volumetric CT with sparse detector arrays (and application to Si-strip photon counters)

NASA Astrophysics Data System (ADS)

Sisniega, A.; Zbijewski, W.; Stayman, J. W.; Xu, J.; Taguchi, K.; Fredenberg, E.; Lundqvist, Mats; Siewerdsen, J. H.

2016-01-01

Novel x-ray medical imaging sensors, such as photon counting detectors (PCDs) and large area CCD and CMOS cameras can involve irregular and/or sparse sampling of the detector plane. Application of such detectors to CT involves undersampling that is markedly different from the commonly considered case of sparse angular sampling. This work investigates volumetric sampling in CT systems incorporating sparsely sampled detectors with axial and helical scan orbits and evaluates performance of model-based image reconstruction (MBIR) with spatially varying regularization in mitigating artifacts due to sparse detector sampling. Volumetric metrics of sampling density and uniformity were introduced. Penalized-likelihood MBIR with a spatially varying penalty that homogenized resolution by accounting for variations in local sampling density (i.e. detector gaps) was evaluated. The proposed methodology was tested in simulations and on an imaging bench based on a Si-strip PCD (total area 5 cm  ×  25 cm) consisting of an arrangement of line sensors separated by gaps of up to 2.5 mm. The bench was equipped with translation/rotation stages allowing a variety of scanning trajectories, ranging from a simple axial acquisition to helical scans with variable pitch. Statistical (spherical clutter) and anthropomorphic (hand) phantoms were considered. Image quality was compared to that obtained with a conventional uniform penalty in terms of structural similarity index (SSIM), image uniformity, spatial resolution, contrast, and noise. Scan trajectories with intermediate helical width (~10 mm longitudinal distance per 360° rotation) demonstrated optimal tradeoff between the average sampling density and the homogeneity of sampling throughout the volume. For a scan trajectory with 10.8 mm helical width, the spatially varying penalty resulted in significant visual reduction of sampling artifacts, confirmed by a 10% reduction in minimum SSIM (from 0.88 to 0.8) and a 40% reduction in the dispersion of SSIM in the volume compared to the constant penalty (both penalties applied at optimal regularization strength). Images of the spherical clutter and wrist phantoms confirmed the advantages of the spatially varying penalty, showing a 25% improvement in image uniformity and 1.8  ×  higher CNR (at matched spatial resolution) compared to the constant penalty. The studies elucidate the relationship between sampling in the detector plane, acquisition orbit, sampling of the reconstructed volume, and the resulting image quality. They also demonstrate the benefit of spatially varying regularization in MBIR for scenarios with irregular sampling patterns. Such findings are important and integral to the incorporation of a sparsely sampled Si-strip PCD in CT imaging.

Volumetric CT with sparse detector arrays (and application to Si-strip photon counters)

PubMed Central

Sisniega, A; Zbijewski, W; Stayman, J W; Xu, J; Taguchi, K; Fredenberg, E; Lundqvist, Mats; Siewerdsen, J H

2016-01-01

Novel x-ray medical imaging sensors, such as photon counting detectors (PCDs) and large area CCD and CMOS cameras can involve irregular and/or sparse sampling of the detector plane. Application of such detectors to CT involves undersampling that is markedly different from the commonly considered case of sparse angular sampling. This work investigates volumetric sampling in CT systems incorporating sparsely sampled detectors with axial and helical scan orbits and evaluates performance of model-based image reconstruction (MBIR) with spatially varying regularization in mitigating artifacts due to sparse detector sampling. Volumetric metrics of sampling density and uniformity were introduced. Penalized-likelihood MBIR with a spatially varying penalty that homogenized resolution by accounting for variations in local sampling density (i.e. detector gaps) was evaluated. The proposed methodology was tested in simulations and on an imaging bench based on a Si-strip PCD (total area 5 cm × 25 cm) consisting of an arrangement of line sensors separated by gaps of up to 2.5 mm. The bench was equipped with translation/rotation stages allowing a variety of scanning trajectories, ranging from a simple axial acquisition to helical scans with variable pitch. Statistical (spherical clutter) and anthropomorphic (hand) phantoms were considered. Image quality was compared to that obtained with a conventional uniform penalty in terms of structural similarity index (SSIM), image uniformity, spatial resolution, contrast, and noise. Scan trajectories with intermediate helical width (~10 mm longitudinal distance per 360° rotation) demonstrated optimal tradeoff between the average sampling density and the homogeneity of sampling throughout the volume. For a scan trajectory with 10.8 mm helical width, the spatially varying penalty resulted in significant visual reduction of sampling artifacts, confirmed by a 10% reduction in minimum SSIM (from 0.88 to 0.8) and a 40% reduction in the dispersion of SSIM in the volume compared to the constant penalty (both penalties applied at optimal regularization strength). Images of the spherical clutter and wrist phantoms confirmed the advantages of the spatially varying penalty, showing a 25% improvement in image uniformity and 1.8 × higher CNR (at matched spatial resolution) compared to the constant penalty. The studies elucidate the relationship between sampling in the detector plane, acquisition orbit, sampling of the reconstructed volume, and the resulting image quality. They also demonstrate the benefit of spatially varying regularization in MBIR for scenarios with irregular sampling patterns. Such findings are important and integral to the incorporation of a sparsely sampled Si-strip PCD in CT imaging. PMID:26611740

Self-assembly of Janus particles into helices with tunable pitch

NASA Astrophysics Data System (ADS)

Fernández, M. Sobrino; Misko, V. R.; Peeters, F. M.

2015-10-01

Janus particles present an important class of building blocks for directional assembly. These are compartmentalized colloids with two different hemispheres. In this work we consider a three-dimensional model of Janus spheres that contain one hydrophobic and one charged hemisphere. Using molecular dynamics simulations, we study the morphology of these particles when confined in a channel-like environment. The interplay between the attractive and repulsive forces on each particle gives rise to a rich phase space where the relative orientation of each particle plays a dominant role in the formation of large-scale clusters. The interest in this system is primarily due to the fact that it could give a better understanding of the mechanisms of the formation of polar membranes. A variety of ordered membranelike morphologies is found consisting of single and multiple connected chain configurations. The helicity of these chains can be chosen by simply changing the salt concentration of the solution. Special attention is given to the formation of Bernal spirals. These helices are composed of regular tetrahedra and are known to exhibit nontrivial translational and rotational symmetry.

The Role of Foreign Domestic Helpers in Hong Kong Chinese Children's English and Chinese Skills: A Longitudinal Study

ERIC Educational Resources Information Center

Dulay, Katrina May; Tong, Xiuhong; McBride, Catherine

2017-01-01

We investigated the influence of nonparental caregivers, such as foreign domestic helpers (FDH), on the home language spoken to the child and its implications for vocabulary and word reading development in Cantonese- and English-speaking bilingual children. Using data collected from ages 5 to 9, we analyzed Chinese vocabulary, Chinese character…

Visualization of evolving laser-generated structures by frequency domain tomography

NASA Astrophysics Data System (ADS)

Chang, Yenyu; Li, Zhengyan; Wang, Xiaoming; Zgadzaj, Rafal; Downer, Michael

2011-10-01

We introduce frequency domain tomography (FDT) for single-shot visualization of time-evolving refractive index structures (e.g. laser wakefields, nonlinear index structures) moving at light-speed. Previous researchers demonstrated single-shot frequency domain holography (FDH), in which a probe-reference pulse pair co- propagates with the laser-generated structure, to obtain snapshot-like images. However, in FDH, information about the structure's evolution is averaged. To visualize an evolving structure, we use several frequency domain streak cameras (FDSCs), in each of which a probe-reference pulse pair propagates at an angle to the propagation direction of the laser-generated structure. The combination of several FDSCs constitutes the FDT system. We will present experimental results for a 4-probe FDT system that has imaged the whole-beam self-focusing of a pump pulse propagating through glass in a single laser shot. Combining temporal and angle multiplexing methods, we successfully processed data from four probe pulses in one spectrometer in a single-shot. The output of data processing is a multi-frame movie of the self- focusing pulse. Our results promise the possibility of visualizing evolving laser wakefield structures that underlie laser-plasma accelerators used for multi-GeV electron acceleration.

Ready to use bioinformatics analysis as a tool to predict immobilisation strategies for protein direct electron transfer (DET).

PubMed

Cazelles, R; Lalaoui, N; Hartmann, T; Leimkühler, S; Wollenberger, U; Antonietti, M; Cosnier, S

2016-11-15

Direct electron transfer (DET) to proteins is of considerable interest for the development of biosensors and bioelectrocatalysts. While protein structure is mainly used as a method of attaching the protein to the electrode surface, we employed bioinformatics analysis to predict the suitable orientation of the enzymes to promote DET. Structure similarity and secondary structure prediction were combined underlying localized amino-acids able to direct one of the enzyme's electron relays toward the electrode surface by creating a suitable bioelectrocatalytic nanostructure. The electro-polymerization of pyrene pyrrole onto a fluorine-doped tin oxide (FTO) electrode allowed the targeted orientation of the formate dehydrogenase enzyme from Rhodobacter capsulatus (RcFDH) by means of hydrophobic interactions. Its electron relays were directed to the FTO surface, thus promoting DET. The reduction of nicotinamide adenine dinucleotide (NAD(+)) generating a maximum current density of 1μAcm(-2) with 10mM NAD(+) leads to a turnover number of 0.09electron/s/molRcFDH. This work represents a practical approach to evaluate electrode surface modification strategies in order to create valuable bioelectrocatalysts. Copyright © 2016 Elsevier B.V. All rights reserved.

Amine dehydrogenases: efficient biocatalysts for the reductive amination of carbonyl compounds.

PubMed

Knaus, Tanja; Böhmer, Wesley; Mutti, Francesco G

2017-01-21

Amines constitute the major targets for the production of a plethora of chemical compounds that have applications in the pharmaceutical, agrochemical and bulk chemical industries. However, the asymmetric synthesis of α-chiral amines with elevated catalytic efficiency and atom economy is still a very challenging synthetic problem. Here, we investigated the biocatalytic reductive amination of carbonyl compounds employing a rising class of enzymes for amine synthesis: amine dehydrogenases (AmDHs). The three AmDHs from this study - operating in tandem with a formate dehydrogenase from Candida boidinii (Cb-FDH) for the recycling of the nicotinamide coenzyme - performed the efficient amination of a range of diverse aromatic and aliphatic ketones and aldehydes with up to quantitative conversion and elevated turnover numbers (TONs). Moreover, the reductive amination of prochiral ketones proceeded with perfect stereoselectivity, always affording the ( R )-configured amines with more than 99% enantiomeric excess. The most suitable amine dehydrogenase, the optimised catalyst loading and the required reaction time were determined for each substrate. The biocatalytic reductive amination with this dual-enzyme system (AmDH-Cb-FDH) possesses elevated atom efficiency as it utilizes the ammonium formate buffer as the source of both nitrogen and reducing equivalents. Inorganic carbonate is the sole by-product.

Holographic Imaging of Evolving Laser-Plasma Structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Downer, Michael; Shvets, G.

In the 1870s, English photographer Eadweard Muybridge captured motion pictures within one cycle of a horse’s gallop, which settled a hotly debated question of his time by showing that the horse became temporarily airborne. In the 1940s, Manhattan project photographer Berlin Brixner captured a nuclear blast at a million frames per second, and resolved a dispute about the explosion’s shape and speed. In this project, we developed methods to capture detailed motion pictures of evolving, light-velocity objects created by a laser pulse propagating through matter. These objects include electron density waves used to accelerate charged particles, laser-induced refractive index changesmore » used for micromachining, and ionization tracks used for atmospheric chemical analysis, guide star creation and ranging. Our “movies”, like Muybridge’s and Brixner’s, are obtained in one shot, since the laser-created objects of interest are insufficiently repeatable for accurate stroboscopic imaging. Our high-speed photographs have begun to resolve controversies about how laser-created objects form and evolve, questions that previously could be addressed only by intensive computer simulations based on estimated initial conditions. Resolving such questions helps develop better tabletop particle accelerators, atmospheric ranging devices and many other applications of laser-matter interactions. Our photographic methods all begin by splitting one or more “probe” pulses from the laser pulse that creates the light-speed object. A probe illuminates the object and obtains information about its structure without altering it. We developed three single-shot visualization methods that differ in how the probes interact with the object of interest or are recorded. (1) Frequency-Domain Holography (FDH). In FDH, there are 2 probes, like “object” and “reference” beams in conventional holography. Our “object” probe surrounds the light-speed object, like a fleas swarming around a sprinting animal. The object modifies the probe, imprinting information about its structure. Meanwhile, our “reference” probe co-propagates ahead of the object, free of its influence. After the interaction, object and reference combine to record a hologram. For technical reasons, our recording device is a spectrometer (a frequency-measuring device), hence the name “frequency-domain” holography. We read the hologram electronically to obtain a “snapshot” of the object’s average structure as it transits the medium. Our published work shows numerous snapshots of electron density waves (“laser wakes”) in ionized gas (“plasma”), analogous to a water wake behind a boat. Such waves are the basis of tabletop particle accelerators, in which charged particles surf on the light-speed wave, gaining energy. Comparing our snapshots to computer simulations deepens understanding of laser wakes. FDH takes snapshots of objects that are quasi-static --- i.e. like Muybridge’s horse standing still on a treadmill. If the object changes shape, FDH images blur, as when a subject moves while a camera shutter is open. Many laser-generated objects of interest do evolve as they propagate. To overcome this limit of FDH, we developed .... (2) Frequency-Domain Tomography (FDT). In FDT, 5 to 10 probe pulses are fired simultaneously across the object’s path at different angles, like a crossfire of bullets. The object imprints a “streaked” record of its evolution on each probe, which we record as in FDH, then recover a multi-frame “movie” of the object’s evolving structure using algorithms of computerized tomography. When propagation distance exceeds a few millimeters, reconstructed FDT images distort. This is because the lenses that image probes to detector have limited depth of field, like cameras that cannot focus simultaneously on both nearby and distant objects. But some laser-generated objects of interest propagate over meters. For these applications we developed … (3) Multi-Object-Plane Phase-Contrast Imaging (MOP-PCI). In MOP-PCI, we image FDT-like probes to the detector from multiple “object planes” --- like recording an event simultaneously with several cameras, some focused on nearby, others on distant, objects. To increase sensitivity, we exploit a phase-contrast imaging technique developed by Dutch Nobel laureate Fritz Zernike in the 1930s. Using MOP-PCI we recorded single-shot movies of laser pulse tracks through more than 10 cm of air. We plan to record images of meter-long tracks of electron bunches propagating through plasma in an experiment at the Stanford Linear Accelerator Center (SLAC). This will help SLAC scientists understand, optimize and scale small plasma-based particle accelerators that have applications in medicine, industry, materials science and high-energy physics.« less

Systematic periodicity in waviness of vertically aligned carbon nanotubes explained by helical buckling

NASA Astrophysics Data System (ADS)

Jahangiri, Mehdi

2017-09-01

A hypothesis is proposed in this work to account for the geometry of individual vertically aligned carbon nanotubes (VACNTs) that not only justifies the directionality of their growth, but also explains the origin of the waviness frequently reported for these nanotube forests. Such waviness has fundamental effects on the transport/conduction properties of VACNTs, either through or along them, regarding phenomena such as mass, stress, heat and electricity. Despite the general opinion about randomness of carbon nanotubes (CNTs) tortuosity, we demonstrate here that rules of helical buckling of tubular strings is applicable to VACNTs, based on which a regular 3D helical geometry is proposed for VACNTs, with a 2D sine wave shape side-profile. In this framework, gradual increase of the total free surface energy by growth of CNTs ensues their partial cohesion, driven by van der Waals interactions, to reduce the excess surface energy. On the other hand, their cohesion is accompanied by their deformation and loss of straightness, which in turn, translates to buildup of an elastic strain energy in the system. The balance of the two energies along with the spatial constraints on each CNT at its contact points with neighboring CNTs, is manifested in its helical buckling, that is systematically influenced by nanostructural characteristics of VACNTs, such as their diameter, wall thickness and inter-CNT spacing.

Systematic periodicity in waviness of vertically aligned carbon nanotubes explained by helical buckling.

PubMed

Jahangiri, Mehdi

2017-09-15

A hypothesis is proposed in this work to account for the geometry of individual vertically aligned carbon nanotubes (VACNTs) that not only justifies the directionality of their growth, but also explains the origin of the waviness frequently reported for these nanotube forests. Such waviness has fundamental effects on the transport/conduction properties of VACNTs, either through or along them, regarding phenomena such as mass, stress, heat and electricity. Despite the general opinion about randomness of carbon nanotubes (CNTs) tortuosity, we demonstrate here that rules of helical buckling of tubular strings is applicable to VACNTs, based on which a regular 3D helical geometry is proposed for VACNTs, with a 2D sine wave shape side-profile. In this framework, gradual increase of the total free surface energy by growth of CNTs ensues their partial cohesion, driven by van der Waals interactions, to reduce the excess surface energy. On the other hand, their cohesion is accompanied by their deformation and loss of straightness, which in turn, translates to buildup of an elastic strain energy in the system. The balance of the two energies along with the spatial constraints on each CNT at its contact points with neighboring CNTs, is manifested in its helical buckling, that is systematically influenced by nanostructural characteristics of VACNTs, such as their diameter, wall thickness and inter-CNT spacing.

Bacillus subtilis MreB paralogues have different filament architectures and lead to shape remodelling of a heterologous cell system.

PubMed

Soufo, Hervé Joël Defeu; Graumann, Peter L

2010-12-01

Like many bacteria, Bacillus subtilis cells contain three actin-like MreB proteins. We show that the three paralogues, MreB, Mbl and MreBH, have different filament architectures in a heterologous cell system, and form straight filaments, helices or ring structures, different from the regular helical arrangement in B. subtilis cells. However, when coexpressed, they colocalize into a single filamentous helical structure, showing that the paralogues influence each other's filament architecture. Ring-like MreBH structures can be converted into MreB-like helical filaments by a single point mutation affecting subunit contacts, showing that MreB paralogues feature flexible filament arrangements. Time-lapse and FRAP experiments show that filaments can extend as well as shrink at both ends, and also show internal rearrangement, suggesting that filaments consist of overlapping bundles of shorter filaments that continuously turn over. Upon induction in Escherichia coli cells, B. subtilis MreB (BsMreB) filaments push the cells into strikingly altered cell morphology, showing that MreB filaments can change cell shape. E. coli cells with a weakened cell wall were ruptured upon induction of BsMreB filaments, suggesting that the bacterial actin orthologue may exert force against the cell membrane and envelope, and thus possibly plays an additional mechanical role in bacteria. © 2010 Blackwell Publishing Ltd.

Postirradiation Testing Laboratory (327 Building)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kammenzind, D.E.

A Standards/Requirements Identification Document (S/RID) is the total list of the Environment, Safety and Health (ES and H) requirements to be implemented by a site, facility, or activity. These requirements are appropriate to the life cycle phase to achieve an adequate level of protection for worker and public health and safety, and the environment during design, construction, operation, decontamination and decommissioning, and environmental restoration. S/RlDs are living documents, to be revised appropriately based on change in the site`s or facility`s mission or configuration, a change in the facility`s life cycle phase, or a change to the applicable standards/requirements. S/RIDs encompassmore » health and safety, environmental, and safety related safeguards and security (S and S) standards/requirements related to the functional areas listed in the US Department of Energy (DOE) Environment, Safety and Health Configuration Guide. The Fluor Daniel Hanford (FDH) Contract S/RID contains standards/requirements, applicable to FDH and FDH subcontractors, necessary for safe operation of Project Hanford Management Contract (PHMC) facilities, that are not the direct responsibility of the facility manager (e.g., a site-wide fire department). Facility S/RIDs contain standards/requirements applicable to a specific facility that are the direct responsibility of the facility manager. S/RlDs are prepared by those responsible for managing the operation of facilities or the conduct of activities that present a potential threat to the health and safety of workers, public, or the environment, including: Hazard Category 1 and 2 nuclear facilities and activities, as defined in DOE 5480.23. Selected Hazard Category 3 nuclear, and Low Hazard non-nuclear facilities and activities, as agreed upon by RL. The Postirradiation Testing Laboratory (PTL) S/RID contains standards/ requirements that are necessary for safe operation of the PTL facility, and other building/areas that are the direct responsibility of the specific facility manager. The specific DOE Orders, regulations, industry codes/standards, guidance documents and good industry practices that serve as the basis for each element/subelement are identified and aligned with each subelement.« less

Percuflex Helical Ureteral Stents Significantly Reduce Patient Analgesic Requirements Compared to Control Stents.

PubMed

Chew, Ben H; Rebullar, Karla A; Harriman, David; McDougall, Elspeth; Paterson, Ryan F; Lange, Dirk

2017-12-01

Ureteral stent symptoms are experienced by the majority of patients with ureteral stents. No one stent or technology has shown a clear advantage. The Helical™ stent, a spirally cut stent made of proprietary Percuflex™ material, was designed to conform to the shape of the ureter and better accommodate patient movement. We prospectively sought to compare unscheduled visits, analgesic use, and pain scores in patients who received a Percuflex Helical ureteral stent following ureteroscopy compared to a historical control group. Fifteen (n = 15) patients undergoing ureteroscopy for the treatment of kidney stones were consented for study. A Percuflex Helical ureteral stent was inserted after treating the urinary stone. The historical control group consisted of 30 patients, from a previous (ketorolac eluting) ureteral stent study utilizing the same protocol and clinical monitoring forms, who received a regular Percuflex ureteral stent. The control patients were matched by age and sex. The primary study outcome was to compare unscheduled visits. Secondary outcomes included comparison of Visual Pain Analog Scale (VPAS) scores and analgesic use between the two groups. There were no differences in the gender, age, BMI, or stone characteristics between groups. Both groups underwent retrograde ureteroscopy using holmium:YAG laser lithotripsy and stone fragmentation. There was a significant reduction in the amount of analgesics required in the Helical stent group (4.4 ± 7.99 mg morphine equivalents) compared to controls (16.75 ± 18.31 mg, p = 0.0035) to achieve similar VPAS scores. There was no difference in unscheduled visits (20%) or VPAS scores (13.84 ± 13.68 helical vs 14.29 ± 11.58 control, p = 0.7910) between groups. Patients who received a Percuflex Helical ureteral stent required significantly fewer analgesics than those who received a Percuflex stent and both had equivalent pain scores.

Coupled reactions on bioparticles: Stereoselective reduction with cofactor regeneration on PhaC inclusion bodies.

PubMed

Spieler, Valerie; Valldorf, Bernhard; Maaß, Franziska; Kleinschek, Alexander; Hüttenhain, Stefan H; Kolmar, Harald

2016-07-01

Chiral alcohols are important building blocks for specialty chemicals and pharmaceuticals. The production of chiral alcohols from ketones can be carried out stereo selectively with alcohol dehydrogenases (ADHs). To establish a process for cost-effective enzyme immobilization on solid phase for application in ketone reduction, we used an established enzyme pair consisting of ADH from Rhodococcus erythropolis and formate dehydrogenase (FDH) from Candida boidinii for NADH cofactor regeneration and co-immobilized them on modified poly-p-hydroxybutyrate synthase (PhaC)-inclusion bodies that were recombinantly produced in Escherichia coli cells. After separate production of genetically engineered and recombinantly produced enzymes and particles, cell lysates were combined and enzymes endowed with a Kcoil were captured on the surface of the Ecoil presenting particles due to coiled-coil interaction. Enzyme-loaded particles could be easily purified by centrifugation. Total conversion of 4'-chloroacetophenone to (S)-4-chloro-α-methylbenzyl alcohol could be accomplished using enzyme-loaded particles, catalytic amounts of NAD(+) and formate as substrates for FDH. Chiral GC-MS analysis revealed that immobilized ADH retained enantioselectivity with 99 % enantiomeric excess. In conclusion, this strategy may become a cost-effective alternative to coupled reactions using purified enzymes. Copyright © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Amine dehydrogenases: efficient biocatalysts for the reductive amination of carbonyl compounds

PubMed Central

Mutti, Francesco G.

2017-01-01

Amines constitute the major targets for the production of a plethora of chemical compounds that have applications in the pharmaceutical, agrochemical and bulk chemical industries. However, the asymmetric synthesis of α-chiral amines with elevated catalytic efficiency and atom economy is still a very challenging synthetic problem. Here, we investigated the biocatalytic reductive amination of carbonyl compounds employing a rising class of enzymes for amine synthesis: amine dehydrogenases (AmDHs). The three AmDHs from this study – operating in tandem with a formate dehydrogenase from Candida boidinii (Cb-FDH) for the recycling of the nicotinamide coenzyme – performed the efficient amination of a range of diverse aromatic and aliphatic ketones and aldehydes with up to quantitative conversion and elevated turnover numbers (TONs). Moreover, the reductive amination of prochiral ketones proceeded with perfect stereoselectivity, always affording the (R)-configured amines with more than 99% enantiomeric excess. The most suitable amine dehydrogenase, the optimised catalyst loading and the required reaction time were determined for each substrate. The biocatalytic reductive amination with this dual-enzyme system (AmDH–Cb-FDH) possesses elevated atom efficiency as it utilizes the ammonium formate buffer as the source of both nitrogen and reducing equivalents. Inorganic carbonate is the sole by-product. PMID:28663713

Representation of viruses in the remediated PDB archive

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lawson, Catherine L., E-mail: cathy.lawson@rutgers.edu; Dutta, Shuchismita; Westbrook, John D.

2008-08-01

A new data model for PDB entries of viruses and other biological assemblies with regular noncrystallographic symmetry is described. A new scheme has been devised to represent viruses and other biological assemblies with regular noncrystallographic symmetry in the Protein Data Bank (PDB). The scheme describes existing and anticipated PDB entries of this type using generalized descriptions of deposited and experimental coordinate frames, symmetry and frame transformations. A simplified notation has been adopted to express the symmetry generation of assemblies from deposited coordinates and matrix operations describing the required point, helical or crystallographic symmetry. Complete correct information for building full assemblies,more » subassemblies and crystal asymmetric units of all virus entries is now available in the remediated PDB archive.« less

Consensus Prediction of Charged Single Alpha-Helices with CSAHserver.

PubMed

Dudola, Dániel; Tóth, Gábor; Nyitray, László; Gáspári, Zoltán

2017-01-01

Charged single alpha-helices (CSAHs) constitute a rare structural motif. CSAH is characterized by a high density of regularly alternating residues with positively and negatively charged side chains. Such segments exhibit unique structural properties; however, there are only a handful of proteins where its existence is experimentally verified. Therefore, establishing a pipeline that is capable of predicting the presence of CSAH segments with a low false positive rate is of considerable importance. Here we describe a consensus-based approach that relies on two conceptually different CSAH detection methods and a final filter based on the estimated helix-forming capabilities of the segments. This pipeline was shown to be capable of identifying previously uncharacterized CSAH segments that could be verified experimentally. The method is available as a web server at http://csahserver.itk.ppke.hu and also a downloadable standalone program suitable to scan larger sequence collections.

Magnetohydrodynamic simulations of noninductive helicity injection in the reversed-field pinch and tokamak

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sovinec, Carl R.

1995-11-01

Numerical computation is used to investigate resistive magnetohydrodynamic (MHD) fluctuations in the reversed-field pinch (RFP) and in tokamak-like configurations driven solely by direct current (DC) helicity injection. A Lundquist number (S) scan of RFP turbulence without plasma pressure produces the weak scaling of S -0.18 for the root-mean-square magnetic fluctuation level for 2.5x10 3≤S≤4x10 4. The temporal behavior of fluctuations and the reversal parameter becomes more regular as S is increased, acquiring a "sawtooth" shape at the largest value of S. Simulations with plasma pressure and anisotropic thermal conduction demonstrate energy transport resulting from parallel heat fluctuations. To investigate meansmore » of improving RFP energy confinement, three forms of current profile modification are tested. Radio frequency (RF) current drive is modeled with an auxiliary electron force, and linear stability calculations are used.« less

Study of Bird Ingestions into Small Inlet Area, Aircraft Turbine Engines

DTIC Science & Technology

1989-12-01

TFE731 3 -0- -0- NONE NONE NONE12/16/1987 -0- -0- -0- RICHMOND, VA-BYRD FIELD YES TFE731 3R A,O 2 NONE NONE NONE12/17/1987 8. -0- FOH FRIEDRICHSHAFEN ...GERMANY NO TPE331 5 A,X 1 -0- NONE RETARE12/17/1987 8. -0- FDH FRIEDRICHSHAFEN , GERMANY NO TPE331 5 A,K I 0 NONE RETARD12/30/1987 -0- -0- -0- CRICIUNA

Zika Virus: Obstetric and Pediatric Anesthesia Considerations.

PubMed

Tutiven, Jacqueline L; Pruden, Benjamin T; Banks, James S; Stevenson, Mario; Birnbach, David J

2017-06-01

As of November 2016, the Florida Department of Health (FDH) and the Centers for Disease Control and Prevention have confirmed more than 4000 travel-related Zika virus (ZIKV) infections in the United States with >700 of those in Florida. There have been 139 cases of locally acquired infection, all occurring in Miami, Florida. Within the US territories (eg, Puerto Rico, US Virgin Islands), >30,000 cases of ZIKV infection have been reported. The projected number of individuals at risk for ZIKV infection in the Caribbean and Latin America approximates 5 million. Similar to Dengue and Chikungunya viruses, ZIKV is spread to humans by infected Aedes aegypti mosquitoes, through travel-associated local transmission, via sexual contact, and through blood transfusions. South Florida is an epicenter for ZIKV infection in the United States and the year-round warm climate along with an abundance of mosquito vectors that can harbor the flavivirus raise health care concerns. ZIKV infection is generally mild with clinical manifestations of fever, rash, conjunctivitis, and arthralgia. Of greatest concern, however, is growing evidence for the relationship between ZIKV infection of pregnant women and increased incidence of abnormal pregnancies and congenital abnormalities in the newborn, now medically termed ZIKA Congenital Syndrome. Federal health officials are observing 899 confirmed Zika-positive pregnancies and the FDH is currently monitoring 110 pregnant women with evidence of Zika infection. The University of Miami/Jackson Memorial Hospital is uniquely positioned just north of downtown Miami and within the vicinity of Liberty City, Little Haiti, and Miami Beach, which are currently "hot spots" for Zika virus exposure and transmissions. As the FDH works fervently to prevent a Zika epidemic in the region, health care providers at the University of Miami and Jackson Memorial Hospital prepare for the clinical spectrum of ZIKV effects as well as the safe perioperative care of the parturients and their affected newborns. In an effort to meet anesthetic preparedness for the care of potential Zika-positive patients and perinatal management of babies born with ZIKA Congenital Syndrome, this review highlights the interim guidelines from the Centers for Disease Control and Prevention and also suggest anesthetic implications and recommendations. In addition, this article reviews guidance for the evaluation and anesthetic management of infants with congenital ZIKV infection. To better manage the perioperative care of affected newborns, this article also reviews the comparative anesthetic implications of babies born with related congenital malformations.

Intramolecular triple helix as a model for regular polyribonucleotide (CAA)(n).

PubMed

Efimov, Alexander V; Spirin, Alexander S

2009-10-09

The regular (CAA)(n) polyribonucleotide, as well as the omega leader sequence containing (CAA)-rich core, have recently been shown to form cooperatively melted and compact structures. In this report, we propose a structural model for the (CAA)(n) sequence in which the polyribonucleotide chain is folded upon itself, so that it forms an intramolecular triple helix. The triple helix is stabilized by hydrogen bonding between bases thus forming coplanar triads, and by stacking interactions between the base triads. A distinctive feature of the proposed triple helix is that it does not contain the canonical double-helix elements. The difference from the known triple helices is that Watson-Crick hydrogen bond pairings do not take place in the interactions between the bases within the base triads.

Molecular dynamics simulations on discoidal HDL particles suggest a mechanism for rotation in the apo A-I belt model.

PubMed

Klon, Anthony E; Segrest, Jere P; Harvey, Stephen C

2002-12-06

Apolipoprotein A-I (apo A-I) is the major protein component of high-density lipoprotein (HDL) particles. Elevated levels of HDL in the bloodstream have been shown to correlate strongly with a reduced risk factor for atherosclerosis. Molecular dynamics simulations have been carried out on three separate model discoidal high-density lipoprotein particles (HDL) containing two monomers of apo A-I and 160 molecules of palmitoyloleoylphosphatidylcholine (POPC), to a time-scale of 1ns. The starting structures were on the basis of previously published molecular belt models of HDL consisting of the lipid-binding C-terminal domain (residues 44-243) wrapped around the circumference of a discoidal HDL particle. Subtle changes between two of the starting structures resulted in significantly different behavior during the course of the simulation. The results provide support for the hypothesis of Segrest et al. that helical registration in the molecular belt model of apo A-I is modulated by intermolecular salt bridges. In addition, we propose an explanation for the presence of proline punctuation in the molecular belt model, and for the presence of two 11-mer helical repeats interrupting the otherwise regular pattern of 22-mer helical repeats in the lipid-binding domain of apo A-I.

Three-dimensional tomographic imaging for dynamic radiation behavior study using infrared imaging video bolometers in large helical device plasma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sano, Ryuichi; Iwama, Naofumi; Peterson, Byron J.

A three-dimensional (3D) tomography system using four InfraRed imaging Video Bolometers (IRVBs) has been designed with a helical periodicity assumption for the purpose of plasma radiation measurement in the large helical device. For the spatial inversion of large sized arrays, the system has been numerically and experimentally examined using the Tikhonov regularization with the criterion of minimum generalized cross validation, which is the standard solver of inverse problems. The 3D transport code EMC3-EIRENE for impurity behavior and related radiation has been used to produce phantoms for numerical tests, and the relative calibration of the IRVB images has been carried outmore » with a simple function model of the decaying plasma in a radiation collapse. The tomography system can respond to temporal changes in the plasma profile and identify the 3D dynamic behavior of radiation, such as the radiation enhancement that starts from the inboard side of the torus, during the radiation collapse. The reconstruction results are also consistent with the output signals of a resistive bolometer. These results indicate that the designed 3D tomography system is available for the 3D imaging of radiation. The first 3D direct tomographic measurement of a magnetically confined plasma has been achieved.« less

Structure-activity relationship of HP (2-20) analog peptide: enhanced antimicrobial activity by N-terminal random coil region deletion.

PubMed

Park, Yoonkyung; Park, Seong-Cheol; Park, Hae-Kyun; Shin, Song Yub; Kim, Yangmee; Hahm, Kyung-Soo

2007-01-01

HP (2-20) (AKKVFKRLEKLFSKIQNDK) is a 19-aa antimicrobial peptide derived from N-terminus of Helicobacter pylori Ribosomal protein L1 (RpL1). In the previous study, several analogs with amino acid substitutions were designed to increase or decrease only the net hydrophobicity. In particular, substitutions of Gln(16) and Asp(18) with Trp (Anal 3) for hydrophobic amino acid caused a dramatic increase in antibiotic activity without a hemolytic effect. HP-A3 is a potent antimicrobial peptide that forms, in a hydrophobic medium, an amphipathic structure consisting of an N-terminal random coil region (residues 2-5) and extended C-terminal regular alpha-helical region (residues 6-20). To obtain the short and potent alpha-helical antimicrobial peptide, we synthesized a N-terminal random coil deleted HP-A3 (A3-NT) and examined their antimicrobial activity and mechanism of action. The resulting 15mer peptide showed increased antibacterial and antifungal activity to 2- and 4-fold, respectively, without hemolysis. Confocal fluorescence microscopy studies showed that A3-NT was accumulated in the plasma membrane. Flow cytometric analysis revealed that A3-NT acted in salt- and energy-independent manner. Furthermore, A3-NT causes significant morphological alterations of the bacterial surfaces as shown by scanning electron microscopy. Circular dichroism (CD) analysis revealed that A3-NT showed higher alpha-helical contents than the HP-A3 peptide in 50% TFE solution. Therefore, the cell-lytic efficiency of HP-A3, which depended on the alpha-helical content of peptide, correlated linearly with their antimicrobial potency.

Growth, nutritional, and gastrointestinal aspects of focal dermal hypoplasia (Goltz-Gorlin syndrome).

PubMed

Motil, Kathleen J; Fete, Mary; Fete, Timothy J

2016-03-01

Focal dermal hypoplasia (FDH) is a rare genetic disorder caused by mutations in the PORCN gene located on the X-chromosome. In the present study, we characterized the pattern of growth, body composition, and the nutritional and gastrointestinal aspects of children and adults (n = 19) affected with this disorder using clinical anthropometry and a survey questionnaire. The mean birth length (P < 0.06) and weight (P < 0.001) z-scores of the participants were lower than the reference population. The mean head circumference (P < 0.001), height (length) (P < 0.001), weight (P < 0.01), and BMI (P < 0.05) for age z-scores of the participants were lower than the reference population. The height-for-age and weight-for-age z-scores of the participants did not differ significantly between birth and current measurements. Three-fourths of the group reported having one or more nutritional or gastrointestinal problems including short stature (65%), underweight (77%), oral motor dysfunction (41%), gastroesophageal reflux (24%), gastroparesis (35%), and constipation (35%). These observations provide novel clinical information about growth, body composition, and nutritional and gastrointestinal aspects of children and adults with FDH and underscore the importance of careful observation and early clinical intervention in the care of individuals affected with this disorder. © 2016 Wiley Periodicals, Inc.

Controlled intramyocardial release of engineered chemokines by biodegradable hydrogels as a treatment approach of myocardial infarction

PubMed Central

Projahn, Delia; Simsekyilmaz, Sakine; Singh, Smriti; Kanzler, Isabella; Kramp, Birgit K; Langer, Marcella; Burlacu, Alexandrina; Bernhagen, Jürgen; Klee, Doris; Zernecke, Alma; Hackeng, Tilman M; Groll, Jürgen; Weber, Christian; Liehn, Elisa A; Koenen, Rory R

2014-01-01

Myocardial infarction (MI) induces a complex inflammatory immune response, followed by the remodelling of the heart muscle and scar formation. The rapid regeneration of the blood vessel network system by the attraction of hematopoietic stem cells is beneficial for heart function. Despite the important role of chemokines in these processes, their use in clinical practice has so far been limited by their limited availability over a long time-span in vivo. Here, a method is presented to increase physiological availability of chemokines at the site of injury over a defined time-span and simultaneously control their release using biodegradable hydrogels. Two different biodegradable hydrogels were implemented, a fast degradable hydrogel (FDH) for delivering Met-CCL5 over 24 hrs and a slow degradable hydrogel (SDH) for a gradual release of protease-resistant CXCL12 (S4V) over 4 weeks. We demonstrate that the time-controlled release using Met-CCL5-FDH and CXCL12 (S4V)-SDH suppressed initial neutrophil infiltration, promoted neovascularization and reduced apoptosis in the infarcted myocardium. Thus, we were able to significantly preserve the cardiac function after MI. This study demonstrates that time-controlled, biopolymer-mediated delivery of chemokines represents a novel and feasible strategy to support the endogenous reparatory mechanisms after MI and may compliment cell-based therapies. PMID:24512349

Helical prospective ECG-gating in cardiac computed tomography: radiation dose and image quality.

PubMed

DeFrance, Tony; Dubois, Eric; Gebow, Dan; Ramirez, Alex; Wolf, Florian; Feuchtner, Gudrun M

2010-01-01

Helical prospective ECG-gating (pECG) may reduce radiation dose while maintaining the advantages of helical image acquisition for coronary computed tomography angiography (CCTA). Aim of this study was to evaluate helical pECG-gating in CCTA in regards to radiation dose and image quality. 86 patients undergoing 64-multislice CCTA were enrolled. pECG-gating was performed in patients with regular heart rates (HR) < 65 bpm; with the gating window set at 70-85% of the cardiac cycle. All patients received oral and some received additional IV beta-blockers to achieve HR < 65 bpm. In patients with higher or irregular HR, or for functional evaluation, retrospective ECG-gating (rECG) was performed. The average X-ray dose was estimated from the dose length product. Each arterial segment (modified AHA/ACC 17-segment-model) was evaluated on a 4-point image quality scale (4 = excellent; 3 = good, mild artefact; 2 = acceptable, some artefact, 1 = uninterpretable). pECG-gating was applied in 57 patients, rECG-gating in 29 patients. There was no difference in age, gender, body mass index, scan length or tube output settings between both groups. HR in the pECG-group was 54.7 bpm (range, 43-64). The effective radiation dose was significantly lower for patients scanned with pECG-gating with mean 6.9 mSv +/- 1.9 (range, 2.9-10.7) compared to rECG with 16.9 mSv +/- 4.1 (P < 0.001), resulting in a mean dose reduction of 59.2%. For pECG-gating, out of 969 coronary segments, 99.3% were interpretable. Image quality was excellent in 90.2%, good in 7.8%, acceptable in 1.3% and non-interpretable in 0.7% (n = 7 segments). For patients with steady heart rates <65 bpm, helical prospective ECG-gating can significantly lower the radiation dose while maintaining high image quality.

Design of a minimal protein oligomerization domain by a structural approach.

PubMed

Burkhard, P; Meier, M; Lustig, A

2000-12-01

Because of the simplicity and regularity of the alpha-helical coiled coil relative to other structural motifs, it can be conveniently used to clarify the molecular interactions responsible for protein folding and stability. Here we describe the de novo design and characterization of a two heptad-repeat peptide stabilized by a complex network of inter- and intrahelical salt bridges. Circular dichroism spectroscopy and analytical ultracentrifugation show that this peptide is highly alpha-helical and 100% dimeric tinder physiological buffer conditions. Interestingly, the peptide was shown to switch its oligomerization state from a dimer to a trimer upon increasing ionic strength. The correctness of the rational design principles used here is supported by details of the atomic structure of the peptide deduced from X-ray crystallography. The structure of the peptide shows that it is not a molten globule but assumes a unique, native-like conformation. This de novo peptide thus represents an attractive model system for the design of a molecular recognition system.

Design of a minimal protein oligomerization domain by a structural approach.

PubMed Central

Burkhard, P.; Meier, M.; Lustig, A.

2000-01-01

Because of the simplicity and regularity of the alpha-helical coiled coil relative to other structural motifs, it can be conveniently used to clarify the molecular interactions responsible for protein folding and stability. Here we describe the de novo design and characterization of a two heptad-repeat peptide stabilized by a complex network of inter- and intrahelical salt bridges. Circular dichroism spectroscopy and analytical ultracentrifugation show that this peptide is highly alpha-helical and 100% dimeric tinder physiological buffer conditions. Interestingly, the peptide was shown to switch its oligomerization state from a dimer to a trimer upon increasing ionic strength. The correctness of the rational design principles used here is supported by details of the atomic structure of the peptide deduced from X-ray crystallography. The structure of the peptide shows that it is not a molten globule but assumes a unique, native-like conformation. This de novo peptide thus represents an attractive model system for the design of a molecular recognition system. PMID:11206050

Helicobacter pylori displays spiral trajectories while swimming like a cork-screw in solutions

NASA Astrophysics Data System (ADS)

Constantino, Maira A.; Hardcastle, Joseph M.; Bansil, Rama; Jabbarzadeh, Mehdi; Fu, Henry C.

Helicobacter pylori is a helical shaped bacterium that causes gastritis, ulcers and gastric cancer in humans and other animals. In order to colonize the harsh acidic environment of the stomach H. pylori has evolved a unique biochemical mechanism to go across the viscoelastic gel-like gastric mucus layer. Many studies have been conducted on the swimming of H. pylori in viscous media. However a yet unanswered question is if the helical cell shape influences bacterial swimming dynamics or confers any advantage when swimming in viscous solution. We will present measurements of H. pylori trajectories displaying corkscrew motion while swimming in solution obtained by tracking single cells using 2-dimensional phase contrast imaging at high magnification and fast frame rates and simultaneously imaging their shape. We observe a linear relationship between swimming speed and rotation rate. The experimental trajectories show good agreement with trajectories calculated using a regularized Stokeslet method to model the low Reynolds number swimming behavior. Supported by NSF PHY 1410798 (PI: RB).

Compaction and binding properties of the intrinsically disordered C-terminal domain of Henipavirus nucleoprotein as unveiled by deletion studies.

PubMed

Blocquel, David; Habchi, Johnny; Gruet, Antoine; Blangy, Stéphanie; Longhi, Sonia

2012-01-01

Henipaviruses are recently emerged severe human pathogens within the Paramyxoviridae family. Their genome is encapsidated by the nucleoprotein (N) within a helical nucleocapsid that recruits the polymerase complex via the phosphoprotein (P). We have previously shown that in Henipaviruses the N protein possesses an intrinsically disordered C-terminal domain, N(TAIL), which undergoes α-helical induced folding in the presence of the C-terminal domain (P(XD)) of the P protein. Using computational approaches, we previously identified within N(TAIL) four putative molecular recognition elements (MoREs) with different structural propensities, and proposed a structural model for the N(TAIL)-P(XD) complex where the MoRE encompassing residues 473-493 adopt an α-helical conformation at the P(XD) surface. In this work, for each N(TAIL) protein, we designed four deletion constructs bearing different combinations of the predicted MoREs. Following purification of the N(TAIL) truncated proteins from the soluble fraction of E. coli, we characterized them in terms of their conformational, spectroscopic and binding properties. These studies provided direct experimental evidence for the structural state of the four predicted MoREs, and showed that two of them have clear α-helical propensities, with the one spanning residues 473-493 being strictly required for binding to P(XD). We also showed that Henipavirus N(TAIL) and P(XD) form heterologous complexes, indicating that the P(XD) binding regions are functionally interchangeable between the two viruses. By combining spectroscopic and conformational analyses, we showed that the content in regular secondary structure is not a major determinant of protein compaction.

A model for straight and helical solar jets: II. Parametric study of the plasma beta.

PubMed

Pariat, E; Dalmasse, K; DeVore, C R; Antiochos, S K; Karpen, J T

2016-12-01

Jets are dynamic, impulsive, well-collimated plasma events that develop at many different scales and in different layers of the solar atmosphere. Jets are believed to be induced by magnetic reconnection, a process central to many astrophysical phenomena. Within the solar atmosphere, jet-like events develop in many different environments, e.g., in the vicinity of active regions as well as in coronal holes, and at various scales, from small photospheric spicules to large coronal jets. In all these events, signatures of helical structure and/or twisting/rotating motions are regularly observed. The present study aims to establish that a single model can generally reproduce the observed properties of these jet-like events. In this study, using our state-of-the-art numerical solver ARMS, we present a parametric study of a numerical tridimensional magnetohydrodynamic (MHD) model of solar jet-like events. Within the MHD paradigm, we study the impact of varying the atmospheric plasma β on the generation and properties of solar-like jets. The parametric study validates our model of jets for plasma β ranging from 10 -3 to 1, typical of the different layers and magnetic environments of the solar atmosphere. Our model of jets can robustly explain the generation of helical solar jet-like events at various β ≤ 1. This study introduces the new original result that the plasma β modifies the morphology of the helical jet, explaining the different observed shapes of jets at different scales and in different layers of the solar atmosphere. Our results allow us to understand the energisation, triggering, and driving processes of jet-like events. Our model allows us to make predictions of the impulsiveness and energetics of jets as determined by the surrounding environment, as well as the morphological properties of the resulting jets.

Prostate Dose Escalation by Innovative Inverse Planning-Driven IMRT

DTIC Science & Technology

2006-11-01

fLJ and at each step, we find the minimizer u,\\ of J’. The Euler-Lagrange equation for the regularized J’ functional is u- div ( 1 Vu )= f E S1,2A...GD, Agazaryan N, Solberg TD . 2003. The effects of tumor motion on planning and delivery of respiratory-gated IMRT. Med Phys 30:1052-1066. Jaffray DA...modulated) radiation therapy: a review. Phys Med Biol 51 :R403-425. Wink NM, McNitt-Gray MF, Solberg TD . 2005. Optimization of multi-slice helical

Sample Based Unit Liter Dose Estimates

DOE Office of Scientific and Technical Information (OSTI.GOV)

JENSEN, L.

The Tank Waste Characterization Program has taken many core samples, grab samples, and auger samples from the single-shell and double-shell tanks during the past 10 years. Consequently, the amount of sample data available has increased, both in terms of quantity of sample results and the number of tanks characterized. More and better data is available than when the current radiological and toxicological source terms used in the Basis for Interim Operation (BIO) (FDH 1999a) and the Final Safety Analysis Report (FSAR) (FDH 1999b) were developed. The Nuclear Safety and Licensing (NS and L) organization wants to use the new datamore » to upgrade the radiological and toxicological source terms used in the BIO and FSAR. The NS and L organization requested assistance in producing a statistically based process for developing the source terms. This report describes the statistical techniques used and the assumptions made to support the development of a new radiological source term for liquid and solid wastes stored in single-shell and double-shell tanks. The results given in this report are a revision to similar results given in an earlier version of the document (Jensen and Wilmarth 1999). The main difference between the results in this document and the earlier version is that the dose conversion factors (DCF) for converting {mu}Ci/g or {mu}Ci/L to Sv/L (sieverts per liter) have changed. There are now two DCFs, one based on ICRP-68 and one based on ICW-71 (Brevick 2000).« less

Radiation dose reduction in medical x-ray CT via Fourier-based iterative reconstruction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fahimian, Benjamin P.; Zhao Yunzhe; Huang Zhifeng

Purpose: A Fourier-based iterative reconstruction technique, termed Equally Sloped Tomography (EST), is developed in conjunction with advanced mathematical regularization to investigate radiation dose reduction in x-ray CT. The method is experimentally implemented on fan-beam CT and evaluated as a function of imaging dose on a series of image quality phantoms and anonymous pediatric patient data sets. Numerical simulation experiments are also performed to explore the extension of EST to helical cone-beam geometry. Methods: EST is a Fourier based iterative algorithm, which iterates back and forth between real and Fourier space utilizing the algebraically exact pseudopolar fast Fourier transform (PPFFT). Inmore » each iteration, physical constraints and mathematical regularization are applied in real space, while the measured data are enforced in Fourier space. The algorithm is automatically terminated when a proposed termination criterion is met. Experimentally, fan-beam projections were acquired by the Siemens z-flying focal spot technology, and subsequently interleaved and rebinned to a pseudopolar grid. Image quality phantoms were scanned at systematically varied mAs settings, reconstructed by EST and conventional reconstruction methods such as filtered back projection (FBP), and quantified using metrics including resolution, signal-to-noise ratios (SNRs), and contrast-to-noise ratios (CNRs). Pediatric data sets were reconstructed at their original acquisition settings and additionally simulated to lower dose settings for comparison and evaluation of the potential for radiation dose reduction. Numerical experiments were conducted to quantify EST and other iterative methods in terms of image quality and computation time. The extension of EST to helical cone-beam CT was implemented by using the advanced single-slice rebinning (ASSR) method. Results: Based on the phantom and pediatric patient fan-beam CT data, it is demonstrated that EST reconstructions with the lowest scanner flux setting of 39 mAs produce comparable image quality, resolution, and contrast relative to FBP with the 140 mAs flux setting. Compared to the algebraic reconstruction technique and the expectation maximization statistical reconstruction algorithm, a significant reduction in computation time is achieved with EST. Finally, numerical experiments on helical cone-beam CT data suggest that the combination of EST and ASSR produces reconstructions with higher image quality and lower noise than the Feldkamp Davis and Kress (FDK) method and the conventional ASSR approach. Conclusions: A Fourier-based iterative method has been applied to the reconstruction of fan-bean CT data with reduced x-ray fluence. This method incorporates advantageous features in both real and Fourier space iterative schemes: using a fast and algebraically exact method to calculate forward projection, enforcing the measured data in Fourier space, and applying physical constraints and flexible regularization in real space. Our results suggest that EST can be utilized for radiation dose reduction in x-ray CT via the readily implementable technique of lowering mAs settings. Numerical experiments further indicate that EST requires less computation time than several other iterative algorithms and can, in principle, be extended to helical cone-beam geometry in combination with the ASSR method.« less

Radiation dose reduction in medical x-ray CT via Fourier-based iterative reconstruction.

PubMed

Fahimian, Benjamin P; Zhao, Yunzhe; Huang, Zhifeng; Fung, Russell; Mao, Yu; Zhu, Chun; Khatonabadi, Maryam; DeMarco, John J; Osher, Stanley J; McNitt-Gray, Michael F; Miao, Jianwei

2013-03-01

A Fourier-based iterative reconstruction technique, termed Equally Sloped Tomography (EST), is developed in conjunction with advanced mathematical regularization to investigate radiation dose reduction in x-ray CT. The method is experimentally implemented on fan-beam CT and evaluated as a function of imaging dose on a series of image quality phantoms and anonymous pediatric patient data sets. Numerical simulation experiments are also performed to explore the extension of EST to helical cone-beam geometry. EST is a Fourier based iterative algorithm, which iterates back and forth between real and Fourier space utilizing the algebraically exact pseudopolar fast Fourier transform (PPFFT). In each iteration, physical constraints and mathematical regularization are applied in real space, while the measured data are enforced in Fourier space. The algorithm is automatically terminated when a proposed termination criterion is met. Experimentally, fan-beam projections were acquired by the Siemens z-flying focal spot technology, and subsequently interleaved and rebinned to a pseudopolar grid. Image quality phantoms were scanned at systematically varied mAs settings, reconstructed by EST and conventional reconstruction methods such as filtered back projection (FBP), and quantified using metrics including resolution, signal-to-noise ratios (SNRs), and contrast-to-noise ratios (CNRs). Pediatric data sets were reconstructed at their original acquisition settings and additionally simulated to lower dose settings for comparison and evaluation of the potential for radiation dose reduction. Numerical experiments were conducted to quantify EST and other iterative methods in terms of image quality and computation time. The extension of EST to helical cone-beam CT was implemented by using the advanced single-slice rebinning (ASSR) method. Based on the phantom and pediatric patient fan-beam CT data, it is demonstrated that EST reconstructions with the lowest scanner flux setting of 39 mAs produce comparable image quality, resolution, and contrast relative to FBP with the 140 mAs flux setting. Compared to the algebraic reconstruction technique and the expectation maximization statistical reconstruction algorithm, a significant reduction in computation time is achieved with EST. Finally, numerical experiments on helical cone-beam CT data suggest that the combination of EST and ASSR produces reconstructions with higher image quality and lower noise than the Feldkamp Davis and Kress (FDK) method and the conventional ASSR approach. A Fourier-based iterative method has been applied to the reconstruction of fan-bean CT data with reduced x-ray fluence. This method incorporates advantageous features in both real and Fourier space iterative schemes: using a fast and algebraically exact method to calculate forward projection, enforcing the measured data in Fourier space, and applying physical constraints and flexible regularization in real space. Our results suggest that EST can be utilized for radiation dose reduction in x-ray CT via the readily implementable technique of lowering mAs settings. Numerical experiments further indicate that EST requires less computation time than several other iterative algorithms and can, in principle, be extended to helical cone-beam geometry in combination with the ASSR method.

Radiation dose reduction in medical x-ray CT via Fourier-based iterative reconstruction

PubMed Central

Fahimian, Benjamin P.; Zhao, Yunzhe; Huang, Zhifeng; Fung, Russell; Mao, Yu; Zhu, Chun; Khatonabadi, Maryam; DeMarco, John J.; Osher, Stanley J.; McNitt-Gray, Michael F.; Miao, Jianwei

2013-01-01

Purpose: A Fourier-based iterative reconstruction technique, termed Equally Sloped Tomography (EST), is developed in conjunction with advanced mathematical regularization to investigate radiation dose reduction in x-ray CT. The method is experimentally implemented on fan-beam CT and evaluated as a function of imaging dose on a series of image quality phantoms and anonymous pediatric patient data sets. Numerical simulation experiments are also performed to explore the extension of EST to helical cone-beam geometry. Methods: EST is a Fourier based iterative algorithm, which iterates back and forth between real and Fourier space utilizing the algebraically exact pseudopolar fast Fourier transform (PPFFT). In each iteration, physical constraints and mathematical regularization are applied in real space, while the measured data are enforced in Fourier space. The algorithm is automatically terminated when a proposed termination criterion is met. Experimentally, fan-beam projections were acquired by the Siemens z-flying focal spot technology, and subsequently interleaved and rebinned to a pseudopolar grid. Image quality phantoms were scanned at systematically varied mAs settings, reconstructed by EST and conventional reconstruction methods such as filtered back projection (FBP), and quantified using metrics including resolution, signal-to-noise ratios (SNRs), and contrast-to-noise ratios (CNRs). Pediatric data sets were reconstructed at their original acquisition settings and additionally simulated to lower dose settings for comparison and evaluation of the potential for radiation dose reduction. Numerical experiments were conducted to quantify EST and other iterative methods in terms of image quality and computation time. The extension of EST to helical cone-beam CT was implemented by using the advanced single-slice rebinning (ASSR) method. Results: Based on the phantom and pediatric patient fan-beam CT data, it is demonstrated that EST reconstructions with the lowest scanner flux setting of 39 mAs produce comparable image quality, resolution, and contrast relative to FBP with the 140 mAs flux setting. Compared to the algebraic reconstruction technique and the expectation maximization statistical reconstruction algorithm, a significant reduction in computation time is achieved with EST. Finally, numerical experiments on helical cone-beam CT data suggest that the combination of EST and ASSR produces reconstructions with higher image quality and lower noise than the Feldkamp Davis and Kress (FDK) method and the conventional ASSR approach. Conclusions: A Fourier-based iterative method has been applied to the reconstruction of fan-bean CT data with reduced x-ray fluence. This method incorporates advantageous features in both real and Fourier space iterative schemes: using a fast and algebraically exact method to calculate forward projection, enforcing the measured data in Fourier space, and applying physical constraints and flexible regularization in real space. Our results suggest that EST can be utilized for radiation dose reduction in x-ray CT via the readily implementable technique of lowering mAs settings. Numerical experiments further indicate that EST requires less computation time than several other iterative algorithms and can, in principle, be extended to helical cone-beam geometry in combination with the ASSR method. PMID:23464329

Null hypersurface quantization, electromagnetic duality and asympotic symmetries of Maxwell theory

NASA Astrophysics Data System (ADS)

Bhattacharyya, Arpan; Hung, Ling-Yan; Jiang, Yikun

2018-03-01

In this paper we consider introducing careful regularization at the quantization of Maxwell theory in the asymptotic null infinity. This allows systematic discussions of the commutators in various boundary conditions, and application of Dirac brackets accordingly in a controlled manner. This method is most useful when we consider asymptotic charges that are not localized at the boundary u → ±∞ like large gauge transformations. We show that our method reproduces the operator algebra in known cases, and it can be applied to other space-time symmetry charges such as the BMS transformations. We also obtain the asymptotic form of the U(1) charge following from the electromagnetic duality in an explicitly EM symmetric Schwarz-Sen type action. Using our regularization method, we demonstrate that the charge generates the expected transformation of a helicity operator. Our method promises applications in more generic theories.

Rotational reorganization of doped cholesteric liquid crystalline films.

PubMed

Eelkema, Rienk; Pollard, Michael M; Katsonis, Nathalie; Vicario, Javier; Broer, Dirk J; Feringa, Ben L

2006-11-08

In this paper an unprecedented rotational reorganization of cholesteric liquid crystalline films is described. This rotational reorganization results from the conversion of a chiral molecular motor dopant to an isomer with a different helical twisting power, leading to a change in the cholesteric pitch. The direction of this reorganization is correlated to the sign of the change in helical twisting power of the dopant. The rotational reorganization of the liquid crystalline film was used to rotate microscopic objects 4 orders of magnitude larger than the bistable dopants in the film, which shows that molecular motors and switches can perform work. The surface of the doped cholesteric liquid crystalline films was found to possess a regular surface relief, whose periodicity coincides with typical cholesteric polygonal line textures. These surface features originate from the cholesteric superstructure in the liquid crystalline film, which in turn is the result of the presence of the chiral dopant. As such, the presence of the dopant is expressed in these distinct surface structures. A possible mechanism at the origin of the rotational reorganization of liquid crystalline films and the cholesteric surface relief is discussed.

Chaotic coordinates for the Large Helical Device

NASA Astrophysics Data System (ADS)

Hudson, Stuart; Suzuki, Yasuhiro

2014-10-01

The study of dynamical systems is facilitated by a coordinate framework with coordinate surfaces that coincide with invariant structures of the dynamical flow. For axisymmetric systems, a continuous family of invariant surfaces is guaranteed and straight-fieldline coordinates may be constructed. For non-integrable systems, e.g. stellarators, perturbed tokamaks, this continuous family is broken. Nevertheless, coordinates can still be constructed that simplify the description of the dynamics. The Poincare-Birkhoff theorem, the Aubry-Mather theorem, and the KAM theorem show that there are important structures that are invariant under the perturbed dynamics; namely the periodic orbits, the cantori, and the irrational flux surfaces. Coordinates adapted to these invariant sets, which we call chaotic coordinates, provide substantial advantages. The regular motion becomes straight, and the irregular motion is bounded by, and dissected by, coordinate surfaces that coincide with surfaces of locally-minimal magnetic-fieldline flux. The chaotic edge of the magnetic field, as calculated by HINT2 code, in the Large Helical Device (LHD) is examined, and a coordinate system is constructed so that the flux surfaces are ``straight'' and the islands become ``square.''

Representation of viruses in the remediated PDB archive

PubMed Central

Lawson, Catherine L.; Dutta, Shuchismita; Westbrook, John D.; Henrick, Kim; Berman, Helen M.

2008-01-01

A new scheme has been devised to represent viruses and other biological assemblies with regular noncrystallographic symmetry in the Protein Data Bank (PDB). The scheme describes existing and anticipated PDB entries of this type using generalized descriptions of deposited and experimental coordinate frames, symmetry and frame transformations. A simplified notation has been adopted to express the symmetry generation of assemblies from deposited coordinates and matrix operations describing the required point, helical or crystallographic symmetry. Complete correct information for building full assemblies, subassemblies and crystal asymmetric units of all virus entries is now available in the remediated PDB archive. PMID:18645236

Multi-enzymatic one-pot reduction of dehydrocholic acid to 12-keto-ursodeoxycholic acid with whole-cell biocatalysts.

PubMed

Sun, Boqiao; Kantzow, Christina; Bresch, Sven; Castiglione, Kathrin; Weuster-Botz, Dirk

2013-01-01

Ursodeoxycholic acid (UDCA) is a bile acid of industrial interest as it is used as an agent for the treatment of primary sclerosing cholangitis and the medicamentous, non-surgical dissolution of gallstones. Currently, it is prepared industrially from cholic acid following a seven-step chemical procedure with an overall yield of <30%. In this study, we investigated the key enzymatic steps in the chemo-enzymatic preparation of UDCA-the two-step reduction of dehydrocholic acid (DHCA) to 12-keto-ursodeoxycholic acid using a mutant of 7β-hydroxysteroid dehydrogenase (7β-HSDH) from Collinsella aerofaciens and 3α-hydroxysteroid dehydrogenase (3α-HSDH) from Comamonas testosteroni. Three different one-pot reaction approaches were investigated using whole-cell biocatalysts in simple batch processes. We applied one-biocatalyst systems, where 3α-HSDH, 7β-HSDH, and either a mutant of formate dehydrogenase (FDH) from Mycobacterium vaccae N10 or a glucose dehydrogenase (GDH) from Bacillus subtilis were expressed in a Escherichia coli BL21(DE3) based host strain. We also investigated two-biocatalyst systems, where 3α-HSDH and 7β-HSDH were expressed separately together with FDH enzymes for cofactor regeneration in two distinct E. coli hosts that were simultaneously applied in the one-pot reaction. The best result was achieved by the one-biocatalyst system with GDH for cofactor regeneration, which was able to completely convert 100 mM DHCA to >99.5 mM 12-keto-UDCA within 4.5 h in a simple batch process on a liter scale. Copyright © 2012 Wiley Periodicals, Inc.

A Model for Straight and Helical Solar Jets: II. Parametric Study of the Plasma Beta

NASA Technical Reports Server (NTRS)

Pariat, E.; Dalmasse, K.; DeVore, C. R.; Antiochos, S. K.; Karpen, J. T.

2016-01-01

Context. Jets are dynamic, impulsive, well-collimated plasma events that develop at many different scales and in different layers of the solar atmosphere. Aims. Jets are believed to be induced by magnetic reconnection, a process central to many astrophysical phenomena. Within the solar atmosphere, jet-like events develop in many different environments, e.g. in the vicinity of active regions as well as in coronal holes, and at various scales, from small photospheric spicules to large coronal jets. In all these events, signatures of helical structure and/or twisting/rotating motions are regularly observed. The present study aims to establish that a single model can generally reproduce the observed properties of these jet-like events. Methods. In this study, using our state-of-the-art numerical solver ARMS, we present a parametric study of a numerical tridimensional magnetohydrodynamic (MHD) model of solar jet-like events. Within the MHD paradigm, we study the impact of varying the atmospheric plasma beta on the generation and properties of solar-like jets. Results. The parametric study validates our model of jets for plasma beta ranging from 10(sup 3) to 1, typical of the different layers and magnetic environments of the solar atmosphere. Our model of jets can robustly explain the generation of helical solar jet-like events at various beta less than or equal to 1. We show that the plasma beta modifies the morphology of the helical jet, explaining the different observed shapes of jets at different scales and in different layers of the solar atmosphere. Conclusions. Our results allow us to understand the energisation, triggering, and driving processes of jet-like events. Our model allows us to make predictions of the impulsiveness and energetics of jets as determined by the surrounding environment, as well as the morphological properties of the resulting jets.

Comparison of breathing gated CT images generated using a 5DCT technique and a commercial clinical protocol in a porcine model

PubMed Central

O’Connell, Dylan P.; Thomas, David H.; Dou, Tai H.; Lamb, James M.; Feingold, Franklin; Low, Daniel A.; Fuld, Matthew K.; Sieren, Jered P.; Sloan, Chelsea M.; Shirk, Melissa A.; Hoffman, Eric A.; Hofmann, Christian

2015-01-01

Purpose: To demonstrate that a “5DCT” technique which utilizes fast helical acquisition yields the same respiratory-gated images as a commercial technique for regular, mechanically produced breathing cycles. Methods: Respiratory-gated images of an anesthetized, mechanically ventilated pig were generated using a Siemens low-pitch helical protocol and 5DCT for a range of breathing rates and amplitudes and with standard and low dose imaging protocols. 5DCT reconstructions were independently evaluated by measuring the distances between tissue positions predicted by a 5D motion model and those measured using deformable registration, as well by reconstructing the originally acquired scans. Discrepancies between the 5DCT and commercial reconstructions were measured using landmark correspondences. Results: The mean distance between model predicted tissue positions and deformably registered tissue positions over the nine datasets was 0.65 ± 0.28 mm. Reconstructions of the original scans were on average accurate to 0.78 ± 0.57 mm. Mean landmark displacement between the commercial and 5DCT images was 1.76 ± 1.25 mm while the maximum lung tissue motion over the breathing cycle had a mean value of 27.2 ± 4.6 mm. An image composed of the average of 30 deformably registered images acquired with a low dose protocol had 6 HU image noise (single standard deviation) in the heart versus 31 HU for the commercial images. Conclusions: An end to end evaluation of the 5DCT technique was conducted through landmark based comparison to breathing gated images acquired with a commercial protocol under highly regular ventilation. The techniques were found to agree to within 2 mm for most respiratory phases and most points in the lung. PMID:26133604

CO2 Photoreduction by Formate Dehydrogenase and a Ru-Complex in a Nanoporous Glass Reactor.

PubMed

Noji, Tomoyasu; Jin, Tetsuro; Nango, Mamoru; Kamiya, Nobuo; Amao, Yutaka

2017-02-01

In this study, we demonstrated the conversion of CO 2 to formic acid under ambient conditions in a photoreduction nanoporous reactor using a photosensitizer, methyl viologen (MV 2+ ), and formate dehydrogenase (FDH). The overall efficiency of this reactor was 14 times higher than that of the equivalent solution. The accumulation rate of formic acid in the nanopores of 50 nm is 83 times faster than that in the equivalent solution. Thus, this CO 2 photoreduction nanoporous glass reactor will be useful as an artificial photosynthesis system that converts CO 2 to fuel.

Training survey -- educational profile for Hanford HANDI 2000 project

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilson, D.

Fluor Daniel Hanford, Inc. (FDH) is currently adopting streamlined business processes through integrated software solutions. Replacing the legacy software (current/replacement systems, attached) also avoids significant maintenance required to resolve Year 2000 issues. This initiative is being referred to as `HANDI 2000`. The software being implemented in the first phase of this project includes Indus International`s PASSPORT Software, Peoplesoft and Primavera P3 Software. The project, which encompasses all the system replacements that will occur, has been named `HANDI 2000.` The PASSPORT applications being implemented are Inventory Management, Purchasing, Contract Management, Accounts Payable, and MSDS (Material Safety Data Sheets).

A generalized analysis of hydrophobic and loop clusters within globular protein sequences

PubMed Central

Eudes, Richard; Le Tuan, Khanh; Delettré, Jean; Mornon, Jean-Paul; Callebaut, Isabelle

2007-01-01

Background Hydrophobic Cluster Analysis (HCA) is an efficient way to compare highly divergent sequences through the implicit secondary structure information directly derived from hydrophobic clusters. However, its efficiency and application are currently limited by the need of user expertise. In order to help the analysis of HCA plots, we report here the structural preferences of hydrophobic cluster species, which are frequently encountered in globular domains of proteins. These species are characterized only by their hydrophobic/non-hydrophobic dichotomy. This analysis has been extended to loop-forming clusters, using an appropriate loop alphabet. Results The structural behavior of hydrophobic cluster species, which are typical of protein globular domains, was investigated within banks of experimental structures, considered at different levels of sequence redundancy. The 294 more frequent hydrophobic cluster species were analyzed with regard to their association with the different secondary structures (frequencies of association with secondary structures and secondary structure propensities). Hydrophobic cluster species are predominantly associated with regular secondary structures, and a large part (60 %) reveals preferences for α-helices or β-strands. Moreover, the analysis of the hydrophobic cluster amino acid composition generally allows for finer prediction of the regular secondary structure associated with the considered cluster within a cluster species. We also investigated the behavior of loop forming clusters, using a "PGDNS" alphabet. These loop clusters do not overlap with hydrophobic clusters and are highly associated with coils. Finally, the structural information contained in the hydrophobic structural words, as deduced from experimental structures, was compared to the PSI-PRED predictions, revealing that β-strands and especially α-helices are generally over-predicted within the limits of typical β and α hydrophobic clusters. Conclusion The dictionary of hydrophobic clusters described here can help the HCA user to interpret and compare the HCA plots of globular protein sequences, as well as provides an original fundamental insight into the structural bricks of protein folds. Moreover, the novel loop cluster analysis brings additional information for secondary structure prediction on the whole sequence through a generalized cluster analysis (GCA), and not only on regular secondary structures. Such information lays the foundations for developing a new and original tool for secondary structure prediction. PMID:17210072

CO 2-fixing one-carbon metabolism in a cellulose-degrading bacterium Clostridium thermocellum

DOE PAGES

Xiong, Wei; Lin, Paul P.; Magnusson, Lauren; ...

2016-10-28

Clostridium thermocellum can ferment cellulosic biomass to formate and other end products, including CO 2. This organism lacks formate dehydrogenase (Fdh), which catalyzes the reduction of CO 2 to formate. However, feeding the bacterium 13C-bicarbonate and cellobiose followed by NMR analysis showed the production of 13C-formate in C. thermocellum culture, indicating the presence of an uncharacterized pathway capable of converting CO 2 to formate. Combining genomic and experimental data, we demonstrated that the conversion of CO 2 to formate serves as a CO 2 entry point into the reductive one-carbon (C1) metabolism, and internalizes CO 2 via two biochemical reactions:more » the reversed pyruvate:ferredoxin oxidoreductase (rPFOR), which incorporates CO 2 using acetyl-CoA as a substrate and generates pyruvate, and pyruvate-formate lyase (PFL) converting pyruvate to formate and acetyl-CoA. We analyzed the labeling patterns of proteinogenic amino acids in individual deletions of all five putative PFOR mutants and in a PFL deletion mutant. We identified two enzymes acting as rPFOR, confirmed the dual activities of rPFOR and PFL crucial for CO 2 uptake, and provided physical evidence of a distinct in vivo 'rPFOR-PFL shunt' to reduce CO 2 to formate while circumventing the lack of Fdh. Such a pathway precedes CO 2 fixation via the reductive C1 metabolic pathway in C. thermocellum. Lastly, these findings demonstrated the metabolic versatility of C. thermocellum, which is thought of as primarily a cellulosic heterotroph but is shown here to be endowed with the ability to fix CO 2 as well.« less

Levels of control exerted by the Isc iron-sulfur cluster system on biosynthesis of the formate hydrogenlyase complex.

PubMed

Pinske, Constanze; Jaroschinsky, Monique; Sawers, R Gary

2013-06-01

The membrane-associated formate hydrogenlyase (FHL) complex of bacteria like Escherichia coli is responsible for the disproportionation of formic acid into the gaseous products carbon dioxide and dihydrogen. It comprises minimally seven proteins including FdhF and HycE, the catalytic subunits of formate dehydrogenase H and hydrogenase 3, respectively. Four proteins of the FHL complex have iron-sulphur cluster ([Fe-S]) cofactors. Biosynthesis of [Fe-S] is principally catalysed by the Isc or Suf systems and each comprises proteins for assembly and for delivery of [Fe-S]. This study demonstrates that the Isc system is essential for biosynthesis of an active FHL complex. In the absence of the IscU assembly protein no hydrogen production or activity of FHL subcomponents was detected. A deletion of the iscU gene also resulted in reduced intracellular formate levels partially due to impaired synthesis of pyruvate formate-lyase, which is dependent on the [Fe-S]-containing regulator FNR. This caused reduced expression of the formate-inducible fdhF gene. The A-type carrier (ATC) proteins IscA and ErpA probably deliver [Fe-S] to specific apoprotein components of the FHL complex because mutants lacking either protein exhibited strongly reduced hydrogen production. Neither ATC protein could compensate for the lack of the other, suggesting that they had independent roles in [Fe-S] delivery to complex components. Together, the data indicate that the Isc system modulates FHL complex biosynthesis directly by provision of [Fe-S] as well as indirectly by influencing gene expression through the delivery of [Fe-S] to key regulators and enzymes that ultimately control the generation and oxidation of formate.

The multi-faceted outcomes of conjunct diabetes and cardiovascular familial history in type 2 diabetes.

PubMed

Hermans, Michel P; Ahn, Sylvie A; Rousseau, Michel F

2012-01-01

Familial history of early-onset CHD (EOCHD) is a major risk factor for CHD. Familial diabetes history (FDH) impacts β-cell function. Some transmissible, accretional gradient of CHD risk may exist when diabetes and EOCHD familial histories combine. We investigated whether the impact of such combination is neutral, additive, or potentiating in T2DM descendants, as regards cardiometabolic phenotype, glucose homeostasis and micro-/macroangiopathies. Cross-sectional retrospective cohort study of 796 T2DM divided according to presence (Diab[+]) or absence (Diab[-]) of 1st-degree diabetes familial history and/or EOCHD (CVD(+) and (-)). Four subgroups: (i) [Diab(-)CVD(-)] (n=355); (ii) [Diab(+)CVD(-)] (n=338); (iii) [Diab(-)CVD(+)] (n=47); and (iv) [Diab(+)CVD(+)] (n=56). No interaction on subgroup distribution between presence of both familial histories, the combination of which translated into additive detrimental outcomes and higher rates of fat mass, sarcopenia, (hs)CRP and retinopathy. FDH(+) had lower insulinemia, insulin secretion, hyperbolic product, and accelerated hyperbolic product loss. An EOCHD family history affected neither insulin secretion nor sensitivity. There were significant differences regarding macroangiopathy/CAD, more prevalent in [Diab(-)CVD(+)] and [Diab(+)CVD(+)]. Among CVD(+), the highest macroangiopathy prevalence was observed in [Diab(-)CVD(+)], who had 66% macroangiopathy, and 57% CAD, rates higher (absolute-relative) by 23%-53% (overall) and 21%-58% (CAD) than [Diab(+)CVD(+)], who inherited the direst cardiometabolic familial history (p 0.0288 and 0.0310). A parental history for diabetes markedly affects residual insulin secretion and secretory loss rate in T2DM offspring without worsening insulin resistance. It paradoxically translated into lower macroangiopathy with concurrent familial EOCHD. Conjunct diabetes and CV familial histories generate multi-faceted vascular outcomes in offspring, including lesser macroangiopathy/CAD. Copyright © 2012 Elsevier Inc. All rights reserved.

Association Between Ultra-Processed Food Consumption and Functional Gastrointestinal Disorders: Results From the French NutriNet-Santé Cohort.

PubMed

Schnabel, Laure; Buscail, Camille; Sabate, Jean-Marc; Bouchoucha, Michel; Kesse-Guyot, Emmanuelle; Allès, Benjamin; Touvier, Mathilde; Monteiro, Carlos A; Hercberg, Serge; Benamouzig, Robert; Julia, Chantal

2018-06-15

Ultra-processed foods (UPF) consumption has increased over the last decades and is raising concerns about potential adverse health effects. Our objective was to assess the association between UPF consumption and four functional gastrointestinal disorders (FGIDs): irritable bowel syndrome (IBS), functional constipation (FC), functional diarrhea (FDh), and functional dyspepsia (FDy), in a large sample of French adults. We analyzed dietary data of 33,343 participants from the web-based NutriNet-Santé cohort, who completed at least three 24 h food records, prior to a Rome III self-administered questionnaire. Proportion (in weight) of UPF in the diet (UPFp) was computed for each subject. The association between UPFp quartiles and FGIDs was estimated by multivariable logistic regression. Participants included in the analysis were mainly women (76.4%), and the mean age was 50.4 (SD = 14.0) years. UPF accounted for 16.0% of food consumed in weight, corresponding to 33.0% of total energy intake. UPF consumption was associated with younger age, living alone, lower incomes, higher BMI, and lower physical activity level (all p < 0.0001). A total of 3516 participants reported IBS (10.5%), 1785 FC (5.4%), 1303 FDy (3.9%), and 396 FDh (1.1%). After adjusting for confounding factors, an increase in UPFp was associated with a higher risk of IBS ( a OR Q4 vs. Q1 [95% CI]: 1.25 [1.12-1.39], p-trend < 0.0001). This study suggests an association between UPF and IBS. Further longitudinal studies are needed to confirm those results and understand the relative impact of the nutritional composition and specific characteristics of UPF in this relationship.

CO 2-fixing one-carbon metabolism in a cellulose-degrading bacterium Clostridium thermocellum

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xiong, Wei; Lin, Paul P.; Magnusson, Lauren

Clostridium thermocellum can ferment cellulosic biomass to formate and other end products, including CO 2. This organism lacks formate dehydrogenase (Fdh), which catalyzes the reduction of CO 2 to formate. However, feeding the bacterium 13C-bicarbonate and cellobiose followed by NMR analysis showed the production of 13C-formate in C. thermocellum culture, indicating the presence of an uncharacterized pathway capable of converting CO 2 to formate. Combining genomic and experimental data, we demonstrated that the conversion of CO 2 to formate serves as a CO 2 entry point into the reductive one-carbon (C1) metabolism, and internalizes CO 2 via two biochemical reactions:more » the reversed pyruvate:ferredoxin oxidoreductase (rPFOR), which incorporates CO 2 using acetyl-CoA as a substrate and generates pyruvate, and pyruvate-formate lyase (PFL) converting pyruvate to formate and acetyl-CoA. We analyzed the labeling patterns of proteinogenic amino acids in individual deletions of all five putative PFOR mutants and in a PFL deletion mutant. We identified two enzymes acting as rPFOR, confirmed the dual activities of rPFOR and PFL crucial for CO 2 uptake, and provided physical evidence of a distinct in vivo 'rPFOR-PFL shunt' to reduce CO 2 to formate while circumventing the lack of Fdh. Such a pathway precedes CO 2 fixation via the reductive C1 metabolic pathway in C. thermocellum. Lastly, these findings demonstrated the metabolic versatility of C. thermocellum, which is thought of as primarily a cellulosic heterotroph but is shown here to be endowed with the ability to fix CO 2 as well.« less

Toward Homosuccinate Fermentation: Metabolic Engineering of Corynebacterium glutamicum for Anaerobic Production of Succinate from Glucose and Formate

PubMed Central

Litsanov, Boris; Brocker, Melanie

2012-01-01

Previous studies have demonstrated the capability of Corynebacterium glutamicum for anaerobic succinate production from glucose under nongrowing conditions. In this work, we have addressed two shortfalls of this process, the formation of significant amounts of by-products and the limitation of the yield by the redox balance. To eliminate acetate formation, a derivative of the type strain ATCC 13032 (strain BOL-1), which lacked all known pathways for acetate and lactate synthesis (Δcat Δpqo Δpta-ackA ΔldhA), was constructed. Chromosomal integration of the pyruvate carboxylase gene pycP458S into BOL-1 resulted in strain BOL-2, which catalyzed fast succinate production from glucose with a yield of 1 mol/mol and showed only little acetate formation. In order to provide additional reducing equivalents derived from the cosubstrate formate, the fdh gene from Mycobacterium vaccae, coding for an NAD+-coupled formate dehydrogenase (FDH), was chromosomally integrated into BOL-2, leading to strain BOL-3. In an anaerobic batch process with strain BOL-3, a 20% higher succinate yield from glucose was obtained in the presence of formate. A temporary metabolic blockage of strain BOL-3 was prevented by plasmid-borne overexpression of the glyceraldehyde 3-phosphate dehydrogenase gene gapA. In an anaerobic fed-batch process with glucose and formate, strain BOL-3/pAN6-gap accumulated 1,134 mM succinate in 53 h with an average succinate production rate of 1.59 mmol per g cells (dry weight) (cdw) per h. The succinate yield of 1.67 mol/mol glucose is one of the highest currently described for anaerobic succinate producers and was accompanied by a very low level of by-products (0.10 mol/mol glucose). PMID:22389371

Synthesis, characterisation and applications of coiled carbon nanotubes.

PubMed

Hanus, Monica J; Harris, Andrew T

2010-04-01

Coiled carbon nanotubes are helical carbon structures formed when heptagonal and pentagonal rings are inserted into the hexagonal backbone of a 'straight' nanotube. Coiled carbon nanotubes have been reported with both regular and irregular helical structures. In this work the structure, growth mechanism(s), synthesis, properties and potential applications of coiled carbon nanotubes are reviewed. Published data suggests that coiled carbon nanotube synthesis occurs due to nonuniform extrusion of carbon from a catalyst surface. To date, coiled carbon nanotubes have been synthesised using catalyst modification techniques including: (i) the addition of S or P containing compounds during synthesis; (ii) the use of binary or ternary metal catalysts; (iii) the use of microwaves to create a local temperature gradient around individual catalyst particles and; (iv) the use of pH control during catalyst preparation. In most instances coiled carbon nanotubes are produced as a by-product; high yield and/or large-scale synthesis of coiled carbon nanotubes remains problematic. The qualitative analysis of coiled carbon nanotubes is currently hindered by the absence of specific characterisation data in the literature, e.g., oxidation profiles measured by thermogravimetric analysis and Raman spectra of pure coiled carbon nanotube samples.

Regeneration of Nicotinamide Coenzymes: Principles and Applications for the Synthesis of Chiral Compounds

NASA Astrophysics Data System (ADS)

Weckbecker, Andrea; Gröger, Harald; Hummel, Werner

Dehydrogenases which depend on nicotinamide coenzymes are of increasing interest for the preparation of chiral compounds, either by reduction of a prochiral precursor or by oxidative resolution of their racemate. The regeneration of oxidized and reduced nicotinamide cofactors is a very crucial step because the use of these cofactors in stoichiometric amounts is too expensive for application. There are several possibilities to regenerate nicotinamide cofactors: established methods such as formate/formate dehydrogenase (FDH) for the regeneration of NADH, recently developed electrochemical methods based on new mediator structures, or the application of gene cloning methods for the construction of "designed" cells by heterologous expression of appropriate genes.

ADP/ATP mitochondrial carrier MD simulations to shed light on the structural-dynamical events that, after an additional mutation, restore the function in a pathological single mutant.

PubMed

Di Marino, Daniele; Oteri, Francesco; Morozzo Della Rocca, Blasco; Chillemi, Giovanni; Falconi, Mattia

2010-12-01

Molecular dynamics simulations of the wild type bovine ADP/ATP mitochondrial carrier, and of the single Ala113Pro and double Ala113Pro/Val180Met mutants, embedded in a lipid bilayer, have been carried out for 30ns to shed light on the structural-dynamical changes induced by the Val180Met mutation restoring the carrier function in the Ala113Pro pathologic mutant. Principal component analysis indicates that, for the three systems, the protein dynamics is mainly characterized by the motion of the matrix loops and of the odd-numbered helices having a conserved proline in their central region. Analysis of the motions shows a different behaviour of single pathological mutant with respect of the other two systems. The single mutation induces a regularization and rigidity of the H3 helix, lost upon the introduction of the second mutation. This is directly correlated to the salt bridge distribution involving residues Arg79, Asp134 and Arg234, hypothesized to interact with the substrate. In fact, in the wild type simulation two stable inter-helices salt bridges, crucial for substrate binding, are present almost over all the simulation time. In line with the impaired ADP transport, one salt interaction is lost in the single mutant trajectory but reappears in the double mutant simulation, where a salt bridge network matching the wild type is restored. Other important structural-dynamical properties, such as the trans-membrane helices mobility, analyzed via the principal component analysis, are similar for the wild type and double mutant while are different for the single mutant, providing a mechanistic explanation for their different functional properties. Copyright © 2010 Elsevier Inc. All rights reserved.

Pathways and intermediates in forced unfolding of spectrin repeats.

PubMed

Altmann, Stephan M; Grünberg, Raik G; Lenne, Pierre-François; Ylänne, Jari; Raae, Arnt; Herbert, Kristina; Saraste, Matti; Nilges, Michael; Hörber, J K Heinrich

2002-08-01

Spectrin repeats are triple-helical coiled-coil domains found in many proteins that are regularly subjected to mechanical stress. We used atomic force microscopy technique and steered molecular dynamics simulations to study the behavior of a wild-type spectrin repeat and two mutants. The experiments indicate that spectrin repeats can form stable unfolding intermediates when subjected to external forces. In the simulations the unfolding proceeded via a variety of pathways. Stable intermediates were associated to kinking of the central helix close to a proline residue. A mutant stabilizing the central helix showed no intermediates in experiments, in agreement with simulation. Spectrin repeats may thus function as elastic elements, extendable to intermediate states at various lengths.

A unified convention for biological assemblies with helical symmetry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tsai, Chung-Jung, E-mail: tsaic@mail.nih.gov; Nussinov, Ruth; Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978

A new representation of helical structure by four parameters, [n{sub 1}, n{sub 2}, twist, rise], is able to generate an entire helical construct from asymmetric units, including cases of helical assembly with a seam. Assemblies with helical symmetry can be conveniently formulated in many distinct ways. Here, a new convention is presented which unifies the two most commonly used helical systems for generating helical assemblies from asymmetric units determined by X-ray fibre diffraction and EM imaging. A helical assembly is viewed as being composed of identical repetitive units in a one- or two-dimensional lattice, named 1-D and 2-D helical systems,more » respectively. The unification suggests that a new helical description with only four parameters [n{sub 1}, n{sub 2}, twist, rise], which is called the augmented 1-D helical system, can generate the complete set of helical arrangements, including coverage of helical discontinuities (seams). A unified four-parameter characterization implies similar parameters for similar assemblies, can eliminate errors in reproducing structures of helical assemblies and facilitates the generation of polymorphic ensembles from helical atomic models or EM density maps. Further, guidelines are provided for such a unique description that reflects the structural signature of an assembly, as well as rules for manipulating the helical symmetry presentation.« less

Statistical analyses and computational prediction of helical kinks in membrane proteins

NASA Astrophysics Data System (ADS)

Huang, Y.-H.; Chen, C.-M.

2012-10-01

We have carried out statistical analyses and computer simulations of helical kinks for TM helices in the PDBTM database. About 59 % of 1562 TM helices showed a significant kink, and 38 % of these kinks are associated with prolines in a range of ±4 residues. Our analyses show that helical kinks are more populated in the central region of helices, particularly in the range of 1-3 residues away from the helix center. Among 1,053 helical kinks analyzed, 88 % of kinks are bends (change in helix axis without loss of helical character) and 12 % are disruptions (change in helix axis and loss of helical character). It is found that proline residues tend to cause larger kink angles in helical bends, while this effect is not observed in helical disruptions. A further analysis of these kinked helices suggests that a kinked helix usually has 1-2 broken backbone hydrogen bonds with the corresponding N-O distance in the range of 4.2-8.7 Å, whose distribution is sharply peaked at 4.9 Å followed by an exponential decay with increasing distance. Our main aims of this study are to understand the formation of helical kinks and to predict their structural features. Therefore we further performed molecular dynamics (MD) simulations under four simulation scenarios to investigate kink formation in 37 kinked TM helices and 5 unkinked TM helices. The representative models of these kinked helices are predicted by a clustering algorithm, SPICKER, from numerous decoy structures possessing the above generic features of kinked helices. Our results show an accuracy of 95 % in predicting the kink position of kinked TM helices and an error less than 10° in the angle prediction of 71.4 % kinked helices. For unkinked helices, based on various structure similarity tests, our predicted models are highly consistent with their crystal structure. These results provide strong supports for the validity of our method in predicting the structure of TM helices.

Evaluation of helicity generation in the tropical storm Gonu

NASA Astrophysics Data System (ADS)

Farahani, Majid M.; Khansalari, Sakineh; Azadi, Majid

2017-06-01

Helicity is a valuable dynamical concept for the study of rotating flows. Consequently helicity flux, indicative of the source or sink of helicity, owns comparable importance. In this study, while reviewing the existing methods, a mathematical relation between helicity and helicity-flux is introduced, discussed and examined. The computed values of helicity and helicity fluxes in an actual case, using the classical and this proposed method are compared. The down-stream helicity flux including sources and sinks of helicity is considered for the tropical storm Gonu that occurred over the coasts of Oman and Iran on June 2-7, 2007. Results show that the buoyancy, through the upper troposphere down to a height within boundary layer, is the main source in producing helicity, and surface friction from earth surface up to a height within boundary layer, is the main dissipating element of helicity. The dominance of buoyancy forcing over the dissipative friction forcing results in generation of vortex or enhancement of it after bouncing the land. Furthermore, the increase (decrease) of helicity results in an increase (decrease) in the height of the level in which maximum helicity flux occurs. It is suggested that the maximum helicity flux occurs at the top of the turbulent boundary layer, so that the height of boundary layer could be obtained.

The activation of fibroblast growth factors (FGFs) by glycosaminoglycans: influence of the sulfation pattern on the biological activity of FGF-1.

PubMed

Angulo, Jesús; Ojeda, Rafael; de Paz, José-Luis; Lucas, Ricardo; Nieto, Pedro M; Lozano, Rosa M; Redondo-Horcajo, Mariano; Giménez-Gallego, Guillermo; Martín-Lomas, Manuel

2004-01-03

Six synthetic heparin-like oligosaccharides have been used to investigate the effect of the oligosaccharide sulfation pattern on the stimulation of acidic fibroblast growth factor (FGF-1) induced mitogenesis signaling and the biological significance of FGF-1 trans dimerization in the FGF-1 activation process. It has been found that some molecules with a sulfation pattern that does not contain the internal trisaccharide motif, which has been proposed for high affinity for FGF-1, stimulate FGF-1 more efficiently than those with the structure of the regular region of heparin. In contrast to regular region oligosaccharides, in which the sulfate groups are distributed on both sides of their helical three-dimensional structures, the molecules containing this particular sulfation pattern display the sulfate groups only on one side of the helix. These results and the fact that these oligosaccharides do not promote FGF-1 dimerization according to sedimentation-equilibrium analysis, confirm the importance of negative-charge distribution in the activation process and strongly suggest that FGF dimerization is not a general and absolute requirement for biological activity.

Bearing capacity of helical pile foundation in peat soil from different, diameter and spacing of helical plates

NASA Astrophysics Data System (ADS)

Fatnanta, F.; Satibi, S.; Muhardi

2018-03-01

In an area dominated by thick peat soil layers, driven piles foundation is often used. These piles are generally skin friction piles where the pile tips do not reach hard stratum. Since the bearing capacity of the piles rely on the resistance of their smooth skin, the bearing capacity of the piles are generally low. One way to increase the bearing capacity of the piles is by installing helical plates around the pile tips. Many research has been performed on helical pile foundation. However, literature on the use of helical pile foundation on peat soil is still hardly found. This research focus on the study of axial bearing capacity of helical pile foundation in peat soil, especially in Riau Province. These full-scale tests on helical pile foundation were performed in a rectangular box partially embedded into the ground. The box is filled with peat soil, which was taken from Rimbo Panjang area in the district of Kampar, Riau Province. Several helical piles with different number, diameter and spacing of the helical plates have been tested and analysed. The tests result show that helical pile with three helical plates of uniform diameter has better bearing capacity compared to other helical piles with varying diameter and different number of helical plates. The bearing capacity of helical pile foundation is affected by the spacing between helical plates. It is found that the effective helical plates spacing for helical pile foundation with diameter of 15cm to 35cm is between 20cm to 30cm. This behaviour may be considered to apply to other type of helical pile foundations in peat soil.

The role of protein homochirality in shaping the energy landscape of folding

PubMed Central

Nanda, Vikas; Andrianarijaona, Aina; Narayanan, Chitra

2007-01-01

The homochirality, or isotacticity, of the natural amino acids facilitates the formation of regular secondary structures such as α-helices and β-sheets. However, many examples exist in nature where novel polypeptide topologies use both l- and d-amino acids. In this study, we explore how stereochemistry of the polypeptide backbone influences basic properties such as compactness and the size of fold space by simulating both lattice and all-atom polypeptide chains. We formulate a rectangular lattice chain model in both two and three dimensions, where monomers are chiral, having the effect of restricting local conformation. Syndiotactic chains with alternating chirality of adjacent monomers have a very large ensemble of accessible conformations characterized predominantly by extended structures. Isotactic chains on the other hand, have far fewer possible conformations and a significant fraction of these are compact. Syndiotactic chains are often unable to access maximally compact states available to their isotactic counterparts of the same length. Similar features are observed in all-atom models of isotactic versus syndiotactic polyalanine. Our results suggest that protein isotacticity has evolved to increase the enthalpy of chain collapse by facilitating compact helical states and to reduce the entropic cost of folding by restricting the size of the unfolded ensemble of competing states. PMID:17600146

Application of 1-aminocyclohexane carboxylic acid to protein nanostructure computer design

PubMed Central

Rodríguez-Ropero, Francisco; Zanuy, David; Casanovas, Jordi; Nussinov, Ruth; Alemán, Carlos

2009-01-01

Conformationally restricted amino acids are promising candidates to serve as basic pieces in redesigned protein motifs which constitute the basic modules in synthetic nanoconstructs. Here we study the ability of constrained cyclic amino acid 1-aminocyclohexane-1-carboxylic acid (Ac6c) to stabilize highly regular β-helical motifs excised from naturally occurring proteins. Calculations indicate that the conformational flexibility observed in both the ring and the main chain is significantly higher than that detected for other 1-aminocycloalkane-1-carboxylic acid (Acnc, where n refers to the size of the ring) with smaller cycles. Incorporation of Ac6c into the flexible loops of β-helical motifs indicates that the stability of such excised building blocks as well as the nano-assemblies derived from them is significantly enhanced. Thus, the intrinsic Ac6c tendency to adopt folded conformations combined with the low structural strain of the cyclohexane ring confers the ability to both self-adapt to the β-helix motif and to stabilize the overall structure by absorbing part of its conformational fluctuations. Comparison with other Acnc residues indicates that the ability to adapt to the targeted position improves considerably with the ring size, i.e. when the rigidity introduced by the strain of the ring decreases. PMID:18201062

Structural analysis of reactionary dentin formed in response to polymicrobial invasion

PubMed Central

Charadram, Nattida; Austin, Christine; Trimby, Patrick; Simonian, Mary; Swain, Michael V.; Hunter, Neil

2013-01-01

In response to microbial invasion of dentin odontoblasts secrete an altered calcified matrix termed reactionary dentin (Rd). 3D reconstruction of focused-ion-beam scanning electron microscopy (FIB-SEM) image slices revealed helical tubular structures in Rd that contrasted with regular cylindrical tubules characteristic of dentin from healthy teeth and affected so-called physiological dentin (Pd) lying exterior to Rd. This helical structure in Rd provided effective constriction of tubule lumen diameter that formed a barrier to bacterial advance towards the dental pulp. SEM of resin cast preparations revealed altered extension of odontoblast processes through Rd. The distribution of key mineral elements was studied by combination of 3D reconstruction of focused-ion-beam based X-ray microanalysis (FIB-EDS), laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) and diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS). There was a marked redistribution of calcium and phosphorous in Rd together with an increase of diffusely deposited magnesium compatible with the mineral deposition phase of synthesis of this altered matrix. Changes in tubule structure and mineral content characteristic of Rd are consistent with reduced hardness and lower elastic modulus reported for this matrix. Findings provide insight into the unique structure of Rd synthesised as a primary response to infection. PMID:23261402

Role of helicity in triad interactions in three-dimensional turbulence investigated by a new shell model

NASA Astrophysics Data System (ADS)

Rathmann, Nicholas M.; Ditlevsen, Peter D.

2016-09-01

Fully developed homogeneous isotropic turbulence in two dimensions is fundamentally different from that in three dimensions. In two dimensions, the simultaneous inviscid conservation of both kinetic energy and enstrophy within the inertial range of scales leads to a forward cascade of enstrophy and a reverse cascade of energy. In three dimensions, helicity, the integral of the scalar product of velocity and vorticity, is also an inviscid flow invariant along with the energy. Unlike the enstrophy, however, the helicity does not block the forward cascade of energy to small scales. Energy and helicity are conserved not only globally but also within each nonlinear triadic interaction between three plane waves in the spectral form of the Navier-Stokes equation (NSE). By decomposing each plane wave into two helical modes of opposite helicities, each triadic interaction is split into a set of eight helical triadic interactions between helical modes [F. Waleffe, Phys. Fluids A 4, 350 (1992), 10.1063/1.858309]. Recently it was found that a subset of these helical interactions, which render both signs of helicity separately conserved (enstrophy-like), leads to an inverse cascade of (part of) the energy [L. Biferale et al., Phys. Rev. Lett. 108, 164501 (2012), 10.1103/PhysRevLett.108.164501]. Motivated by this finding we introduce a new shell model, obtained from the NSE expressed in the helical basis, allowing the eight helical interactions to be coupled as in the NSE and their relative contributions evaluated as a function of both the net helicity input and triad geometry. By numerically integrating the new model, we find that the intermittency of the energy cascade decreases with the net helicity input. Studying the partitioning of the energy cascade between the eight helical interactions, we find that the decrease in intermittency is related to a shift in the dominating helical interactions when helically forced, two of which exhibit a larger cascade intermittency than the other six interactions. Among the relatively local triad geometries considered here, the partitioning of the energy and helicity cascades between the eight helical interactions shows no sign of change with triad geometry.

DNS of helicity-induced stratified turbulent flow

NASA Astrophysics Data System (ADS)

Chandy, Abhilash J.; Rahimi, Abbas

2013-11-01

Helical flows undergoing density stratification have wide applications in meteorological phenomena such as dust devils, tornadoes, and hurricanes due to the complexity and disasters caused by them. Direct numerical simulations (DNS) of transition to turbulence in a stably stratified Boussinesq fluid are presented for different rotation and stratification intensities. In order to understand the effect of velocity on the energy cascade, comparisons are made between helicity initiated and non-helical flows. Results show that stratification decelerates the helicity decay and causes velocity and vorticity to align with each other. With respect to the helical and non-helical flow comparisons, the total energy in the presence of stratification decays faster with helicity. In addition, the behavior of length scales were examined by comparing temporal variations of the vertical shearing of velocities. Results showed a growing asymmetry with time in the case of helical flow, while non-helical flow stayed close to begin symmetric.

Self-assembly of a double-helical complex of sodium.

PubMed

Bell, T W; Jousselin, H

1994-02-03

Spontaneous self-organization of helical and multiple-helical molecular structures occurs on several levels in living organisms. Key examples are alpha-helical polypeptides, double-helical nucleic acids and helical protein structures, including F-actin, microtubules and the protein sheath of the tobacco mosaic virus. Although the self-assembly of double-helical transition-metal complexes bears some resemblance to the molecular organization of double-stranded DNA, selection between monohelical, double-helical and triple-helical structures is determined largely by the size and geometrical preference of the tightly bound metal. Here we present an example of double-helical assembly induced by the weaker and non-directional interactions of an alkali-metal ion with an organic ligand that is pre-organized into a coil. We have characterized the resulting complex by two-dimensional NMR and fast-atom-bombardment mass spectrometry. These results provide a step toward the creation of molecular tubes or ion channels consisting of intertwined coils.

Magnetic design constraints of helical solenoids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lopes, M. L.; Krave, S. T.; Tompkins, J. C.

2015-01-30

Helical solenoids have been proposed as an option for a Helical Cooling Channel for muons in a proposed Muon Collider. Helical solenoids can provide the required three main field components: solenoidal, helical dipole, and a helical gradient. In general terms, the last two are a function of many geometric parameters: coil aperture, coil radial and longitudinal dimensions, helix period and orbit radius. In this paper, we present design studies of a Helical Solenoid, addressing the geometric tunability limits and auxiliary correction system.

Helical localized wave solutions of the scalar wave equation.

PubMed

Overfelt, P L

2001-08-01

A right-handed helical nonorthogonal coordinate system is used to determine helical localized wave solutions of the homogeneous scalar wave equation. Introducing the characteristic variables in the helical system, i.e., u = zeta - ct and v = zeta + ct, where zeta is the coordinate along the helical axis, we can use the bidirectional traveling plane wave representation and obtain sets of elementary bidirectional helical solutions to the wave equation. Not only are these sets bidirectional, i.e., based on a product of plane waves, but they may also be broken up into right-handed and left-handed solutions. The elementary helical solutions may in turn be used to create general superpositions, both Fourier and bidirectional, from which new solutions to the wave equation may be synthesized. These new solutions, based on the helical bidirectional superposition, are members of the class of localized waves. Examples of these new solutions are a helical fundamental Gaussian focus wave mode, a helical Bessel-Gauss pulse, and a helical acoustic directed energy pulse train. Some of these solutions have the interesting feature that their shape and localization properties depend not only on the wave number governing propagation along the longitudinal axis but also on the normalized helical pitch.

Dosimetric aspects of breast radiotherapy with three-dimensional and intensity-modulated radiotherapy helical tomotherapy planning modules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yadav, Poonam; Service of Radiation Therapy, University of Wisconsin Aspirus Cancer Center, Wisconsin Rapids, WI; Yan, Yue, E-mail: yyan5@mdanderson.org

In this work, we investigated the dosimetric differences between the intensity-modulated radiotherapy (IMRT) plans and the three-dimensional (3D) helical plans based on the TomoTherapy system. A total of 15 patients with supine setup were randomly selected from the data base. For patients with lumpectomy planning target volume (PTV), regional lymph nodes were also included as part of the target. For dose sparing, the significant differences between the helical IMRT and helical 3D were only found in the heart and contralateral breast. For the dose to the heart, helical IMRT reduced the maximum point dose by 6.98 Gy compared to themore » helical 3D plan (p = 0.01). For contralateral breast, the helical IMRT plans significantly reduced the maximum point dose by 5.6 Gy compared to the helical 3D plan. However, compared to the helical 3D plan, the helical IMRT plan increased the volume for lower dose (13.08% increase in V{sub 5} {sub Gy}, p = 0.01). In general, there are no significant differences in dose sparing between helical IMRT and helical 3D plans.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wemmer, D.E.; Kumar, N.V.; Metrione, R.M.

Toxin II from Radianthus paumotensis (Rp/sub II/) has been investigated by high-resolution NMR and chemical sequencing methods. Resonance assignments have been obtained for this protein by the sequential approach. NMR assignments could not be made consistent with the previously reported primary sequence for this protein, and chemical methods have been used to determine a sequence with which the NMR data are consistent. Analysis of the 2D NOE spectra shows that the protein secondary structure is comprised of two sequences of ..beta..-sheet, probably joined into a distorted continuous sheet, connected by turns and extended loops, without any regular ..cap alpha..-helical segments.more » The residues previously implicated in activity in this class of proteins, D8 and R13, occur in a loop region.« less

Regulation of pokemon 1 activity by sumoylation.

PubMed

Roh, Hee-Eun; Lee, Min-Nyung; Jeon, Bu-Nam; Choi, Won-Il; Kim, Yoo-Jin; Yu, Mi-Young; Hur, Man-Wook

2007-01-01

Pokemon 1 is a proto-oncogenic transcriptional regulator that contains a POZ domain at the N-terminus and four Kruppel-like zinc fingers at the C-terminus. Pokemon 1 plays an important role in adipogenesis, osteogenesis, oncogenesis, and transcription of NF-kB responsive genes. Recent reports have shown that biological activities of transcription factors are regulated by sumolylation. We investigated whether Pokemon 1 is post-translationally modified by sumoylation and whether the modification affects Pokemon 1's transcriptional properties. We found that Pokemon 1 is sumoylated in vitro and in vivo. Upon careful analysis of the amino acid sequence of Pokemon 1, we found ten potential sumoylation sites located at lysines 61, 354, 371, 379, 383, 396, 486, 487, 536 and 539. We mutated each of these amino acids into arginine and tested whether the mutation could affect the transcriptional properties of Pokemon 1 on the Pokemon 1 responsive genes, such as ADH5/FDH and pG5-FRE-Luc. Wild-type Pokemon 1 potently represses transcription of ADH5/FDH. Most of the mutants, however, were weaker transcription repressors and repressed transcription 1.3-3.3 fold less effective. Although potential sumoylation sites were located close to the DNA binding domain or the nuclear localization sequence, the mutations did not alter nuclear localization or DNA binding activity. In addition, on the pG5-FRE-Luc test promoter construct, ectopic SUMO-1 repressed transcription in the presence of Pokemon 1. The sumoylation target lysine residue at amino acid 61, which is located in the middle of the POZ-domain, is important because K61R mutation resulted in a much weaker molecular interaction with corepressors. Our data suggest that Pokemon 1's activity as a transcription factor may involve sumoylation, and that sumoylation might be important in the regulation of transcription by Pokemon 1.

NADP-Specific Electron-Bifurcating [FeFe]-Hydrogenase in a Functional Complex with Formate Dehydrogenase in Clostridium autoethanogenum Grown on CO

PubMed Central

Wang, Shuning; Huang, Haiyan; Kahnt, Jörg; Mueller, Alexander P.; Köpke, Michael

2013-01-01

Flavin-based electron bifurcation is a recently discovered mechanism of coupling endergonic to exergonic redox reactions in the cytoplasm of anaerobic bacteria and archaea. Among the five electron-bifurcating enzyme complexes characterized to date, one is a heteromeric ferredoxin- and NAD-dependent [FeFe]-hydrogenase. We report here a novel electron-bifurcating [FeFe]-hydrogenase that is NADP rather than NAD specific and forms a complex with a formate dehydrogenase. The complex was found in high concentrations (6% of the cytoplasmic proteins) in the acetogenic Clostridium autoethanogenum autotrophically grown on CO, which was fermented to acetate, ethanol, and 2,3-butanediol. The purified complex was composed of seven different subunits. As predicted from the sequence of the encoding clustered genes (fdhA/hytA-E) and from chemical analyses, the 78.8-kDa subunit (FdhA) is a selenocysteine- and tungsten-containing formate dehydrogenase, the 65.5-kDa subunit (HytB) is an iron-sulfur flavin mononucleotide protein harboring the NADP binding site, the 51.4-kDa subunit (HytA) is the [FeFe]-hydrogenase proper, and the 18.1-kDa (HytC), 28.6-kDa (HytD), 19.9-kDa (HytE1), and 20.1-kDa (HytE2) subunits are iron-sulfur proteins. The complex catalyzed both the reversible coupled reduction of ferredoxin and NADP+ with H2 or formate and the reversible formation of H2 and CO2 from formate. We propose the complex to have two functions in vivo, namely, to normally catalyze CO2 reduction to formate with NADPH and reduced ferredoxin in the Wood-Ljungdahl pathway and to catalyze H2 formation from NADPH and reduced ferredoxin when these redox mediators get too reduced during unbalanced growth of C. autoethanogenum on CO (E0′ = −520 mV). PMID:23893107

NADP-specific electron-bifurcating [FeFe]-hydrogenase in a functional complex with formate dehydrogenase in Clostridium autoethanogenum grown on CO.

PubMed

Wang, Shuning; Huang, Haiyan; Kahnt, Jörg; Mueller, Alexander P; Köpke, Michael; Thauer, Rudolf K

2013-10-01

Flavin-based electron bifurcation is a recently discovered mechanism of coupling endergonic to exergonic redox reactions in the cytoplasm of anaerobic bacteria and archaea. Among the five electron-bifurcating enzyme complexes characterized to date, one is a heteromeric ferredoxin- and NAD-dependent [FeFe]-hydrogenase. We report here a novel electron-bifurcating [FeFe]-hydrogenase that is NADP rather than NAD specific and forms a complex with a formate dehydrogenase. The complex was found in high concentrations (6% of the cytoplasmic proteins) in the acetogenic Clostridium autoethanogenum autotrophically grown on CO, which was fermented to acetate, ethanol, and 2,3-butanediol. The purified complex was composed of seven different subunits. As predicted from the sequence of the encoding clustered genes (fdhA/hytA-E) and from chemical analyses, the 78.8-kDa subunit (FdhA) is a selenocysteine- and tungsten-containing formate dehydrogenase, the 65.5-kDa subunit (HytB) is an iron-sulfur flavin mononucleotide protein harboring the NADP binding site, the 51.4-kDa subunit (HytA) is the [FeFe]-hydrogenase proper, and the 18.1-kDa (HytC), 28.6-kDa (HytD), 19.9-kDa (HytE1), and 20.1-kDa (HytE2) subunits are iron-sulfur proteins. The complex catalyzed both the reversible coupled reduction of ferredoxin and NADP(+) with H2 or formate and the reversible formation of H2 and CO2 from formate. We propose the complex to have two functions in vivo, namely, to normally catalyze CO2 reduction to formate with NADPH and reduced ferredoxin in the Wood-Ljungdahl pathway and to catalyze H2 formation from NADPH and reduced ferredoxin when these redox mediators get too reduced during unbalanced growth of C. autoethanogenum on CO (E0' = -520 mV).

Chloramphenicol Biosynthesis: The Structure of CmlS, a Flavin-Dependent Halogenase Shwing a Covalent Flavin-Aspartate Bond

DOE Office of Scientific and Technical Information (OSTI.GOV)

Podzelinska, K.; Latimer, R; Bhattacharya, A

2010-01-01

Chloramphenicol is a halogenated natural product bearing an unusual dichloroacetyl moiety that is critical for its antibiotic activity. The operon for chloramphenicol biosynthesis in Streptomyces venezuelae encodes the chloramphenicol halogenase CmlS, which belongs to the large and diverse family of flavin-dependent halogenases (FDH's). CmlS was previously shown to be essential for the formation of the dichloroacetyl group. Here we report the X-ray crystal structure of CmlS determined at 2.2 {angstrom} resolution, revealing a flavin monooxygenase domain shared by all FDHs, but also a unique 'winged-helix' C-terminal domain that creates a T-shaped tunnel leading to the halogenation active site. Intriguingly, themore » C-terminal tail of this domain blocks access to the halogenation active site, suggesting a structurally dynamic role during catalysis. The halogenation active site is notably nonpolar and shares nearly identical residues with Chondromyces crocatus tyrosyl halogenase (CndH), including the conserved Lys (K71) that forms the reactive chloramine intermediate. The exception is Y350, which could be used to stabilize enolate formation during substrate halogenation. The strictly conserved residue E44, located near the isoalloxazine ring of the bound flavin adenine dinucleotide (FAD) cofactor, is optimally positioned to function as a remote general acid, through a water-mediated proton relay, which could accelerate the reaction of the chloramine intermediate during substrate halogenation, or the oxidation of chloride by the FAD(C4{alpha})-OOH intermediate. Strikingly, the 8{alpha} carbon of the FAD cofactor is observed to be covalently attached to D277 of CmlS, a residue that is highly conserved in the FDH family. In addition to representing a new type of flavin modification, this has intriguing implications for the mechanism of FDHs. Based on the crystal structure and in analogy to known halogenases, we propose a reaction mechanism for CmlS.« less

Meta-Analyses of Dehalococcoides mccartyi Strain 195 Transcriptomic Profiles Identify a Respiration Rate-Related Gene Expression Transition Point and Interoperon Recruitment of a Key Oxidoreductase Subunit

PubMed Central

Mansfeldt, Cresten B.; Rowe, Annette R.; Heavner, Gretchen L. W.; Zinder, Stephen H.

2014-01-01

A cDNA-microarray was designed and used to monitor the transcriptomic profile of Dehalococcoides mccartyi strain 195 (in a mixed community) respiring various chlorinated organics, including chloroethenes and 2,3-dichlorophenol. The cultures were continuously fed in order to establish steady-state respiration rates and substrate levels. The organization of array data into a clustered heat map revealed two major experimental partitions. This partitioning in the data set was further explored through principal component analysis. The first two principal components separated the experiments into those with slow (1.6 ± 0.6 μM Cl−/h)- and fast (22.9 ± 9.6 μM Cl−/h)-respiring cultures. Additionally, the transcripts with the highest loadings in these principal components were identified, suggesting that those transcripts were responsible for the partitioning of the experiments. By analyzing the transcriptomes (n = 53) across experiments, relationships among transcripts were identified, and hypotheses about the relationships between electron transport chain members were proposed. One hypothesis, that the hydrogenases Hup and Hym and the formate dehydrogenase-like oxidoreductase (DET0186-DET0187) form a complex (as displayed by their tight clustering in the heat map analysis), was explored using a nondenaturing protein separation technique combined with proteomic sequencing. Although these proteins did not migrate as a single complex, DET0112 (an FdhB-like protein encoded in the Hup operon) was found to comigrate with DET0187 rather than with the catalytic Hup subunit DET0110. On closer inspection of the genome annotations of all Dehalococcoides strains, the DET0185-to-DET0187 operon was found to lack a key subunit, an FdhB-like protein. Therefore, on the basis of the transcriptomic, genomic, and proteomic evidence, the place of the missing subunit in the DET0185-to-DET0187 operon is likely filled by recruiting a subunit expressed from the Hup operon (DET0112). PMID:25063656

Roles of effective helical ripple rates in nonlinear stability of externally induced magnetic islands

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nishimura, Seiya, E-mail: n-seiya@kobe-kosen.ac.jp

Magnetic islands are externally produced by resonant magnetic perturbations (RMPs) in toroidal plasmas. Spontaneous annihilation of RMP-induced magnetic islands called self-healing has been observed in helical systems. A possible mechanism of the self-healing is shielding of RMP penetration by helical ripple-induced neoclassical flows, which give rise to neoclassical viscous torques. In this study, effective helical ripple rates in multi-helicity helical systems are revisited, and a multi-helicity effect on the self-healing is investigated, based on a theoretical model of rotating magnetic islands. It is confirmed that effective helical ripple rates are sensitive to magnetic axis positions. It is newly found thatmore » self-healing thresholds also strongly depend on magnetic axis positions, which is due to dependence of neoclassical viscous torques on effective helical ripple rates.« less

Fluid-Dynamic Optimal Design of Helical Vascular Graft for Stenotic Disturbed Flow

PubMed Central

Ha, Hojin; Hwang, Dongha; Choi, Woo-Rak; Baek, Jehyun; Lee, Sang Joon

2014-01-01

Although a helical configuration of a prosthetic vascular graft appears to be clinically beneficial in suppressing thrombosis and intimal hyperplasia, an optimization of a helical design has yet to be achieved because of the lack of a detailed understanding on hemodynamic features in helical grafts and their fluid dynamic influences. In the present study, the swirling flow in a helical graft was hypothesized to have beneficial influences on a disturbed flow structure such as stenotic flow. The characteristics of swirling flows generated by helical tubes with various helical pitches and curvatures were investigated to prove the hypothesis. The fluid dynamic influences of these helical tubes on stenotic flow were quantitatively analysed by using a particle image velocimetry technique. Results showed that the swirling intensity and helicity of the swirling flow have a linear relation with a modified Germano number (Gn*) of the helical pipe. In addition, the swirling flow generated a beneficial flow structure at the stenosis by reducing the size of the recirculation flow under steady and pulsatile flow conditions. Therefore, the beneficial effects of a helical graft on the flow field can be estimated by using the magnitude of Gn*. Finally, an optimized helical design with a maximum Gn* was suggested for the future design of a vascular graft. PMID:25360705

Helical vortices: Quasiequilibrium states and their time evolution

NASA Astrophysics Data System (ADS)

Selçuk, Can; Delbende, Ivan; Rossi, Maurice

2017-08-01

The time evolution of a viscous helical vortex is investigated by direct numerical simulations of the Navier-Stokes equations where helical symmetry is enforced. Using conservation laws in the framework of helical symmetry, we elaborate an initial condition consisting in a finite core vortex, the time evolution of which leads to a generic quasiequilibrium state independent of the initial core size. Numerical results at different helical pitch values provide an accurate characterization in time for such helical states, for which specific techniques have been introduced: helix radius, angular velocity, stream function-velocity-vorticity relationships, and core properties (size, self-similarity, and ellipticity). Viscosity is shown to be at the origin of a small helical velocity component, which we relate to the helical vorticity component. Finally, changes in time of the flow topology are studied using the helical stream function and three-dimensional Lagrangian orbits.

Spectral CT of the extremities with a silicon strip photon counting detector

NASA Astrophysics Data System (ADS)

Sisniega, A.; Zbijewski, W.; Stayman, J. W.; Xu, J.; Taguchi, K.; Siewerdsen, J. H.

2015-03-01

Purpose: Photon counting x-ray detectors (PCXDs) are an important emerging technology for spectral imaging and material differentiation with numerous potential applications in diagnostic imaging. We report development of a Si-strip PCXD system originally developed for mammography with potential application to spectral CT of musculoskeletal extremities, including challenges associated with sparse sampling, spectral calibration, and optimization for higher energy x-ray beams. Methods: A bench-top CT system was developed incorporating a Si-strip PCXD, fixed anode x-ray source, and rotational and translational motions to execute complex acquisition trajectories. Trajectories involving rotation and translation combined with iterative reconstruction were investigated, including single and multiple axial scans and longitudinal helical scans. The system was calibrated to provide accurate spectral separation in dual-energy three-material decomposition of soft-tissue, bone, and iodine. Image quality and decomposition accuracy were assessed in experiments using a phantom with pairs of bone and iodine inserts (3, 5, 15 and 20 mm) and an anthropomorphic wrist. Results: The designed trajectories improved the sampling distribution from 56% minimum sampling of voxels to 75%. Use of iterative reconstruction (viz., penalized likelihood with edge preserving regularization) in combination with such trajectories resulted in a very low level of artifacts in images of the wrist. For large bone or iodine inserts (>5 mm diameter), the error in the estimated material concentration was <16% for (50 mg/mL) bone and <8% for (5 mg/mL) iodine with strong regularization. For smaller inserts, errors of 20-40% were observed and motivate improved methods for spectral calibration and optimization of the edge-preserving regularizer. Conclusion: Use of PCXDs for three-material decomposition in joint imaging proved feasible through a combination of rotation-translation acquisition trajectories and iterative reconstruction with optimized regularization.

An Amino Acid Packing Code for α-helical Structure and Protein Design

PubMed Central

Joo, Hyun; Chavan, Archana G.; Phan, Jamie; Day, Ryan; Tsai, Jerry

2012-01-01

This work demonstrates that all packing in α-helices can be simplified to repetitive patterns of a single motif: the knob-socket. Using the precision of Voronoi Polyhedra/Deluaney Tessellations to identify contacts, the knob-socket is a 4 residue tetrahedral motif: a knob residue on one α-helix packs into the 3 residue socket on another α-helix. The principle of the knob-socket model relates the packing between levels of protein structure: the intra-helical packing arrangements within secondary structure that permit inter-helix tertiary packing interactions. Within an α-helix, the 3 residue sockets arrange residues into a uniform packing lattice. Inter-helix packing results from a definable pattern of interdigitated knob-socket motifs between 2 α-helices. Furthermore, the knob-socket model classifies 3 types of sockets: 1) free: favoring only intra-helical packing, 2) filled: favoring inter-helical interactions and 3) non: disfavoring α-helical structure. The amino acid propensities in these 3 socket classes essentially represent an amino acid code for structure in α-helical packing. Using this code, a novel yet straightforward approach for the design of α-helical structure was used to validate the knob-socket model. Unique sequences for 3 peptides were created to produce a predicted amount of α-helical structure: mostly helical, some helical, and no-helix. These 3 peptides were synthesized and helical content assessed using CD spectroscopy. The measured α-helicity of each peptide was consistent with the expected predictions. These results and analysis demonstrate that the knob-socket motif functions as the basic unit of packing and presents an intuitive tool to decipher the rules governing packing in protein structure. PMID:22426125

Dissection and engineering of the Escherichia coli formate hydrogenlyase complex.

PubMed

McDowall, Jennifer S; Hjersing, M Charlotte; Palmer, Tracy; Sargent, Frank

2015-10-07

The Escherichia coli formate hydrogenlyase (FHL) complex is produced under fermentative conditions and couples formate oxidation to hydrogen production. In this work, the architecture of FHL has been probed by analysing affinity-tagged complexes from various genetic backgrounds. In a successful attempt to stabilize the complex, a strain encoding a fusion between FdhF and HycB has been engineered and characterised. Finally, site-directed mutagenesis of the hycG gene was performed, which is predicted to encode a hydrogenase subunit important for regulating sensitivity to oxygen. This work helps to define the core components of FHL and provides solutions to improving the stability of the enzyme. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

A Combined Study of Photospheric Magnetic and Current Helicities and Subsurface Kinetic Helicities of Solar Active Regions during 2006-2013

NASA Astrophysics Data System (ADS)

Seligman, D.; Petrie, G. J. D.; Komm, R.

2014-11-01

We compare the average photospheric current helicity Hc , photospheric twist parameter α (a well-known proxy for the full relative magnetic helicity), and subsurface kinetic helicity Hk for 194 active regions observed between 2006-2013. We use 2440 Hinode photospheric vector magnetograms, and the corresponding subsurface fluid velocity data derived from GONG (2006-2012) and Helioseismic and Magnetic Imager (2010-2013) dopplergrams. We find a significant hemispheric bias in all three parameters. The subsurface kinetic helicity is preferentially positive in the southern hemisphere and negative in the northern hemisphere. The photospheric current helicity and the α parameter have the same bias for strong fields (|B| > 1000 G) and no significant bias for weak fields (100 G <|B| < 500 G). We find no significant region-by-region correlation between the subsurface kinetic helicity and either the strong-field current helicity or α. Subsurface fluid motions of a given handedness correspond to photospheric helicities of both signs in approximately equal numbers. However, common variations appear in annual averages of these quantities over all regions. Furthermore, in a subset of 77 regions, we find significant correlations between the temporal profiles of the subsurface and photospheric helicities. In these cases, the sign of the linear correlation coefficient matches the sign relationship between the helicities, indicating that the photospheric magnetic field twist is sensitive to the twisting motions below the surface.

SU-F-J-117: Impact of Motion Artifacts On Image Quality and Accuracy of Tumor Motion Reconstruction in 4D CT-On-Rails and MV-CBCT Scans: A Phantom Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, T; Ma, C

Purpose: To compare and quantify respiratory motion artifacts in images from free breathing 4D-CT-on-Rails(CTOR) and those from MV-Cone-beam-CT(MVCB) and facilitate respiratory motion guided radiation therapy. Methods: 4D-CTOR: Siemens Somatom CT-on-Rails system with Anzai belt loaded with pressure sensor load cells. 4D scans were performed in helical mode, pitch 0.1, gantry rotation time 0.5s, 1.5mm slice thickness, 120kVp, 400 mAs. Normal and fast breathing (>12rpm) scanning protocols were investigated. Helical scan, AIP(average intensity projection) and MIP(maximum intensity projection) were generated from 4D-CTOR scans with amplitude sorting into 10 phases.MVCB: Siemens Artiste diamond view(1MV)MVCB was performed with 5MU thorax protocol with 60more » second of full rotation.Phantom: Anzai AZ-733V respiratory phantom. The settings were set to normal and resp. modes with repetition rates at 15 rpm and 10 rpm. Surgical clips, acrylic, wooden, rubber and lung density, total six mock-ups were scanned and compared in this study.Signal-to-noise ratio(SNR), contrast-to-noise ratio(CNR) and reconstructed motion volume were compared to different respiratory setups for the mock-ups. Results: Reconstructed motion volume was compared to the real object volume for the six test mock-ups. It shows that free breathing helical in all instances underestimates the object excursions largest to −67.4% and least −6.3%. Under normal breathing settings, MIP can predict very precise motion volume with minimum 0.4% and largest −13.9%. MVCB shows underestimate of the motion volume with −1.11% minimum and −18.0% maximum. With fast breathing, AIP provides bad representation of the object motion; however, the MIP can predict the motion volume with −2.0% to −11.4% underestimate. Conclusion: Respiratory motion guided radiation therapy requires good motion recording. This study shows that regular CTOR helical scans provides bad guidance, 4D CTOR AIP cannot represent the fast breathing pattern, MIP can represent the best motion volume, MVCBCT can only be used for normal breathing with acceptable uncertainties.« less

Development of self-assembling nanowires containing electronically active oligothiophenes

NASA Astrophysics Data System (ADS)

Tsai, Wei-Wen

This dissertation discusses the development of conductive one-dimensional nanowires from self-assembling oligothiophene molecules. Self-assembly has been demonstrated to be a promising alternative approach towards high performance, solution processable, and low-cost organic electronics. One of the many challenges in this field is the control of supramolecular morphologies of ordered structures containing pi-conjugated moieties. This research demonstrated several successful strategies to achieve self assembly of conductive nanowires using synergistic interactions combining pi stacking and hydrogen bonding. The first approach used was to develop a hairpin-shaped sexithiophene molecule, which features two arms of the conjugated structure. The diamidocyclohexyl headgroup of this molecule successfully directs the self-assembly from hydrogen bonding among the amides, forming high-aspect-ratio one-dimensional nanowires with well-defined diameters of 3.0 +/- 0.3 nm. The molecular orientation in the nanostructures promotes formation of sexithiophene H and J aggregates that facilitate efficient charge transport. Organic field-effect transistors were fabricated to reveal improved intrinsic hole mobility from films of the nanostructures, 3.46 x 10-6 cm2V-1s-1, which is one order of magnitude higher than films cast from unassembled molecules. Bulk heterojunction solar cells were developed from this molecule and fullerenes utilizing solution-phase fabrication methods. Intimate mix of the molecule and phenyl-C61-butyric acid methyl ester creates structured interfaces for efficient exciton splitting. The charge carrier mobilities of each material are improved by self-assembly in solution and thermal-energy assisted phase separation.The photovoltaic devices achieved the highest open-circuit voltage of 0.62 V, short-circuit current of 1.79 mA/cm2, fill factor of 35%, and power conversion efficiency of 0.48%. Another strategy to one-dimensional nanowires studied here involved the modification of a class of peptide lipids. The tripeptide segments in the molecular structure promote beta-sheet formation in nonpolar organic solvents, which is the main driving force for their self-assembly into 1D nanowires. Left-handed helical nanowires were formed with diameters of 8.9 nm and pitches between 50--150 nm. Substitutions of oligothiophenes lead to unprecedented supercoiling phenomena manifested as the transformation from helical to coiled or curved nanowires. We proposed that the curving of the nanowires is the consequence of relaxation from torsionally strained nanohelices, a process similar to supercoiling of strained DNA double helix. This process is governed by the mismatch in intermolecular distances required for peptide beta-sheets vs. pi-pi interactions of the conjugated segments decorating the periphery of the nanowires. Circular dichroism revealed helical arrangements of the conjugated moieties in these peptide lipids manifesting supercoiling phenomena. Peptide lipids without helical arrangement of the conjugated segments only exhibit helical morphologies. The self-assembly process of peptide lipids also leads to hierarchical assemblies of energetically favored single, double, and triple-helical nanostructures with well-defined dimensions. Self-assembled nanowires from oligothiophene-substituted peptide lipids revealed increased conductivity of 1.39--1.41 x 10-5 S/cm, two orders of magnitude higher than unassembled films and one order of magnitude higher than unsubstituted peptide lipids. The role of the primary beta-helix in controlling supramolecular organization was investigated by varying the chirality of the tripeptide segments, GAA. Four diastereomers of a peptide lipid substituted with p-toluene carboxylates were compared using L or D-alanines. Molecules with all L residues self-assemble into left-handed helical nanofibers with a pitch of 160 +/- 30 nm. Substitution of one or two D-alanines leads to assemblies of cylindrical nanofibers without any twisting, left-handed helices with smaller pitches (40 +/- 6 nm), or aggregates without regular shapes. We believe these effects are steric in nature that changes the beta-sheet sub-structure within the nanofibers. These principles could be utilized as strategies to optimize the morphologies and properties of nanostructures based on these amphiphilic molecules.

Effects of Magnetic and Kinetic Helicities on the Growth of Magnetic Fields in Laminar and Turbulent Flows by Helical Fourier Decomposition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Linkmann, Moritz; Sahoo, Ganapati; Biferale, Luca

We present a numerical and analytical study of incompressible homogeneous conducting fluids using a helical Fourier representation. We analytically study both small- and large-scale dynamo properties, as well as the inverse cascade of magnetic helicity, in the most general minimal subset of interacting velocity and magnetic fields on a closed Fourier triad. We mainly focus on the dependency of magnetic field growth as a function of the distribution of kinetic and magnetic helicities among the three interacting wavenumbers. By combining direct numerical simulations of the full magnetohydrodynamics equations with the helical Fourier decomposition, we numerically confirm that in the kinematicmore » dynamo regime the system develops a large-scale magnetic helicity with opposite sign compared to the small-scale kinetic helicity, a sort of triad-by-triad α -effect in Fourier space. Concerning the small-scale perturbations, we predict theoretically and confirm numerically that the largest instability is achived for the magnetic component with the same helicity of the flow, in agreement with the Stretch–Twist–Fold mechanism. Vice versa, in the presence of Lorentz feedback on the velocity, we find that the inverse cascade of magnetic helicity is mostly local if magnetic and kinetic helicities have opposite signs, while it is more nonlocal and more intense if they have the same sign, as predicted by the analytical approach. Our analytical and numerical results further demonstrate the potential of the helical Fourier decomposition to elucidate the entangled dynamics of magnetic and kinetic helicities both in fully developed turbulence and in laminar flows.« less

Extending Three-Dimensional Weighted Cone Beam Filtered Backprojection (CB-FBP) Algorithm for Image Reconstruction in Volumetric CT at Low Helical Pitches

PubMed Central

Hsieh, Jiang; Nilsen, Roy A.; McOlash, Scott M.

2006-01-01

A three-dimensional (3D) weighted helical cone beam filtered backprojection (CB-FBP) algorithm (namely, original 3D weighted helical CB-FBP algorithm) has already been proposed to reconstruct images from the projection data acquired along a helical trajectory in angular ranges up to [0, 2 π]. However, an overscan is usually employed in the clinic to reconstruct tomographic images with superior noise characteristics at the most challenging anatomic structures, such as head and spine, extremity imaging, and CT angiography as well. To obtain the most achievable noise characteristics or dose efficiency in a helical overscan, we extended the 3D weighted helical CB-FBP algorithm to handle helical pitches that are smaller than 1: 1 (namely extended 3D weighted helical CB-FBP algorithm). By decomposing a helical over scan with an angular range of [0, 2π + Δβ] into a union of full scans corresponding to an angular range of [0, 2π], the extended 3D weighted function is a summation of all 3D weighting functions corresponding to each full scan. An experimental evaluation shows that the extended 3D weighted helical CB-FBP algorithm can improve noise characteristics or dose efficiency of the 3D weighted helical CB-FBP algorithm at a helical pitch smaller than 1: 1, while its reconstruction accuracy and computational efficiency are maintained. It is believed that, such an efficient CB reconstruction algorithm that can provide superior noise characteristics or dose efficiency at low helical pitches may find its extensive applications in CT medical imaging. PMID:23165031

The positive inside rule is stronger when followed by a transmembrane helix.

PubMed

Virkki, Minttu T; Peters, Christoph; Nilsson, Daniel; Sörensen, Therese; Cristobal, Susana; Wallner, Björn; Elofsson, Arne

2014-08-12

The translocon recognizes transmembrane helices with sufficient level of hydrophobicity and inserts them into the membrane. However, sometimes less hydrophobic helices are also recognized. Positive inside rule, orientational preferences of and specific interactions with neighboring helices have been shown to aid in the recognition of these helices, at least in artificial systems. To better understand how the translocon inserts marginally hydrophobic helices, we studied three naturally occurring marginally hydrophobic helices, which were previously shown to require the subsequent helix for efficient translocon recognition. We find no evidence for specific interactions when we scan all residues in the subsequent helices. Instead, we identify arginines located at the N-terminal part of the subsequent helices that are crucial for the recognition of the marginally hydrophobic transmembrane helices, indicating that the positive inside rule is important. However, in two of the constructs, these arginines do not aid in the recognition without the rest of the subsequent helix; that is, the positive inside rule alone is not sufficient. Instead, the improved recognition of marginally hydrophobic helices can here be explained as follows: the positive inside rule provides an orientational preference of the subsequent helix, which in turn allows the marginally hydrophobic helix to be inserted; that is, the effect of the positive inside rule is stronger if positively charged residues are followed by a transmembrane helix. Such a mechanism obviously cannot aid C-terminal helices, and consequently, we find that the terminal helices in multi-spanning membrane proteins are more hydrophobic than internal helices. Copyright © 2014 Elsevier Ltd. All rights reserved.

Cryo-EM Structure Determination Using Segmented Helical Image Reconstruction.

PubMed

Fromm, S A; Sachse, C

2016-01-01

Treating helices as single-particle-like segments followed by helical image reconstruction has become the method of choice for high-resolution structure determination of well-ordered helical viruses as well as flexible filaments. In this review, we will illustrate how the combination of latest hardware developments with optimized image processing routines have led to a series of near-atomic resolution structures of helical assemblies. Originally, the treatment of helices as a sequence of segments followed by Fourier-Bessel reconstruction revealed the potential to determine near-atomic resolution structures from helical specimens. In the meantime, real-space image processing of helices in a stack of single particles was developed and enabled the structure determination of specimens that resisted classical Fourier helical reconstruction and also facilitated high-resolution structure determination. Despite the progress in real-space analysis, the combination of Fourier and real-space processing is still commonly used to better estimate the symmetry parameters as the imposition of the correct helical symmetry is essential for high-resolution structure determination. Recent hardware advancement by the introduction of direct electron detectors has significantly enhanced the image quality and together with improved image processing procedures has made segmented helical reconstruction a very productive cryo-EM structure determination method. © 2016 Elsevier Inc. All rights reserved.

Geometry Dynamics of α-Helices in Different Class I Major Histocompatibility Complexes

PubMed Central

Karch, Rudolf; Schreiner, Wolfgang

2015-01-01

MHC α-helices form the antigen-binding cleft and are of particular interest for immunological reactions. To monitor these helices in molecular dynamics simulations, we applied a parsimonious fragment-fitting method to trace the axes of the α-helices. Each resulting axis was fitted by polynomials in a least-squares sense and the curvature integral was computed. To find the appropriate polynomial degree, the method was tested on two artificially modelled helices, one performing a bending movement and another a hinge movement. We found that second-order polynomials retrieve predefined parameters of helical motion with minimal relative error. From MD simulations we selected those parts of α-helices that were stable and also close to the TCR/MHC interface. We monitored the curvature integral, generated a ruled surface between the two MHC α-helices, and computed interhelical area and surface torsion, as they changed over time. We found that MHC α-helices undergo rapid but small changes in conformation. The curvature integral of helices proved to be a sensitive measure, which was closely related to changes in shape over time as confirmed by RMSD analysis. We speculate that small changes in the conformation of individual MHC α-helices are part of the intrinsic dynamics induced by engagement with the TCR. PMID:26649324

Fine Structure and Dynamics of Sunspot Penumbra

NASA Astrophysics Data System (ADS)

Ryutova, M.; Berger, T.; Title, A.

2007-08-01

A mature sunspot is usually surrounded by a penumbra: strong vertical magnetic field in the umbra, the dark central region of sunspot, becomes more and more horizontal toward the periphery forming an ensemble of a thin magnetic filaments of varying inclinations. Recent high resolution observations with the 1-meter Swedish Solar Telescope (SST) on La Palma revealed a fine substructure of penumbral filaments and new regularities in their dynamics.1 These findings provide both the basis and constraints for an adequate model of the penumbra whose origin still remains enigmatic. We present results of recent observations obtained with the SST. Our data, taken simultaneously in 4305 Å G-band and 4396 Å continuum bandpasses and compiled in high cadence movies, confirm previous results and reveal new features of the penumbra. We find e.g. that individual filaments are cylindrical helices with a pitch/radius ratio providing their dynamic stability. We propose a mechanism that may explain the fine structure of penumbral filaments, the observed regularities, and their togetherness with sunspot formation. The mechanism is based on the anatomy of sunspots in which not only penumbra has a filamentary structure but umbra itself is a dense conglomerate of twisted interlaced flux tubes.

Systematic size study of an insect antifreeze protein and its interaction with ice.

PubMed

Liu, Kai; Jia, Zongchao; Chen, Guangju; Tung, Chenho; Liu, Ruozhuang

2005-02-01

Because of their remarkable ability to depress the freezing point of aqueous solutions, antifreeze proteins (AFPs) play a critical role in helping many organisms survive subzero temperatures. The beta-helical insect AFP structures solved to date, consisting of multiple repeating circular loops or coils, are perhaps the most regular protein structures discovered thus far. Taking an exceptional advantage of the unusually high structural regularity of insect AFPs, we have employed both semiempirical and quantum mechanics computational approaches to systematically investigate the relationship between the number of AFP coils and the AFP-ice interaction energy, an indicator of antifreeze activity. We generated a series of AFP models with varying numbers of 12-residue coils (sequence TCTxSxxCxxAx) and calculated their interaction energies with ice. Using several independent computational methods, we found that the AFP-ice interaction energy increased as the number of coils increased, until an upper bound was reached. The increase of interaction energy was significant for each of the first five coils, and there was a clear synergism that gradually diminished and even decreased with further increase of the number of coils. Our results are in excellent agreement with the recently reported experimental observations.

Systematic Size Study of an Insect Antifreeze Protein and Its Interaction with Ice

PubMed Central

Liu, Kai; Jia, Zongchao; Chen, Guangju; Tung, Chenho; Liu, Ruozhuang

2005-01-01

Because of their remarkable ability to depress the freezing point of aqueous solutions, antifreeze proteins (AFPs) play a critical role in helping many organisms survive subzero temperatures. The β-helical insect AFP structures solved to date, consisting of multiple repeating circular loops or coils, are perhaps the most regular protein structures discovered thus far. Taking an exceptional advantage of the unusually high structural regularity of insect AFPs, we have employed both semiempirical and quantum mechanics computational approaches to systematically investigate the relationship between the number of AFP coils and the AFP-ice interaction energy, an indicator of antifreeze activity. We generated a series of AFP models with varying numbers of 12-residue coils (sequence TCTxSxxCxxAx) and calculated their interaction energies with ice. Using several independent computational methods, we found that the AFP-ice interaction energy increased as the number of coils increased, until an upper bound was reached. The increase of interaction energy was significant for each of the first five coils, and there was a clear synergism that gradually diminished and even decreased with further increase of the number of coils. Our results are in excellent agreement with the recently reported experimental observations. PMID:15713600

Topological properties of microwave magnetoelectric fields.

PubMed

Berezin, M; Kamenetskii, E O; Shavit, R

2014-02-01

Collective excitations of electron spins in a ferromagnetic sample dominated by the magnetic dipole-dipole interaction strongly influence the field structure of microwave radiation. A small quasi-two-dimensional ferrite disk with magnetic-dipolar-mode (MDM) oscillation spectra can behave as a source of specific fields in vacuum, termed magnetoelectric (ME) fields. A coupling between the time-varying electric and magnetic fields in the ME-field structures is different from such a coupling in regular electromagnetic fields. The ME fields are characterized by strong energy confinement at a subwavelength region of microwave radiation, topologically distinctive power-flow vortices, and helicity parameters [E. O. Kamenetskii, R. Joffe, and R. Shavit, Phys. Rev. E 87, 023201 (2013)]. We study topological properties of microwave ME fields by loading a MDM ferrite particle with different dielectric samples. We establish a close connection between the permittivity parameters of dielectric environment and the topology of ME fields. We show that the topology of ME fields is strongly correlated with the Fano-resonance spectra observed at terminals of a microwave structure. We reveal specific thresholds in the Fano-resonance spectra appearing at certain permittivity parameters of dielectric samples. We show that ME fields originated from MDM ferrite disks can be distinguished by topological portraits of the helicity parameters and can have a torsion degree of freedom. Importantly, the ME-field phenomena can be viewed as implementations of space-time coordinate transformations on waves.

Dynamical characteristics of an electromagnetic field under conditions of total reflection

NASA Astrophysics Data System (ADS)

Bekshaev, Aleksandr Ya

2018-04-01

The dynamical characteristics of electromagnetic fields include energy, momentum, angular momentum (spin) and helicity. We analyze their spatial distributions near the planar interface between two transparent and non-dispersive media, when the incident monochromatic plane wave with arbitrary polarization is totally reflected, and an evanescent wave is formed in the medium with lower optical density. Based on the recent arguments in favor of the Minkowski definition of the electromagnetic momentum in a material medium (Philbin 2011 Phys. Rev. A 83 013823; Philbin and Allanson 2012 86 055802; Bliokh et al 2017 Phys. Rev. Lett. 119 073901), we derive the explicit expressions for the dynamical characteristics in both media, with special attention to their behavior at the interface. In particular, the ‘extraordinary’ spin and momentum components orthogonal to the plane of incidence are described, and a canonical (spin-orbital) momentum decomposition is performed that contains no singular terms. The field energy, helicity, the spin momentum and orbital momentum components are everywhere regular but experience discontinuities at the interface; the spin components parallel to the interface appear to be continuous, which testifies to the consistency of the adopted Minkowski picture. The results supply a meaningful example of the electromagnetic momentum decomposition, with separation of spatial and polarization degrees of freedom, in inhomogeneous media, and can be used in engineering the structured fields designed for optical sorting, dispatching and micromanipulation.

Orientation determination of interfacial beta-sheet structures in situ.

PubMed

Nguyen, Khoi Tan; King, John Thomas; Chen, Zhan

2010-07-01

Structural information such as orientations of interfacial proteins and peptides is important for understanding properties and functions of such biological molecules, which play crucial roles in biological applications and processes such as antimicrobial selectivity, membrane protein activity, biocompatibility, and biosensing performance. The alpha-helical and beta-sheet structures are the most widely encountered secondary structures in peptides and proteins. In this paper, for the first time, a method to quantify the orientation of the interfacial beta-sheet structure using a combined attenuated total reflectance Fourier transformation infrared spectroscopic (ATR-FTIR) and sum frequency generation (SFG) vibrational spectroscopic study was developed. As an illustration of the methodology, the orientation of tachyplesin I, a 17 amino acid peptide with an antiparallel beta-sheet, adsorbed to polymer surfaces as well as associated with a lipid bilayer was determined using the regular and chiral SFG spectra, together with polarized ATR-FTIR amide I signals. Both the tilt angle (theta) and the twist angle (psi) of the beta-sheet at interfaces are determined. The developed method in this paper can be used to obtain in situ structural information of beta-sheet components in complex molecules. The combination of this method and the existing methodology that is currently used to investigate alpha-helical structures will greatly broaden the application of optical spectroscopy in physical chemistry, biochemistry, biophysics, and structural biology.

Two-fluid and finite Larmor radius effects on helicity evolution in a plasma pinch

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sauppe, J. P., E-mail: jpsauppe@gmail.com; Department of Physics, University of Wisconsin-Madison, 1150 University Avenue, Madison, Wisconsin 53706; Sovinec, C. R., E-mail: csovinec@wisc.edu

2016-03-15

The evolution of magnetic energy, helicity, and hybrid helicity during nonlinear relaxation of a driven-damped plasma pinch is compared in visco-resistive magnetohydrodynamics and two-fluid models with and without the ion gyroviscous stress tensor. Magnetic energy and helicity are supplied via a boundary electric field which initially balances the resistive dissipation, and the plasma undergoes multiple relaxation events during the nonlinear evolution. The magnetic helicity is well conserved relative to the magnetic energy over each event, which is short compared with the global resistive diffusion time. The magnetic energy decreases by roughly 1.5% of its initial value over a relaxation event,more » while the magnetic helicity changes by at most 0.2% of the initial value. The hybrid helicity is dominated by magnetic helicity in low-β pinch conditions and is also well conserved. Differences of less than 1% between magnetic helicity and hybrid helicity are observed with two-fluid modeling and result from cross helicity evolution. The cross helicity is found to change appreciably due to the first-order finite Larmor radius effects which have not been included in contemporary relaxation theories. The plasma current evolves towards the flat parallel current state predicted by Taylor relaxation theory but does not achieve it. Plasma flow develops significant structure for two-fluid models, and the flow perpendicular to the magnetic field is much more substantial than the flow along it.« less

A combined study of photospheric magnetic and current helicities and subsurface kinetic helicities of solar active regions during 2006-2013

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seligman, D.; Petrie, G. J. D.; Komm, R.

2014-11-10

We compare the average photospheric current helicity H{sub c} , photospheric twist parameter α (a well-known proxy for the full relative magnetic helicity), and subsurface kinetic helicity H{sub k} for 194 active regions observed between 2006-2013. We use 2440 Hinode photospheric vector magnetograms, and the corresponding subsurface fluid velocity data derived from GONG (2006-2012) and Helioseismic and Magnetic Imager (2010-2013) dopplergrams. We find a significant hemispheric bias in all three parameters. The subsurface kinetic helicity is preferentially positive in the southern hemisphere and negative in the northern hemisphere. The photospheric current helicity and the α parameter have the same biasmore » for strong fields (|B| > 1000 G) and no significant bias for weak fields (100 G <|B| < 500 G). We find no significant region-by-region correlation between the subsurface kinetic helicity and either the strong-field current helicity or α. Subsurface fluid motions of a given handedness correspond to photospheric helicities of both signs in approximately equal numbers. However, common variations appear in annual averages of these quantities over all regions. Furthermore, in a subset of 77 regions, we find significant correlations between the temporal profiles of the subsurface and photospheric helicities. In these cases, the sign of the linear correlation coefficient matches the sign relationship between the helicities, indicating that the photospheric magnetic field twist is sensitive to the twisting motions below the surface.« less

Stimuli-Driven Control of the Helical Axis of Self-Organized Soft Helical Superstructures.

PubMed

Bisoyi, Hari Krishna; Bunning, Timothy J; Li, Quan

2018-06-01

Supramolecular and macromolecular functional helical superstructures are ubiquitous in nature and display an impressive catalog of intriguing and elegant properties and performances. In materials science, self-organized soft helical superstructures, i.e., cholesteric liquid crystals (CLCs), serve as model systems toward the understanding of morphology- and orientation-dependent properties of supramolecular dynamic helical architectures and their potential for technological applications. Moreover, most of the fascinating device applications of CLCs are primarily determined by different orientations of the helical axis. Here, the control of the helical axis orientation of CLCs and its dynamic switching in two and three dimensions using different external stimuli are summarized. Electric-field-, magnetic-field-, and light-irradiation-driven orientation control and reorientation of the helical axis of CLCs are described and highlighted. Different techniques and strategies developed to achieve a uniform lying helix structure are explored. Helical axis control in recently developed heliconical cholesteric systems is examined. The control of the helical axis orientation in spherical geometries such as microdroplets and microshells fabricated from these enticing photonic fluids is also explored. Future challenges and opportunities in this exciting area involving anisotropic chiral liquids are then discussed. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The global distribution of magnetic helicity in the solar corona

NASA Astrophysics Data System (ADS)

Yeates, A. R.; Hornig, G.

2016-10-01

By defining an appropriate field line helicity, we apply the powerful concept of magnetic helicity to the problem of global magnetic field evolution in the Sun's corona. As an ideal-magnetohydrodynamic invariant, the field line helicity is a meaningful measure of how magnetic helicity is distributed within the coronal volume. It may be interpreted, for each magnetic field line, as a magnetic flux linking with that field line. Using magneto-frictional simulations, we investigate how field line helicity evolves in the non-potential corona as a result of shearing by large-scale motions on the solar surface. On open magnetic field lines, the helicity injected by the Sun is largely output to the solar wind, provided that the coronal relaxation is sufficiently fast. But on closed magnetic field lines, helicity is able to build up. We find that the field line helicity is non-uniformly distributed, and is highly concentrated in twisted magnetic flux ropes. Eruption of these flux ropes is shown to lead to sudden bursts of helicity output, in contrast to the steady flux along the open magnetic field lines. Movies are available at http://www.aanda.org

Hidden topological constellations and polyvalent charges in chiral nematic droplets

NASA Astrophysics Data System (ADS)

Posnjak, Gregor; Čopar, Simon; Muševič, Igor

2017-02-01

Topology has an increasingly important role in the physics of condensed matter, quantum systems, material science, photonics and biology, with spectacular realizations of topological concepts in liquid crystals. Here we report on long-lived hidden topological states in thermally quenched, chiral nematic droplets, formed from string-like, triangular and polyhedral constellations of monovalent and polyvalent singular point defects. These topological defects are regularly packed into a spherical liquid volume and stabilized by the elastic energy barrier due to the helical structure and confinement of the liquid crystal in the micro-sphere. We observe, for the first time, topological three-dimensional point defects of the quantized hedgehog charge q=-2, -3. These higher-charge defects act as ideal polyvalent artificial atoms, binding the defects into polyhedral constellations representing topological molecules.

Hidden topological constellations and polyvalent charges in chiral nematic droplets

PubMed Central

Posnjak, Gregor; Čopar, Simon; Muševič, Igor

2017-01-01

Topology has an increasingly important role in the physics of condensed matter, quantum systems, material science, photonics and biology, with spectacular realizations of topological concepts in liquid crystals. Here we report on long-lived hidden topological states in thermally quenched, chiral nematic droplets, formed from string-like, triangular and polyhedral constellations of monovalent and polyvalent singular point defects. These topological defects are regularly packed into a spherical liquid volume and stabilized by the elastic energy barrier due to the helical structure and confinement of the liquid crystal in the micro-sphere. We observe, for the first time, topological three-dimensional point defects of the quantized hedgehog charge q=−2, −3. These higher-charge defects act as ideal polyvalent artificial atoms, binding the defects into polyhedral constellations representing topological molecules. PMID:28220770

Autonomously folded α-helical lockers promote RNAi*

NASA Astrophysics Data System (ADS)

Guyader, Christian P. E.; Lamarre, Baptiste; de Santis, Emiliana; Noble, James E.; Slater, Nigel K.; Ryadnov, Maxim G.

2016-10-01

RNAi is an indispensable research tool with a substantial therapeutic potential. However, the complete transition of the approach to an applied capability remains hampered due to poorly understood relationships between siRNA delivery and gene suppression. Here we propose that interfacial tertiary contacts between α-helices can regulate siRNA cytoplasmic delivery and RNAi. We introduce a rationale of helical amphipathic lockers that differentiates autonomously folded helices, which promote gene silencing, from helices folded with siRNA, which do not. Each of the helical designs can deliver siRNA into cells via energy-dependent endocytosis, while only autonomously folded helices with pre-locked hydrophobic interfaces were able to promote statistically appreciable gene silencing. We propose that it is the amphipathic locking of interfacing helices prior to binding to siRNA that enables RNAi. The rationale offers structurally balanced amphipathic scaffolds to advance the exploitation of functional RNAi.

Autonomously folded α-helical lockers promote RNAi*

PubMed Central

Guyader, Christian P. E.; Lamarre, Baptiste; De Santis, Emiliana; Noble, James E.; Slater, Nigel K.; Ryadnov, Maxim G.

2016-01-01

RNAi is an indispensable research tool with a substantial therapeutic potential. However, the complete transition of the approach to an applied capability remains hampered due to poorly understood relationships between siRNA delivery and gene suppression. Here we propose that interfacial tertiary contacts between α-helices can regulate siRNA cytoplasmic delivery and RNAi. We introduce a rationale of helical amphipathic lockers that differentiates autonomously folded helices, which promote gene silencing, from helices folded with siRNA, which do not. Each of the helical designs can deliver siRNA into cells via energy-dependent endocytosis, while only autonomously folded helices with pre-locked hydrophobic interfaces were able to promote statistically appreciable gene silencing. We propose that it is the amphipathic locking of interfacing helices prior to binding to siRNA that enables RNAi. The rationale offers structurally balanced amphipathic scaffolds to advance the exploitation of functional RNAi. PMID:27721465

Autonomously folded α-helical lockers promote RNAi.

PubMed

Guyader, Christian P E; Lamarre, Baptiste; De Santis, Emiliana; Noble, James E; Slater, Nigel K; Ryadnov, Maxim G

2016-10-10

RNAi is an indispensable research tool with a substantial therapeutic potential. However, the complete transition of the approach to an applied capability remains hampered due to poorly understood relationships between siRNA delivery and gene suppression. Here we propose that interfacial tertiary contacts between α-helices can regulate siRNA cytoplasmic delivery and RNAi. We introduce a rationale of helical amphipathic lockers that differentiates autonomously folded helices, which promote gene silencing, from helices folded with siRNA, which do not. Each of the helical designs can deliver siRNA into cells via energy-dependent endocytosis, while only autonomously folded helices with pre-locked hydrophobic interfaces were able to promote statistically appreciable gene silencing. We propose that it is the amphipathic locking of interfacing helices prior to binding to siRNA that enables RNAi. The rationale offers structurally balanced amphipathic scaffolds to advance the exploitation of functional RNAi.

Self-Assembly of Helical Ribbons

NASA Astrophysics Data System (ADS)

Zastavker, Yevgeniya V.; Asherie, Neer; Lomakin, Aleksey; Pande, Jayanti; Donovan, Joanne M.; Schnur, Joel M.; Benedek, George B.

1999-07-01

The self-assembly of helical ribbons is examined in a variety of multicomponent enantiomerically pure systems that contain a bile salt or a nonionic detergent, a phosphatidylcholine or a fatty acid, and a steroid analog of cholesterol. In almost all systems, two different pitch types of helical ribbons are observed: high pitch, with a pitch angle of 54± 2 degrees, and low pitch, with a pitch angle of 11± 2 degrees. Although the majority of these helices are right-handed, a small proportion of left-handed helices is observed. Additionally, a third type of helical ribbon, with a pitch angle in the range 30-47 degrees, is occasionally found. These experimental findings suggest that the helical ribbons are crystalline rather than liquid crystal in nature and also suggest that molecular chirality may not be the determining factor in helix formation. The large yields of helices produced will permit a systematic investigation of their individual kinetic evolution and their elastic moduli.

Cascades of energy and helicity in axisymmetric turbulence

NASA Astrophysics Data System (ADS)

Qu, Bo; Naso, Aurore; Bos, Wouter J. T.

2018-01-01

A spectral analysis of strictly axisymmetric turbulence is performed. Both freely decaying and statistically steady flows are considered. In helical flows we identify a dual cascade, where energy is transferred towards the large scales and helicity to the smallest ones. It is shown that even in the absence of net helicity, a dual cascade persists, transferring energy backward and positively and negatively polarized helicity fluctuations forward.

Measurements of Magnetic Helicity within Two Interacting Flux Ropes

NASA Astrophysics Data System (ADS)

Dehaas, Timothy; Gekelman, Walter

2016-10-01

Magnetic helicity (HM) has become a useful tool in the exploration of astrophysical plasmas. Its conservation in the MHD limit (and even some fluid approaches) constrains the global behavior of large plasma structures. One such astrophysical structure is a magnetic flux rope: a rope-like, current-carrying plasma embedded in an external magnetic field. Bundles of these ropes are commonly observed extending from the solar surface and can be found in the near-earth environment. In this well-diagnosed experiment (3D measurements of ne, Te, Vp, B, J, E, uflow) , two magnetic flux ropes were generated in the Large Plasma Device at UCLA. These ropes were driven kink-unstable, commencing complex motion. As they interact, helicity conservation is broken in regions of reconnection, turbulence, and instabilities. The changes in helicity can be visualized as 1) the transport of helicity (ϕB +E × A) and 2) the dissipation of the helicity (-2EB). Magnetic helicity is observed to have a negative sign and its counterpart, cross helicity, a positive one. These qualities oscillate 8% peak-to-peak. As the ropes move and the topology of the field lines change, a quasi-separatrix layer (QSL) is formed. The volume averaged HM and the largest value of Q both oscillate but not in phase. In addition to magnetic helicity, similar quantities such as self-helicity, mutual-helicity, vorticity, and canonical helicity are derived and will be presented. This work is supported by LANL-UC research Grant and done at the Basic Plasma Science Facility, which is funded by DOE and NSF.

Computational prediction of kink properties of helices in membrane proteins

NASA Astrophysics Data System (ADS)

Mai, T.-L.; Chen, C.-M.

2014-02-01

We have combined molecular dynamics simulations and fold identification procedures to investigate the structure of 696 kinked and 120 unkinked transmembrane (TM) helices in the PDBTM database. Our main aim of this study is to understand the formation of helical kinks by simulating their quasi-equilibrium heating processes, which might be relevant to the prediction of their structural features. The simulated structural features of these TM helices, including the position and the angle of helical kinks, were analyzed and compared with statistical data from PDBTM. From quasi-equilibrium heating processes of TM helices with four very different relaxation time constants, we found that these processes gave comparable predictions of the structural features of TM helices. Overall, 95 % of our best kink position predictions have an error of no more than two residues and 75 % of our best angle predictions have an error of less than 15°. Various structure assessments have been carried out to assess our predicted models of TM helices in PDBTM. Our results show that, in 696 predicted kinked helices, 70 % have a RMSD less than 2 Å, 71 % have a TM-score greater than 0.5, 69 % have a MaxSub score greater than 0.8, 60 % have a GDT-TS score greater than 85, and 58 % have a GDT-HA score greater than 70. For unkinked helices, our predicted models are also highly consistent with their crystal structure. These results provide strong supports for our assumption that kink formation of TM helices in quasi-equilibrium heating processes is relevant to predicting the structure of TM helices.

Numerical simulation of helical flow in a cylindrical channel

NASA Astrophysics Data System (ADS)

Vasiliev, A.; Sukhanovskii, A.; Stepanov, R.

2017-06-01

Numerical simulation of the helical flow in a cylindrical channel with diverter was carried out using open-source software OpenFOAM Extend 4.0. The velocity, vorticity and helicity density distributions were analyzed. It was shown that azimithal contribution of helicity is negative near the wall and positive in the center. In opposite axial helicity contribution is negative in the center and positive near the wall. Analysis of helicity of non-axisymmetric part of the flow showed that it has substantial values near the diverter but than rapidly decreases with y (axial coordinate) and further downstream it can be neglected. Dependencies of integrated values of azimuthal Hϕ and axial Hy contributions of helicity density on y show a remarkable quantitative similarity. It was found that integral values of Hϕ and Hy are negative for all y. Magnitudes of Hϕ and Hy decrease after the diverter up to y ≈ 70 mm and after that monotonically increase. The flow behind the diverter is characterized by substantial amount of helicity and can be used as a helicity generator.

Ruby-Helix: an implementation of helical image processing based on object-oriented scripting language.

PubMed

Metlagel, Zoltan; Kikkawa, Yayoi S; Kikkawa, Masahide

2007-01-01

Helical image analysis in combination with electron microscopy has been used to study three-dimensional structures of various biological filaments or tubes, such as microtubules, actin filaments, and bacterial flagella. A number of packages have been developed to carry out helical image analysis. Some biological specimens, however, have a symmetry break (seam) in their three-dimensional structure, even though their subunits are mostly arranged in a helical manner. We refer to these objects as "asymmetric helices". All the existing packages are designed for helically symmetric specimens, and do not allow analysis of asymmetric helical objects, such as microtubules with seams. Here, we describe Ruby-Helix, a new set of programs for the analysis of "helical" objects with or without a seam. Ruby-Helix is built on top of the Ruby programming language and is the first implementation of asymmetric helical reconstruction for practical image analysis. It also allows easier and semi-automated analysis, performing iterative unbending and accurate determination of the repeat length. As a result, Ruby-Helix enables us to analyze motor-microtubule complexes with higher throughput to higher resolution.

Inhomogeneous helicity effect in the solar angular-momentum transport

NASA Astrophysics Data System (ADS)

Yokoi, Nobumitsu

2017-04-01

Coupled with mean absolute vorticity Ω∗ (rotation and mean relative vorticity), inhomogeneous turbulent helicity is expected to contribute to the generation of global flow structure against the linear and angular momentum mixing due to turbulent or eddy viscosity. This inhomogeneous helicity effect was originally derived in Yokoi & Yoshizawa (1993) [1], and recently has been validated by direct numerical simulations (DNSs) of rotating helical turbulence [2]. Turbulence effect enters the mean-vorticity equation through the turbulent vortexmotive force ⟨u'×ω'⟩ [u': velocity fluctuation, ω'(= ∇× u'): vorticity fluctuation], which is the vorticity counterpart of the electromotive force ⟨u'× b'⟩ (b': magnetic fluctuation) in the mean magnetic-field induction. The mean velocity induction δU is proportional to the vortexmotive force. According to the theoretical result [1,2], it is expressed as δU = -νT∇×Ω∗-ηT(∇2H)Ω∗, where ηT is the transport coefficient, H = ⟨u'ṡω'⟩ the turbulent helicity, and Ω∗ the mean absolute vorticity. The first term corresponds to the enhanced diffusion due to turbulent viscosity νT. The second term expresses the large-scale flow generation due to inhomogeneous helicity. Since helicity is self-generated in rotating stratified turbulence [3], an inhomogeneous helicity distribution is expected to exist in the solar convection zone. A rising flow with expansion near the surface of the Sun generates a strongly negative helicity there [4]. This spatial distribution of helicity would lead to a positive Laplacian of turbulent helicity (∇2H > 0) in the subsurface layer of the Sun. In the combination with the large-scale vorticity associated with the meridional circulation, the inhomogeneous helicity effect works for accelerating the mean velocity in the azimuthal direction. The relevance of this inhomogeneous helicity effect in the solar convection zone is discussed further. References [1] Yokoi, N. and Yoshizawa, A., "Statistical analysis of the effects of helicity in inhomogeneous turbulence," Phys. Fluids A, 5, 464-477 (1993). [2] Yokoi, N. and Brandenburg, A., "Large-scale flow generation by inhomogeneous helicity," Phys. Rev. E, 93, 033125-1-14 (2016). [3] Marino, R., Mininni, P., Rosenberg, D., and Pouquet, A., "Emergence of helicity in rotating stratified turbulence," Phys. Rev. E, 87, 033016-1-9 (2013). [4] Duarte, L. D. V., Wicht, J., Browning, M. K., and Gastine, T., "Helicity inversion in spherical convection as a means for equatorward dynamo wave propagation," Mon. Not. Roy. Astron. Soc. 456, 1708-1722 (2016).

Enhanced heat transfer and frictional losses in heat exchanger tube with modified helical coiled inserts

NASA Astrophysics Data System (ADS)

Verma, Aditya; Kumar, Manoj; Patil, Anil Kumar

2018-04-01

The application of compact heat exchangers in any thermal system improves overall performance with a considerable reduction in size and weight. Inserts of different geometrical features have been used as turbulence promoting devices to increase the heat transfer rates. The present study deals with the experimental investigation of heat transfer and fluid flow characteristics of a tubular heat exchanger fitted with modified helical coiled inserts. Experiments have been carried out for a smooth tube without insert, tube fitted with helical coiled inserts, and modified helical coiled inserts. The helical coiled inserts are tested by varying the pitch ratio and wire diameter ratio from 0.5-1.5, and 0.063-0.125, respectively for the Reynolds number range of 1400 to 11,000. Experimental data have also been collected for the modified helical coiled inserts with gradually increasing pitch (GIP) and gradually decreasing pitch (GDP) configurations. The Nusselt number and friction factor values for helical coiled inserts are enhanced in the range of 1.42-2.62, 3.4-27.4, relative to smooth tube, respectively. The modified helical coiled insert showed enhancements in Nusselt number and friction factor values in the range of 1.49-3.14, 11.2-19.9, relative to smooth tube, respectively. The helical coiled and modified helical coiled inserts have thermo-hydraulic performance factor in the range of 0.59-1.29, 0.6-1.39, respectively. The empirical correlations of Nusselt number and friction factor for helical coiled inserts are proposed.

Faraday signature of magnetic helicity from reduced depolarization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brandenburg, Axel; Stepanov, Rodion

2014-05-10

Using one-dimensional models, we show that a helical magnetic field with an appropriate sign of helicity can compensate the Faraday depolarization resulting from the superposition of Faraday-rotated polarization planes from a spatially extended source. For radio emission from a helical magnetic field, the polarization as a function of the square of the wavelength becomes asymmetric with respect to zero. Mathematically speaking, the resulting emission occurs then either at observable or at unobservable (imaginary) wavelengths. We demonstrate that rotation measure (RM) synthesis allows for the reconstruction of the underlying Faraday dispersion function in the former case, but not in the latter.more » The presence of positive magnetic helicity can thus be detected by observing positive RM in highly polarized regions in the sky and negative RM in weakly polarized regions. Conversely, negative magnetic helicity can be detected by observing negative RM in highly polarized regions and positive RM in weakly polarized regions. The simultaneous presence of two magnetic constituents with opposite signs of helicity is shown to possess signatures that can be quantified through polarization peaks at specific wavelengths and the gradient of the phase of the Faraday dispersion function. Similar polarization peaks can tentatively also be identified for the bi-helical magnetic fields that are generated self-consistently by a dynamo from helically forced turbulence, even though the magnetic energy spectrum is then continuous. Finally, we discuss the possibility of detecting magnetic fields with helical and non-helical properties in external galaxies using the Square Kilometre Array.« less

Hydrodynamic studies of CNT nanofluids in helical coil heat exchanger

NASA Astrophysics Data System (ADS)

Babita; Sharma, S. K.; Mital Gupta, Shipra; Kumar, Arinjay

2017-12-01

Helical coils are extensively used in several industrial processes such as refrigeration systems, chemical reactors, recovery processes etc to accommodate a large heat transfer area within a smaller space. Nanofluids are getting great attention due to their enhanced heat transfer capability. In heat transfer equipments, pressure drop is one of the major factors of consideration for pumping power calculations. So, the present work is aimed to study hydrodynamics of CNT nanofluids in helical coils. In this study, pressure drop characteristics of CNT nanofluid flowing inside horizontal helical coils are investigated experimentally. The helical coil to tube diameter was varied from 11.71 to 27.34 keeping pitch of the helical coil constant. Double distilled water was used as basefluid. SDBS and GA surfactants were added to stablilize CNT nanofluids. The volumetric fraction of CNT nanofluid was varied from 0.003 vol% to 0.051 vol%. From the experimental data, it was analyzed that the friction factor in helical coils is greater than that of straight tubes. Concentration of CNT in nanofluids also has a significant influence on the pressure drop/friction factor of helical coils. At a constant concentration of CNT, decreasing helical coil to tube diameter from 27.24 to 11.71, fanning friction factor of helical coil; f c increases for a constant value of p/d t. This increase in the value of fanning friction factor can be attributed to the secondary flow of CNT nanofluid in helical coils.

Magnetic field generation by pointwise zero-helicity three-dimensional steady flow of an incompressible electrically conducting fluid

NASA Astrophysics Data System (ADS)

Rasskazov, Andrey; Chertovskih, Roman; Zheligovsky, Vladislav

2018-04-01

We introduce six families of three-dimensional space-periodic steady solenoidal flows, whose kinetic helicity density is zero at any point. Four families are analytically defined. Flows in four families have zero helicity spectrum. Sample flows from five families are used to demonstrate numerically that neither zero kinetic helicity density nor zero helicity spectrum prohibit generation of large-scale magnetic field by the two most prominent dynamo mechanisms: the magnetic α -effect and negative eddy diffusivity. Our computations also attest that such flows often generate small-scale field for sufficiently small magnetic molecular diffusivity. These findings indicate that kinetic helicity and helicity spectrum are not the quantities controlling the dynamo properties of a flow regardless of whether scale separation is present or not.

Structures of the transmembrane helices of the G-protein coupled receptor, rhodopsin.

PubMed

Katragadda, M; Chopra, A; Bennett, M; Alderfer, J L; Yeagle, P L; Albert, A D

2001-07-01

An hypothesis is tested that individual peptides corresponding to the transmembrane helices of the membrane protein, rhodopsin, would form helices in solution similar to those in the native protein. Peptides containing the sequences of helices 1, 4 and 5 of rhodopsin were synthesized. Two peptides, with overlapping sequences at their termini, were synthesized to cover each of the helices. The peptides from helix 1 and helix 4 were helical throughout most of their length. The N- and C-termini of all the peptides were disordered and proline caused opening of the helical structure in both helix 1 and helix 4. The peptides from helix 5 were helical in the middle segment of each peptide, with larger disordered regions in the N- and C-termini than for helices 1 and 4. These observations show that there is a strong helical propensity in the amino acid sequences corresponding to the transmembrane domain of this G-protein coupled receptor. In the case of the peptides from helix 4, it was possible to superimpose the structures of the overlapping sequences to produce a construct covering the whole of the sequence of helix 4 of rhodopsin. As similar superposition for the peptides from helix 1 also produced a construct, but somewhat less successfully because of the disordering in the region of sequence overlap. This latter problem was more severe for helix 5 and therefore a single peptide was synthesized for the entire sequence of this helix, and its structure determined. It proved to be helical throughout. Comparison of all these structures with the recent crystal structure of rhodopsin revealed that the peptide structures mimicked the structures seen in the whole protein. Thus similar studies of peptides may provide useful information on the secondary structure of other transmembrane proteins built around helical bundles.

PRODUCTIVITY OF SOLAR FLARES AND MAGNETIC HELICITY INJECTION IN ACTIVE REGIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, Sung-hong; Wang Haimin; Chae, Jongchul, E-mail: sp295@njit.ed

The main objective of this study is to better understand how magnetic helicity injection in an active region (AR) is related to the occurrence and intensity of solar flares. We therefore investigate the magnetic helicity injection rate and unsigned magnetic flux, as a reference. In total, 378 ARs are analyzed using SOHO/MDI magnetograms. The 24 hr averaged helicity injection rate and unsigned magnetic flux are compared with the flare index and the flare-productive probability in the next 24 hr following a measurement. In addition, we study the variation of helicity over a span of several days around the times ofmore » the 19 flares above M5.0 which occurred in selected strong flare-productive ARs. The major findings of this study are as follows: (1) for a sub-sample of 91 large ARs with unsigned magnetic fluxes in the range from (3-5) x 10{sup 22} Mx, there is a difference in the magnetic helicity injection rate between flaring ARs and non-flaring ARs by a factor of 2; (2) the GOES C-flare-productive probability as a function of helicity injection displays a sharp boundary between flare-productive ARs and flare-quiet ones; (3) the history of helicity injection before all the 19 major flares displayed a common characteristic: a significant helicity accumulation of (3-45) x 10{sup 42} Mx{sup 2} during a phase of monotonically increasing helicity over 0.5-2 days. Our results support the notion that helicity injection is important in flares, but it is not effective to use it alone for the purpose of flare forecast. It is necessary to find a way to better characterize the time history of helicity injection as well as its spatial distribution inside ARs.« less

Productivity of Solar Flares and Magnetic Helicity Injection in Active Regions

NASA Astrophysics Data System (ADS)

Park, Sung-hong; Chae, Jongchul; Wang, Haimin

2010-07-01

The main objective of this study is to better understand how magnetic helicity injection in an active region (AR) is related to the occurrence and intensity of solar flares. We therefore investigate the magnetic helicity injection rate and unsigned magnetic flux, as a reference. In total, 378 ARs are analyzed using SOHO/MDI magnetograms. The 24 hr averaged helicity injection rate and unsigned magnetic flux are compared with the flare index and the flare-productive probability in the next 24 hr following a measurement. In addition, we study the variation of helicity over a span of several days around the times of the 19 flares above M5.0 which occurred in selected strong flare-productive ARs. The major findings of this study are as follows: (1) for a sub-sample of 91 large ARs with unsigned magnetic fluxes in the range from (3-5) × 1022 Mx, there is a difference in the magnetic helicity injection rate between flaring ARs and non-flaring ARs by a factor of 2; (2) the GOES C-flare-productive probability as a function of helicity injection displays a sharp boundary between flare-productive ARs and flare-quiet ones; (3) the history of helicity injection before all the 19 major flares displayed a common characteristic: a significant helicity accumulation of (3-45) × 1042 Mx2 during a phase of monotonically increasing helicity over 0.5-2 days. Our results support the notion that helicity injection is important in flares, but it is not effective to use it alone for the purpose of flare forecast. It is necessary to find a way to better characterize the time history of helicity injection as well as its spatial distribution inside ARs.

A remarkable solvent effect on the nuclearity of neutral titanium(IV)-based helicate assemblies.

PubMed

Weekes, David Michael; Diebold, Carine; Mobian, Pierre; Huguenard, Clarisse; Allouche, Lionel; Henry, Marc

2014-04-22

The spontaneous self-assembly of a neutral circular trinuclear Ti(IV) -based helicate is described through the reaction of titanium(IV) isopropoxide with a rationally designed tetraphenolic ligand. The trimeric ring helicate was obtained after diffusion of n-pentane into a solution with dichloromethane. The circular helicate has been characterized by using single-crystal X-ray diffraction study, (13) C CP-MAS NMR and (1) H NMR DOSY solution spectroscopic, and positive electrospray ionization mass-spectrometric analysis. These analytical data were compared with those obtained from a previously reported double-stranded helicate that crystallizes in toluene. The trimeric ring was unstable in a pure solution with dichloromethane and transformed into the double-stranded helicate. Thermodynamic analysis by means of the PACHA software revealed that formation of the double-stranded helicates was characterized by ΔH(toluene)=-30 kJ mol(-1) and ΔS(toluene)=+357 J K(-1)  mol(-1) , whereas these values were ΔH(CH2 Cl2 )=-75 kJ mol(-1) and ΔS(CH2 Cl2 )=-37 J K(-1)  mol(-1) for the ring helicate. The transformation of the ring helicate into the double-stranded helicate was a strongly endothermic process characterized by ΔH(CH2 Cl2 )=+127 kJ mol(-1) and ΔH(n-pentane)=+644 kJ mol(-1) associated with a large positive entropy change ΔS=+1115 J K(-1) ⋅mol(-1) . Consequently, the instability of the ring helicate in pure dichloromethane was attributed to the rather high dielectric constant and dipole moment of dichloromethane relative to n-pentane. Suggestions for increasing the stability of the ring helicate are given. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

CURRENT AND KINETIC HELICITY OF LONG-LIVED ACTIVITY COMPLEXES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Komm, Rudolf; Gosain, Sanjay, E-mail: komm@nso.edu

2015-01-01

We study long-lived activity complexes and their current helicity at the solar surface and their kinetic helicity below the surface. The current helicity has been determined from synoptic vector magnetograms from the NSO/SOLIS facility, and the kinetic helicity of subsurface flows has been determined with ring-diagram analysis applied to full-disk Dopplergrams from NSO/GONG and SDO/HMI. Current and kinetic helicity of activity complexes follow the hemispheric helicity rule with mainly positive values (78%; 78%, respectively, with a 95% confidence level of 31%) in the southern hemisphere and negative ones (80%; 93%, respectively, with a 95% confidence level of 22% and 14%,more » respectively) in the northern hemisphere. The locations with the dominant sign of kinetic helicity derived from Global Oscillation Network Group (GONG) and SDO/HMI data are more organized than those of the secondary sign even if they are not part of an activity complex, while locations with the secondary sign are more fragmented. This is the case for both hemispheres even for the northern one where it is not as obvious visually due to the large amount of magnetic activity present as compared to the southern hemisphere. The current helicity shows a similar behavior. The dominant sign of current helicity is the same as that of kinetic helicity for the majority of the activity complexes (83% with a 95% confidence level of 15%). During the 24 Carrington rotations analyzed here, there is at least one longitude in each hemisphere where activity complexes occur repeatedly throughout the epoch. These ''active'' longitudes are identifiable as locations of strong current and kinetic helicity of the same sign.« less

On the resilience of helical magnetic fields to turbulent diffusion and the astrophysical implications

NASA Astrophysics Data System (ADS)

Blackman, Eric G.; Subramanian, Kandaswamy

2013-02-01

The extent to which large-scale magnetic fields are susceptible to turbulent diffusion is important for interpreting the need for in situ large-scale dynamos in astrophysics and for observationally inferring field strengths compared to kinetic energy. By solving coupled evolution equations for magnetic energy and magnetic helicity in a system initialized with isotropic turbulence and an arbitrarily helical large-scale field, we quantify the decay rate of the latter for a bounded or periodic system. The magnetic energy associated with the non-helical large-scale field decays at least as fast as the kinematically estimated turbulent diffusion rate, but the decay rate of the helical part depends on whether the ratio of its magnetic energy to the turbulent kinetic energy exceeds a critical value given by M1, c = (k1/k2)2, where k1 and k2 are the wavenumbers of the large and forcing scales. Turbulently diffusing helical fields to small scales while conserving magnetic helicity requires a rapid increase in total magnetic energy. As such, only when the helical field is subcritical can it so diffuse. When supercritical, it decays slowly, at a rate determined by microphysical dissipation even in the presence of macroscopic turbulence. In effect, turbulent diffusion of such a large-scale helical field produces small-scale helicity whose amplification abates further turbulent diffusion. Two curious implications are that (1) standard arguments supporting the need for in situ large-scale dynamos based on the otherwise rapid turbulent diffusion of large-scale fields require re-thinking since only the large-scale non-helical field is so diffused in a closed system. Boundary terms could however provide potential pathways for rapid change of the large-scale helical field. (2) Since M1, c ≪ 1 for k1 ≪ k2, the presence of long-lived ordered large-scale helical fields as in extragalactic jets do not guarantee that the magnetic field dominates the kinetic energy.

Tire

NASA Technical Reports Server (NTRS)

Benzing, II, James Alfred (Inventor); Kish, James Christopher (Inventor); Asnani, Vivake Manohar (Inventor)

2012-01-01

A tire includes a plurality of helical springs. Each helical spring includes a first end portion, a second end portion, and an arching middle portion. Each helical spring is interlaced with at least one other helical spring thereby forming a laced toroidal structure extending about an entire circumference of the tire.

Helical bottleneck effect in 3D homogeneous isotropic turbulence

NASA Astrophysics Data System (ADS)

Stepanov, Rodion; Golbraikh, Ephim; Frick, Peter; Shestakov, Alexander

2018-02-01

We present the results of modelling the development of homogeneous and isotropic turbulence with a large-scale source of energy and a source of helicity distributed over scales. We use the shell model for numerical simulation of the turbulence at high Reynolds number. The results show that the helicity injection leads to a significant change in the behavior of the energy and helicity spectra in scales larger and smaller than the energy injection scale. We suggest the phenomenology for direct turbulent cascades with the helicity effect, which reduces the efficiency of the spectral energy transfer. Therefore the energy is accumulated and redistributed so that non-linear interactions will be sufficient to provide a constant energy flux. It can be interpreted as the ‘helical bottleneck effect’ which, depending on the parameters of the injection helicity, reminds one of the well-known bottleneck effect at the end of inertial range. Simulations which included the infrared part of the spectrum show that the inverse cascade hardly develops under distributed helicity forcing.

Dynamics of zonal flows in helical systems.

PubMed

Sugama, H; Watanabe, T-H

2005-03-25

A theory for describing collisionless long-time behavior of zonal flows in helical systems is presented and its validity is verified by gyrokinetic-Vlasov simulation. It is shown that, under the influence of particles trapped in helical ripples, the response of zonal flows to a given source becomes weaker for lower radial wave numbers and deeper helical ripples while a high-level zonal-flow response, which is not affected by helical-ripple-trapped particles, can be maintained for a longer time by reducing their bounce-averaged radial drift velocity. This implies a possibility that helical configurations optimized for reducing neoclassical ripple transport can simultaneously enhance zonal flows which lower anomalous transport.

Accurate Cold-Test Model of Helical TWT Slow-Wave Circuits

NASA Technical Reports Server (NTRS)

Kory, Carol L.; Dayton, James A., Jr.

1997-01-01

Recently, a method has been established to accurately calculate cold-test data for helical slow-wave structures using the three-dimensional electromagnetic computer code, MAFIA. Cold-test parameters have been calculated for several helical traveling-wave tube (TWT) slow-wave circuits possessing various support rod configurations, and results are presented here showing excellent agreement with experiment. The helical models include tape thickness, dielectric support shapes and material properties consistent with the actual circuits. The cold-test data from this helical model can be used as input into large-signal helical TWT interaction codes making it possible, for the first time, to design a complete TWT via computer simulation.

ON THE INJECTION OF HELICITY BY THE SHEARING MOTION OF FLUXES IN RELATION TO FLARES AND CORONAL MASS EJECTIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vemareddy, P.; Ambastha, A.; Maurya, R. A.

An investigation of helicity injection by photospheric shear motions is carried out for two active regions (ARs), NOAA 11158 and 11166, using line-of-sight magnetic field observations obtained from the Helioseismic and Magnetic Imager on board the Solar Dynamics Observatory. We derived the horizontal velocities in the ARs from the differential affine velocity estimator (DAVE) technique. Persistent strong shear motions at maximum velocities in the range of 0.6-0.9 km s{sup -1} along the magnetic polarity inversion line and outward flows from the peripheral regions of the sunspots were observed in the two ARs. The helicities injected in NOAA 11158 and 11166more » during their six-day evolution period were estimated as 14.16 Multiplication-Sign 10{sup 42} Mx{sup 2} and 9.5 Multiplication-Sign 10{sup 42} Mx{sup 2}, respectively. The estimated injection rates decreased up to 13% by increasing the time interval between the magnetograms from 12 minutes to 36 minutes, and increased up to 9% by decreasing the DAVE window size from 21 Multiplication-Sign 18 to 9 Multiplication-Sign 6 pixel{sup 2}, resulting in 10% variation in the accumulated helicity. In both ARs, the flare-prone regions (R2) had inhomogeneous helicity flux distribution with mixed helicities of both signs and coronal mass ejection (CME) prone regions had almost homogeneous distribution of helicity flux dominated by a single sign. The temporal profiles of helicity injection showed impulsive variations during some flares/CMEs due to negative helicity injection into the dominant region of positive helicity flux. A quantitative analysis reveals a marginally significant association of helicity flux with CMEs but not flares in AR 11158, while for the AR 11166, we find a marginally significant association of helicity flux with flares but not CMEs, providing evidence of the role of helicity injection at localized sites of the events. These short-term variations of helicity flux are further discussed in view of possible flare-related effects. This study suggests that flux motions and spatial distribution of helicity injection are important to understanding the complex nature of the magnetic flux system of the AR, and how it can lead to conditions favorable for eruptive events.« less

Frequency-Domain Streak Camera and Tomography for Ultrafast Imaging of Evolving and Channeled Plasma Accelerator Structures

NASA Astrophysics Data System (ADS)

Li, Zhengyan; Zgadzaj, Rafal; Wang, Xiaoming; Reed, Stephen; Dong, Peng; Downer, Michael C.

2010-11-01

We demonstrate a prototype Frequency Domain Streak Camera (FDSC) that can capture the picosecond time evolution of the plasma accelerator structure in a single shot. In our prototype Frequency-Domain Streak Camera, a probe pulse propagates obliquely to a sub-picosecond pump pulse that creates an evolving nonlinear index "bubble" in fused silica glass, supplementing a conventional Frequency Domain Holographic (FDH) probe-reference pair that co-propagates with the "bubble". Frequency Domain Tomography (FDT) generalizes Frequency-Domain Streak Camera by probing the "bubble" from multiple angles and reconstructing its morphology and evolution using algorithms similar to those used in medical CAT scans. Multiplexing methods (Temporal Multiplexing and Angular Multiplexing) improve data storage and processing capability, demonstrating a compact Frequency Domain Tomography system with a single spectrometer.

76 FR 57075 - Helical Spring Lock Washers From China and Taiwan

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-15

... INTERNATIONAL TRADE COMMISSION [Investigation Nos. 731-TA-624-625; Third Review] Helical Spring... duty orders on helical spring lock washers from China and Taiwan. AGENCY: United States International...) to determine whether revocation of the antidumping duty orders on helical spring lock washers from...

Effects of Helicity on Lagrangian and Eulerian Time Correlations in Turbulence

NASA Technical Reports Server (NTRS)

Rubinstein, Robert; Zhou, Ye

1998-01-01

Taylor series expansions of turbulent time correlation functions are applied to show that helicity influences Eulerian time correlations more strongly than Lagrangian time correlations: to second order in time, the helicity effect on Lagrangian time correlations vanishes, but the helicity effect on Eulerian time correlations is nonzero. Fourier analysis shows that the helicity effect on Eulerian time correlations is confined to the largest inertial range scales. Some implications for sound radiation by swirling flows are discussed.

Processing and plating helical metallic coils

NASA Technical Reports Server (NTRS)

1972-01-01

The results of research efforts to develop an optimized nickel cobalt coating suitable as a recording medium are outlined. The coating is to be used directly on a BeCu helical coil substrate of a helical coil NASA recorder. Specifically, efforts were made to: optimize the coating thickness; establish processes and techniques adaptable for the production of finalized plated helical coils; design and fabricate the equipment required for production and testing of the coils; and deliver finalized helical coils to NASA.

Transferability of different classical force fields for right and left handed α-helices constructed from enantiomeric amino acids.

PubMed

Biswas, Santu; Sarkar, Sujit; Pandey, Prithvi Raj; Roy, Sudip

2016-02-21

Amino acids can form d and l enantiomers, of which the l enantiomer is abundant in nature. The naturally occurring l enantiomer has a greater preference for a right handed helical conformation, and the d enantiomer for a left handed helical conformation. The other conformations, that is, left handed helical conformations of the l enantiomers and right handed helical conformations of the d enantiomers, are not common. The energetic differences between left and right handed alpha helical peptide chains constructed from enantiomeric amino acids are investigated using quantum chemical calculations (using the M06/6-311g(d,p) level of theory). Further, the performances of commonly used biomolecular force fields (OPLS/AA, CHARMM27/CMAP and AMBER) to represent the different helical conformations (left and right handed) constructed from enantiomeric (D and L) amino acids are evaluated. 5- and 10-mer chains from d and l enantiomers of alanine, leucine, lysine, and glutamic acid, in right and left handed helical conformations, are considered in the study. Thus, in total, 32 α-helical polypeptides (4 amino acids × 4 conformations of 5-mer and 10-mer) are studied. Conclusions, with regards to the performance of the force fields, are derived keeping the quantum optimized geometry as the benchmark, and on the basis of phi and psi angle calculations, hydrogen bond analysis, and different long range helical order parameters.

Data on diverse roles of helix perturbations in membrane proteins.

PubMed

Shelar, Ashish; Bansal, Manju

2016-12-01

The various structural variations observed in TM helices of membrane proteins have been deconstructed into 9 distinct types of helix perturbations. These perturbations are defined by the deviation of TM helices from the predominantly observed linear α-helical conformation, to form 3 10 - and π-helices, as well as adopting curved and kinked geometries. The data presented here supplements the article 'Helix perturbations in Membrane Proteins Assist in Inter-helical Interactions and Optimal Helix Positioning in the Bilayer' (A. Shelar, M. Bansal, 2016) [1]. This data provides strong evidence for the role of various helix perturbations in influencing backbone torsion angles of helices, mediating inter-helical interactions, oligomer formation and accommodation of hydrophobic residues within the bilayer. The methodology used for creation of various datasets of membrane protein families (Sodium/Calcium exchanger and Heme Copper Oxidase) has also been mentioned.

Two-phase pressure drop in a helical coil flow boiling system

NASA Astrophysics Data System (ADS)

Hardik, B. K.; Prabhu, S. V.

2018-05-01

The objective of the present work is to study the two-phase pressure drop in helical coils. Literature on the two-phase pressure drop in a helical coil suggests the complexity in flow boiling inside a helical coil due to secondary flow. Most of correlations reported in the literature on the two-phase pressure drop in a helical coil are limited to a specific operating range. No general correlation is available for a helical coil which is applicable for all fluids. In the present study, an experimental databank collected containing a total of 832 data points includes the data from the present study and from the literature. The data includes diabatic pressure drop of two fluids namely water and R123. Data covers a range of parameters namely a mass flux of 120-2058 kg/m2 s, a heat flux of 18-2831 kW/m2, an exit quality of 0.03-1, a density ratio of 32-1404 and a coil to tube diameter ratio of 14-58. The databank is compared with eighteen empirical correlations which include well referred correlations of straight tubes and the available correlations of helical coils. The straight tube correlations are not working well for the present data set. The helical coil correlations work reasonably well for the present databank. A correlation is suggested to predict the two-phase pressure drop in helical coils. The present study suggests that the influence of a helical coil is completely included in the single phase pressure drop correlation for helical coils.

Conversion from mutual helicity to self-helicity observed with IRIS

NASA Astrophysics Data System (ADS)

Li, L. P.; Peter, H.; Chen, F.; Zhang, J.

2014-10-01

Context. In the upper atmosphere of the Sun observations show convincing evidence for crossing and twisted structures, which are interpreted as mutual helicity and self-helicity. Aims: We use observations with the new Interface Region Imaging Spectrograph (IRIS) to show the conversion of mutual helicity into self-helicity in coronal structures on the Sun. Methods: Using far UV spectra and slit-jaw images from IRIS and coronal images and magnetograms from SDO, we investigated the evolution of two crossing loops in an active region, in particular, the properties of the Si IV line profile in cool loops. Results: In the early stage two cool loops cross each other and accordingly have mutual helicity. The Doppler shifts in the loops indicate that they wind around each other. As a consequence, near the crossing point of the loops (interchange) reconnection sets in, which heats the plasma. This is consistent with the observed increase of the line width and of the appearance of the loops at higher temperatures. After this interaction, the two new loops run in parallel, and in one of them shows a clear spectral tilt of the Si IV line profile. This is indicative of a helical (twisting) motion, which is the same as to say that the loop has self-helicity. Conclusions: The high spatial and spectral resolution of IRIS allowed us to see the conversion of mutual helicity to self-helicity in the (interchange) reconnection of two loops. This is observational evidence for earlier theoretical speculations. Movie associated with Fig. 1 and Appendix A are available in electronic form at http://www.aanda.org

Heat Transfer Measurements of Internally Finned Rotating Heat Pipes.

DTIC Science & Technology

1983-12-01

42 C. RESULTS OF STRAIGHT 22 FIN CONDENSER o . o . 51 D. RESULTS OF HELICAL 14 AND 16 FIN CONDENSER o 51 E. RESULTS OF HELICAL 36 FIN...88 C.6 RESULTS OF STRAIGHT 22 FIN CONDENSER AT 2800 RPM . . . . . . . . . . . . . . . . . . . . 89 C.7 RESULTS OF HELICAL 16 FIN CONDENSER ...AT 700 RPM . 90 C.8 RESULTS OF HELICAL 16 PIN CONDENSER AT 1600 RPM . 91 C.9 RESULTS OF HELICAL 16 PIN CONDENSER AT 2800 RPM . 92 C. 10 RESULTS OF

Approaches to ab initio molecular replacement of α-helical transmembrane proteins.

PubMed

Thomas, Jens M H; Simkovic, Felix; Keegan, Ronan; Mayans, Olga; Zhang, Chengxin; Zhang, Yang; Rigden, Daniel J

2017-12-01

α-Helical transmembrane proteins are a ubiquitous and important class of proteins, but present difficulties for crystallographic structure solution. Here, the effectiveness of the AMPLE molecular replacement pipeline in solving α-helical transmembrane-protein structures is assessed using a small library of eight ideal helices, as well as search models derived from ab initio models generated both with and without evolutionary contact information. The ideal helices prove to be surprisingly effective at solving higher resolution structures, but ab initio-derived search models are able to solve structures that could not be solved with the ideal helices. The addition of evolutionary contact information results in a marked improvement in the modelling and makes additional solutions possible.

Real-space processing of helical filaments in SPARX

PubMed Central

Behrmann, Elmar; Tao, Guozhi; Stokes, David L.; Egelman, Edward H.; Raunser, Stefan; Penczek, Pawel A.

2012-01-01

We present a major revision of the iterative helical real-space refinement (IHRSR) procedure and its implementation in the SPARX single particle image processing environment. We built on over a decade of experience with IHRSR helical structure determination and we took advantage of the flexible SPARX infrastructure to arrive at an implementation that offers ease of use, flexibility in designing helical structure determination strategy, and high computational efficiency. We introduced the 3D projection matching code which now is able to work with non-cubic volumes, the geometry better suited for long helical filaments, we enhanced procedures for establishing helical symmetry parameters, and we parallelized the code using distributed memory paradigm. Additional feature includes a graphical user interface that facilitates entering and editing of parameters controlling the structure determination strategy of the program. In addition, we present a novel approach to detect and evaluate structural heterogeneity due to conformer mixtures that takes advantage of helical structure redundancy. PMID:22248449

On the Mysterious Propulsion of Synechococcus

PubMed Central

Ehlers, Kurt; Oster, George

2012-01-01

We propose a model for the self-propulsion of the marine bacterium Synechococcus utilizing a continuous looped helical track analogous to that found in Myxobacteria [1]. In our model cargo-carrying protein motors, driven by proton-motive force, move along a continuous looped helical track. The movement of the cargo creates surface distortions in the form of small amplitude traveling ridges along the S-layer above the helical track. The resulting fluid motion adjacent to the helical ribbon provides the propulsive thrust. A variation on the helical rotor model of [1] allows the motors to be anchored to the peptidoglycan layer, where they drive rotation of the track creating traveling helical waves along the S-layer. We derive expressions relating the swimming speed to the amplitude, wavelength, and velocity of the surface waves induced by the helical rotor, and show that they fall in reasonable ranges to explain the velocity and rotation rate of swimming Synechococcus. PMID:22567124

75 FR 9159 - Certain Helical Spring Lock Washers from the People's Republic of China: Extension of Time Limit...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-01

... DEPARTMENT OF COMMERCE International Trade Administration [A-570-822] Certain Helical Spring Lock... of the administrative review of the antidumping duty order on certain helical spring lock washers... September 30, 2008. See Certain Helical Spring Lock Washers from the People's Republic of China: Preliminary...

Godbillon Vey Helicity and Magnetic Helicity in Magnetohydrodynamics

NASA Astrophysics Data System (ADS)

Webb, G. M.; Hu, Q.; Anco, S.; Zank, G. P.

2017-12-01

The Godbillon-Vey invariant arises in homology theory, and algebraic topology, where conditions for a layered family of 2D surfaces forms a 3D manifold were elucidated. The magnetic Godbillon-Vey helicity invariant in magnetohydrodynamics (MHD) is a helicity invariant that occurs for flows, in which the magnetic helicity density hm= A\\cdotB=0 where A is the magnetic vector potential and B is the magnetic induction. Our purpose is to elucidate the evolution of the magnetic Godbillon-Vey field η =A×B/|A|2 and the Godbillon-Vey helicity hgv}= η \\cdot∇ × η in general MHD flows in which the magnetic helicity hm≠q 0. It is shown that hm acts as a source term in the Godbillon-Vey helicity transport equation, in which hm is coupled to hgv via the shear tensor of the background flow. The transport equation for hgv depends on the electric field potential ψ , which is related to the gauge for A, which takes its simplest form for the advected A gauge in which ψ =A\\cdot u where u is the fluid velocity.

The helical MreB cytoskeleton in Escherichia coli MC1000/pLE7 is an artifact of the N-Terminal yellow fluorescent protein tag.

PubMed

Swulius, Matthew T; Jensen, Grant J

2012-12-01

Based on fluorescence microscopy, the actin homolog MreB has been thought to form extended helices surrounding the cytoplasm of rod-shaped bacterial cells. The presence of these and other putative helices has come to dominate models of bacterial cell shape regulation, chromosome segregation, polarity, and motility. Here we use electron cryotomography to show that MreB does in fact form extended helices and filaments in Escherichia coli when yellow fluorescent protein (YFP) is fused to its N terminus but native (untagged) MreB expressed to the same levels does not. In contrast, mCherry fused to an internal loop (MreB-RFP(SW)) does not induce helices. The helices are therefore an artifact of the placement of the fluorescent protein tag. YFP-MreB helices were also clearly distinguishable from the punctate, "patchy" localization patterns of MreB-RFP(SW), even by standard light microscopy. The many interpretations in the literature of such punctate patterns as helices should therefore be reconsidered.

Helicity transformation under the collision and merging of two magnetic flux ropes

NASA Astrophysics Data System (ADS)

DeHaas, Timothy; Gekelman, Walter

2017-07-01

Magnetic helicity has become a useful tool in the analysis of astrophysical plasmas. Its conservation in the magnetohydrodynamic limit (and other fluid approaches) constrains the global behavior of large plasma structures. One such astrophysical structure is a magnetic flux rope: a tube-like, current-carrying plasma embedded in an external magnetic field. Bundles of these ropes are commonly observed in the near-earth environment and solar atmosphere. In this well-diagnosed experiment (three-dimensional measurements of ne, Te, Vp, B, J, E, and uflow), two magnetic flux ropes are generated in the Large Plasma Device at UCLA. These ropes are driven kink-unstable to trigger complex motion. As they interact, helicity conservation is examined in regions of reconnection. We examine (1) the transport of helicity and (2) the dissipation of the helicity. As the ropes move and the topology of the field lines diverge, a quasi-separatrix layer (QSL) is formed. As the QSL forms, magnetic helicity is dissipated within this region. At the same time, there is an influx of canonical helicity into the region such that the temporal derivative of magnetic helicity is zero.

Comparison of forcing functions in magnetohydrodynamics

NASA Astrophysics Data System (ADS)

McKay, Mairi E.; Linkmann, Moritz; Clark, Daniel; Chalupa, Adam A.; Berera, Arjun

2017-11-01

Results are presented of direct numerical simulations of incompressible, homogeneous magnetohydrodynamic turbulence without a mean magnetic field, subject to different mechanical forcing functions commonly used in the literature. Specifically, the forces are negative damping (which uses the large-scale velocity field as a forcing function), a nonhelical random force, and a nonhelical static sinusoidal force (analogous to helical ABC forcing). The time evolution of the three ideal invariants (energy, magnetic helicity, and cross helicity), the time-averaged energy spectra, the energy ratios, and the dissipation ratios are examined. All three forcing functions produce qualitatively similar steady states with regard to the time evolution of the energy and magnetic helicity. However, differences in the cross-helicity evolution are observed, particularly in the case of the static sinusoidal method of energy injection. Indeed, an ensemble of sinusoidally forced simulations with identical parameters shows significant variations in the cross helicity over long time periods, casting some doubt on the validity of the principle of ergodicity in systems in which the injection of helicity cannot be controlled. Cross helicity can unexpectedly enter the system through the forcing function and must be carefully monitored.

Helicity conservation by flow across scales in reconnecting vortex links and knots

PubMed Central

Scheeler, Martin W.; Kleckner, Dustin; Kindlmann, Gordon L.; Irvine, William T. M.

2014-01-01

The conjecture that helicity (or knottedness) is a fundamental conserved quantity has a rich history in fluid mechanics, but the nature of this conservation in the presence of dissipation has proven difficult to resolve. Making use of recent advances, we create vortex knots and links in viscous fluids and simulated superfluids and track their geometry through topology-changing reconnections. We find that the reassociation of vortex lines through a reconnection enables the transfer of helicity from links and knots to helical coils. This process is remarkably efficient, owing to the antiparallel orientation spontaneously adopted by the reconnecting vortices. Using a new method for quantifying the spatial helicity spectrum, we find that the reconnection process can be viewed as transferring helicity between scales, rather than dissipating it. We also infer the presence of geometric deformations that convert helical coils into even smaller scale twist, where it may ultimately be dissipated. Our results suggest that helicity conservation plays an important role in fluids and related fields, even in the presence of dissipation. PMID:25326419

Studying the Transfer of Magnetic Helicity in Solar Active Regions with the Connectivity-based Helicity Flux Density Method

NASA Astrophysics Data System (ADS)

Dalmasse, K.; Pariat, É.; Valori, G.; Jing, J.; Démoulin, P.

2018-01-01

In the solar corona, magnetic helicity slowly and continuously accumulates in response to plasma flows tangential to the photosphere and magnetic flux emergence through it. Analyzing this transfer of magnetic helicity is key for identifying its role in the dynamics of active regions (ARs). The connectivity-based helicity flux density method was recently developed for studying the 2D and 3D transfer of magnetic helicity in ARs. The method takes into account the 3D nature of magnetic helicity by explicitly using knowledge of the magnetic field connectivity, which allows it to faithfully track the photospheric flux of magnetic helicity. Because the magnetic field is not measured in the solar corona, modeled 3D solutions obtained from force-free magnetic field extrapolations must be used to derive the magnetic connectivity. Different extrapolation methods can lead to markedly different 3D magnetic field connectivities, thus questioning the reliability of the connectivity-based approach in observational applications. We address these concerns by applying this method to the isolated and internally complex AR 11158 with different magnetic field extrapolation models. We show that the connectivity-based calculations are robust to different extrapolation methods, in particular with regard to identifying regions of opposite magnetic helicity flux. We conclude that the connectivity-based approach can be reliably used in observational analyses and is a promising tool for studying the transfer of magnetic helicity in ARs and relating it to their flaring activity.

Optimization of view weighting in tilted-plane-based reconstruction algorithms to minimize helical artifacts in multi-slice helical CT

NASA Astrophysics Data System (ADS)

Tang, Xiangyang

2003-05-01

In multi-slice helical CT, the single-tilted-plane-based reconstruction algorithm has been proposed to combat helical and cone beam artifacts by tilting a reconstruction plane to fit a helical source trajectory optimally. Furthermore, to improve the noise characteristics or dose efficiency of the single-tilted-plane-based reconstruction algorithm, the multi-tilted-plane-based reconstruction algorithm has been proposed, in which the reconstruction plane deviates from the pose globally optimized due to an extra rotation along the 3rd axis. As a result, the capability of suppressing helical and cone beam artifacts in the multi-tilted-plane-based reconstruction algorithm is compromised. An optomized tilted-plane-based reconstruction algorithm is proposed in this paper, in which a matched view weighting strategy is proposed to optimize the capability of suppressing helical and cone beam artifacts and noise characteristics. A helical body phantom is employed to quantitatively evaluate the imaging performance of the matched view weighting approach by tabulating artifact index and noise characteristics, showing that the matched view weighting improves both the helical artifact suppression and noise characteristics or dose efficiency significantly in comparison to the case in which non-matched view weighting is applied. Finally, it is believed that the matched view weighting approach is of practical importance in the development of multi-slive helical CT, because it maintains the computational structure of fan beam filtered backprojection and demands no extra computational services.

On the inverse transfer of (non-)helical magnetic energy in a decaying magnetohydrodynamic turbulence

NASA Astrophysics Data System (ADS)

Park, Kiwan

2017-12-01

In our conventional understanding, large-scale magnetic fields are thought to originate from an inverse cascade in the presence of magnetic helicity, differential rotation or a magneto-rotational instability. However, as recent simulations have given strong indications that an inverse cascade (transfer) may occur even in the absence of magnetic helicity, the physical origin of this inverse cascade is still not fully understood. We here present two simulations of freely decaying helical and non-helical magnetohydrodynamic (MHD) turbulence. We verified the inverse transfer of helical and non-helical magnetic fields in both cases, but we found the underlying physical principles to be fundamentally different. In the former case, the helical magnetic component leads to an inverse cascade of magnetic energy. We derived a semi-analytic formula for the evolution of large-scale magnetic field using α coefficient and compared it with the simulation data. But in the latter case, the α effect, including other conventional dynamo theories, is not suitable to describe the inverse transfer of non-helical magnetic energy. To obtain a better understanding of the physics at work here, we introduced a 'field structure model' based on the magnetic induction equation in the presence of inhomogeneities. This model illustrates how the curl of the electromotive force leads to the build up of a large-scale magnetic field without the requirement of magnetic helicity. And we applied a quasi-normal approximation to the inverse transfer of magnetic energy.

Segregation of helicity in inertial wave packets

NASA Astrophysics Data System (ADS)

Ranjan, A.

2017-03-01

Inertial waves are known to exist in the Earth's rapidly rotating outer core and could be important for the dynamo generation. It is well known that a monochromatic inertial plane wave traveling parallel to the rotation axis (along positive z ) has negative helicity while the wave traveling antiparallel (negative z ) has positive helicity. Such a helicity segregation, north and south of the equator, is necessary for the α2-dynamo model based on inertial waves [Davidson, Geophys. J. Int. 198, 1832 (2014), 10.1093/gji/ggu220] to work. The core is likely to contain a myriad of inertial waves of different wave numbers and frequencies. In this study, we investigate whether this characteristic of helicity segregation also holds for an inertial wave packet comprising waves with the same sign of Cg ,z, the z component of group velocity. We first derive the polarization relations for inertial waves and subsequently derive the resultant helicity in wave packets forming as a result of superposition of two or more waves. We find that the helicity segregation does hold for an inertial wave packet unless the wave numbers of the constituent waves are widely separated. In the latter case, regions of opposite color helicity do appear, but the mean helicity retains the expected sign. An illustration of this observation is provided by (a) calculating the resultant helicity for a wave packet formed by superposition of four upward-propagating inertial waves with different wave vectors and (b) conducting the direct numerical simulation of a Gaussian eddy under rapid rotation. Last, the possible effects of other forces such as the viscous dissipation, the Lorentz force, buoyancy stratification, and nonlinearity on helicity are investigated and discussed. The helical structure of the wave packet is likely to remain unaffected by dissipation or the magnetic field, but can be modified by the presence of linearly stable stratification and nonlinearity.

Crystal structure of tandem type III fibronectin domains from Drosophila neuroglian at 2.0 A.

PubMed

Huber, A H; Wang, Y M; Bieber, A J; Bjorkman, P J

1994-04-01

We report the crystal structure of two adjacent fibronectin type III repeats from the Drosophila neural cell adhesion molecule neuroglian. Each domain consists of two antiparallel beta sheets and is folded topologically identically to single fibronectin type III domains from the extracellular matrix proteins tenascin and fibronectin. beta bulges and left-handed polyproline II helices disrupt the regular beta sheet structure of both neuroglian domains. The hydrophobic interdomain interface includes a metal-binding site, presumably involved in stabilizing the relative orientation between domains and predicted by sequence comparision to be present in the vertebrate homolog molecule L1. The neuroglian domains are related by a near perfect 2-fold screw axis along the longest molecular dimension. Using this relationship, a model for arrays of tandem fibronectin type III repeats in neuroglian and other molecules is proposed.

SSEP: secondary structural elements of proteins

PubMed Central

Shanthi, V.; Selvarani, P.; Kiran Kumar, Ch.; Mohire, C. S.; Sekar, K.

2003-01-01

SSEP is a comprehensive resource for accessing information related to the secondary structural elements present in the 25 and 90% non-redundant protein chains. The database contains 1771 protein chains from 1670 protein structures and 6182 protein chains from 5425 protein structures in 25 and 90% non-redundant protein chains, respectively. The current version provides information about the α-helical segments and β-strand fragments of varying lengths. In addition, it also contains the information about 310-helix, β- and ν-turns and hairpin loops. The free graphics program RASMOL has been interfaced with the search engine to visualize the three-dimensional structures of the user queried secondary structural fragment. The database is updated regularly and is available through Bioinformatics web server at http://cluster.physics.iisc.ernet.in/ssep/ or http://144.16.71.148/ssep/. PMID:12824336

Secondary Structural Changes of Intact and Disulfide Bridges-Cleaved Human Serum Albumins in Thermal Denaturation up to 130°C - Additive Effects of Sodium Dodecyl Sulfate on the Changes.

PubMed

Moriyama, Yoshiko; Takeda, Kunio

2017-05-01

The secondary structural changes of human serum albumin with the intact 17 disulfide bridges (HSA) and the disulfide bridges-cleaved human serum albumin (RCM-HSA) in thermal denaturation were examined. Most of the helical structures of HSA, whose original helicity was 66%, were sharply disrupted between 50 and 100°C. However, 14% helicity remained even at 130°C. The temperature dependence of the degree of disrupted helical structures of HSA was discussed in connection with questions about a general protein denaturation model. When HSA lost the disulfide bridges, about two-thirds of the original helices were disrupted. Although the helices of RCM-HSA remaining after the cleavage of the disulfide bridges were relatively resistant against the heat treatment, the helicity changed from 22% at 25°C to 14% at 130℃. The helicity of RCM-HSA at 130°C agreed with the helicity of HSA at the same temperature, indicating that the same helical moieties of the polypeptides remained unaffected at this high temperature. The additive effects of sodium dodecyl sulfate (SDS) on the structural changes of HSA and RCM-HSA in thermal denaturation were also examined. A slight amount of SDS protected the helical structures of HSA from thermal denaturation below 80°C. Upon cooling to 25°C after heat treatment at temperatures below 70°C with the coexistence of SDS of low concentrations, the helical structures of HSA were reformed to the original level at 25°C before heating. A similar tendency was also observed after heat treatment at 80°C. In contrast, the helical structures of the RCM-HSA complexes with SDS are completely recovered upon cooling to 25°C even after heat treatment up to 100°C. Similar investigations were also carried out on bovine serum albumins which had the intact 17 disulfide bridges and lost all of the bridges.

EVOLUTION OF SPINNING AND BRAIDING HELICITY FLUXES IN SOLAR ACTIVE REGION NOAA 10930

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ravindra, B.; Yoshimura, Keiji; Dasso, Sergio, E-mail: ravindra@iiap.res.in, E-mail: yosimura@solar.physics.montana.edu, E-mail: dasso@df.uba.ar

2011-12-10

The line-of-sight magnetograms from Solar Optical Telescope Narrowband Filter Imager observations of NOAA Active Region 10930 have been used to study the evolution of spinning and braiding helicities over a period of five days starting from 2006 December 9. The north (N) polarity sunspot was the follower and the south (S) polarity sunspot was the leader. The N-polarity sunspot in the active region was rotating in the counterclockwise direction. The rate of rotation was small during the first two days of observations and it increased up to 8 Degree-Sign hr{sup -1} on the third day of the observations. On themore » fourth and fifth days it remained at 4 Degree-Sign hr{sup -1} with small undulations in its magnitude. The sunspot rotated about 260 Degree-Sign in the last three days. The S-polarity sunspot did not complete more than 20 Degree-Sign in five days. However, it changed its direction of rotation five times over a period of five days and injected both the positive and negative type of spin helicity fluxes into the corona. Through the five days, both the positive and negative sunspot regions injected equal amounts of spin helicity. The total injected helicity is predominantly negative in sign. However, the sign of the spin and braiding helicity fluxes computed over all the regions were reversed from negative to positive five times during the five-day period of observations. The reversal in spinning helicity flux was found before the onset of the X3.4-class flare, too. Though, the rotating sunspot has been observed in this active region, the braiding helicity has contributed more to the total accumulated helicity than the spinning helicity. The accumulated helicity is in excess of -7 Multiplication-Sign 10{sup 43} Mx{sup 2} over a period of five days. Before the X3.4-class flare that occurred on 2006 December 13, the rotation speed and spin helicity flux increased in the S-polarity sunspot. Before the flare, the total injected helicity was larger than -6 Multiplication-Sign 10{sup 43} Mx{sup 2}. The observed reversal in the sign of spinning and braiding helicity fluxes could be the signature of the emergence of a twisted flux tube, which acquires the writhe of an opposite sign. The magnetic cloud associated with the ejected mass has carried about -7 Multiplication-Sign 10{sup 41} Mx{sup 2} of helicity. A time integration of helicity flux of about 1.2 hr integrated backward in time of the observation of the coronal mass ejection is sufficient for this event.« less

Binary black hole spacetimes with a helical Killing vector

DOE Office of Scientific and Technical Information (OSTI.GOV)

Klein, Christian

Binary black hole spacetimes with a helical Killing vector, which are discussed as an approximation for the early stage of a binary system, are studied in a projection formalism. In this setting the four-dimensional Einstein equations are equivalent to a three-dimensional gravitational theory with a SL(2,R)/SO(1,1) sigma model as the material source. The sigma model is determined by a complex Ernst equation. 2+1 decompositions of the three-metric are used to establish the field equations on the orbit space of the Killing vector. The two Killing horizons of spherical topology which characterize the black holes, the cylinder of light where themore » Killing vector changes from timelike to spacelike, and infinity are singular points of the equations. The horizon and the light cylinder are shown to be regular singularities, i.e., the metric functions can be expanded in a formal power series in the vicinity. The behavior of the metric at spatial infinity is studied in terms of formal series solutions to the linearized Einstein equations. It is shown that the spacetime is not asymptotically flat in the strong sense to have a smooth null infinity under the assumption that the metric tends asymptotically to the Minkowski metric. In this case the metric functions have an oscillatory behavior in the radial coordinate in a nonaxisymmetric setting, the asymptotic multipoles are not defined. The asymptotic behavior of the Weyl tensor near infinity shows that there is no smooth null infinity.« less

Optimizing Immobilized Enzyme Performance in Cell-Free Environments to Produce Liquid Fuels

DOE Office of Scientific and Technical Information (OSTI.GOV)

Belfort, Georges; Grimaldi, Joseph J.

2015-01-27

Limitations on biofuel production using cell culture (Escherichia coli, Clostridium, Saccharomyces cerevisiae, brown microalgae, blue-green algae and others) include low product (alcohol) concentrations (≤0.2 vol%) due to feedback inhibition, instability of cells, and lack of economical product recovery processes. To overcome these challenges, an alternate simplified biofuel production scheme was tested based on a cell-free immobilized enzyme system. Using this cell free system, we were able to obtain about 2.6 times higher concentrations of iso-butanol using our non-optimized system as compared with live cell systems. This process involved two steps: (i) converts acid to aldehyde using keto-acid decarboxylase (KdcA), andmore » (ii) produces alcohol from aldehyde using alcohol dehydrogenase (ADH) with a cofactor (NADH) conversion from inexpensive formate using a third enzyme, formate dehydrogenase (FDH). To increase stability and conversion efficiency with easy separations, the first two enzymes were immobilized onto methacrylate resin. Fusion proteins of labile KdcA (fKdcA) were expressed to stabilize the covalently immobilized KdcA. Covalently immobilized ADH exhibited long-term stability and efficient conversion of aldehyde to alcohol over multiple batch cycles without fusions. High conversion rates and low protein leaching were achieved by covalent immobilization of enzymes on methacrylate resin. The complete reaction scheme was demonstrated by immobilizing both ADH and fKdcA and using FDH free in solution. The new system without in situ removal of isobutanol achieved a 55% conversion of ketoisovaleric acid to isobutanol at a concentration of 0.5 % (v/v). Further increases in titer will require continuous removal of the isobutanol using our novel brush membrane system that exhibits a 1.5 fold increase in the separation factor of isobutanol from water versus that obtained for commercial silicone rubber membranes. These bio-inspired brush membranes are based on the presence of glycocalyx filaments coating the luminal surface of our vasculature and represent a new class of synthetic membranes. They thus meet the requirements/scope of the Bimolecular Materials program, Materials Science and Engineering Div., Office of Science, US DOE.« less

Chiral self-assembly of helical particles.

PubMed

Kolli, Hima Bindu; Cinacchi, Giorgio; Ferrarini, Alberta; Giacometti, Achille

2016-01-01

The shape of the building blocks plays a crucial role in directing self-assembly towards desired architectures. Out of the many different shapes, the helix has a unique position. Helical structures are ubiquitous in nature and a helical shape is exhibited by the most important biopolymers like polynucleotides, polypeptides and polysaccharides as well as by cellular organelles like flagella. Helical particles can self-assemble into chiral superstructures, which may have a variety of applications, e.g. as photonic (meta)materials. However, a clear and definite understanding of these structures has not been entirely achieved yet. We have recently undertaken an extensive investigation on the phase behaviour of hard helical particles, using numerical simulations and classical density functional theory. Here we present a detailed study of the phase diagram of hard helices as a function of their morphology. This includes a variety of liquid-crystal phases, with different degrees of orientational and positional ordering. We show how, by tuning the helix parameters, it is possible to control the organization of the system. Starting from slender helices, whose phase behaviour is similar to that of rodlike particles, an increase in curliness leads to the onset of azimuthal correlations between the particles and the formation of phases specific to helices. These phases feature a new kind of screw order, of which there is experimental evidence in colloidal suspensions of helical flagella.

Finite element analysis of helical flows in human aortic arch: A novel index

PubMed Central

Lee, Cheng-Hung; Liu, Kuo-Sheng; Jhong, Guan-Heng; Liu, Shih-Jung; Hsu, Ming-Yi; Wang, Chao-Jan; Hung, Kuo-Chun

2014-01-01

This study investigates the helical secondary flows in the aortic arch using finite element analysis. The relationship between helical flow and the configuration of the aorta in patients of whose three-dimensional images constructed from computed tomography scans was examined. A finite element model of the pressurized root, arch, and supra-aortic vessels was developed to simulate the pattern of helical secondary flows. Calculations indicate that most of the helical secondary flow was formed in the ascending aorta. Angle α between the zero reference point and the aortic ostium (correlation coefficient (r) = −0.851, P = 0.001), the dispersion index of the cross section of the ascending (r = 0.683, P = 0.021) and descending aorta (r = 0.732, P = 0.010), all correlated closely with the presence of helical flow (P < 0.05). Stepwise multiple linear regression analysis confirmed angel α to be independently associated with the helical flow pattern in therein (standardized coefficients = −0.721, P = 0.023). The presence of helical fluid motion based on the atherosclerotic risks of patients, including those associated with diabetes, hypertension, hyperlipidemia, or renal insufficiency, was also evaluated. Numerical simulation of the flow patterns in aortas incorporating the atherosclerotic risks may better explain the mechanism of formation of helical flows and provide insight into causative factors that underlie them. PMID:24803960

Maintenance of electrostatic stabilization in altered tubulin lateral contacts may facilitate formation of helical filaments in foraminifera.

PubMed

Bassen, David M; Hou, Yubo; Bowser, Samuel S; Banavali, Nilesh K

2016-08-19

Microtubules in foraminiferan protists (forams) can convert into helical filament structures, in which longitudinal intraprotofilament interactions between tubulin heterodimers are thought to be lost, while lateral contacts across protofilaments are still maintained. The coarse geometric features of helical filaments are known through low-resolution negative stain electron microscopy (EM). In this study, geometric restraints derived from these experimental data were used to generate an average atomic-scale helical filament model, which anticipated a modest reorientation in the lateral tubulin heterodimer interface. Restrained molecular dynamics (MD) simulations of the nearest neighbor interactions combined with a Genalized Born implicit solvent model were used to assess the lateral, longitudinal, and seam contacts in 13-3 microtubules and the reoriented lateral contacts in the helical filament model. This electrostatic analysis suggests that the change in the lateral interface in the helical filament does not greatly diminish the lateral electrostatic interaction. After longitudinal dissociation, the 13-3 seam interaction is much weaker than the reoriented lateral interface in the helical filament model, providing a plausible atomic-detail explanation for seam-to-lateral contact transition that enables the transition to a helical filament structure.

Maintenance of electrostatic stabilization in altered tubulin lateral contacts may facilitate formation of helical filaments in foraminifera

NASA Astrophysics Data System (ADS)

Bassen, David M.; Hou, Yubo; Bowser, Samuel S.; Banavali, Nilesh K.

2016-08-01

Microtubules in foraminiferan protists (forams) can convert into helical filament structures, in which longitudinal intraprotofilament interactions between tubulin heterodimers are thought to be lost, while lateral contacts across protofilaments are still maintained. The coarse geometric features of helical filaments are known through low-resolution negative stain electron microscopy (EM). In this study, geometric restraints derived from these experimental data were used to generate an average atomic-scale helical filament model, which anticipated a modest reorientation in the lateral tubulin heterodimer interface. Restrained molecular dynamics (MD) simulations of the nearest neighbor interactions combined with a Genalized Born implicit solvent model were used to assess the lateral, longitudinal, and seam contacts in 13-3 microtubules and the reoriented lateral contacts in the helical filament model. This electrostatic analysis suggests that the change in the lateral interface in the helical filament does not greatly diminish the lateral electrostatic interaction. After longitudinal dissociation, the 13-3 seam interaction is much weaker than the reoriented lateral interface in the helical filament model, providing a plausible atomic-detail explanation for seam-to-lateral contact transition that enables the transition to a helical filament structure.

Magnetic Helicities and Dynamo Action in Magneto-rotational Turbulence

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bodo, G.; Rossi, P.; Cattaneo, F.

We examine the relationship between magnetic flux generation, taken as an indicator of large-scale dynamo action, and magnetic helicity, computed as an integral over the dynamo volume, in a simple dynamo. We consider dynamo action driven by magneto-rotational turbulence (MRT) within the shearing-box approximation. We consider magnetically open boundary conditions that allow a flux of helicity in or out of the computational domain. We circumvent the problem of the lack of gauge invariance in open domains by choosing a particular gauge—the winding gauge—that provides a natural interpretation in terms of the average winding number of pairwise field lines. We usemore » this gauge precisely to define and measure the helicity and the helicity flux for several realizations of dynamo action. We find in these cases that the system as a whole does not break reflectional symmetry and that the total helicity remains small even in cases when substantial magnetic flux is generated. We find no particular connection between the generation of magnetic flux and the helicity or the helicity flux through the boundaries. We suggest that this result may be due to the essentially nonlinear nature of the dynamo processes in MRT.« less

Theoretical model of chirality-induced helical self-propulsion

NASA Astrophysics Data System (ADS)

Yamamoto, Takaki; Sano, Masaki

2018-01-01

We recently reported the experimental realization of a chiral artificial microswimmer exhibiting helical self-propulsion [T. Yamamoto and M. Sano, Soft Matter 13, 3328 (2017), 10.1039/C7SM00337D]. In the experiment, cholesteric liquid crystal (CLC) droplets dispersed in surfactant solutions swam spontaneously, driven by the Marangoni flow, in helical paths whose handedness is determined by the chirality of the component molecules of CLC. To study the mechanism of the emergence of the helical self-propelled motion, we propose a phenomenological model of the self-propelled helical motion of the CLC droplets. Our model is constructed by symmetry argument in chiral systems, and it describes the dynamics of CLC droplets with coupled time-evolution equations in terms of a velocity, an angular velocity, and a tensor variable representing the symmetry of the helical director field of the droplet. We found that helical motions as well as other chiral motions appear in our model. By investigating bifurcation behaviors between each chiral motion, we found that the chiral coupling terms between the velocity and the angular velocity, the structural anisotropy of the CLC droplet, and the nonlinearity of model equations play a crucial role in the emergence of the helical motion of the CLC droplet.

Helicity within the vortex filament model.

PubMed

Hänninen, R; Hietala, N; Salman, H

2016-11-24

Kinetic helicity is one of the invariants of the Euler equations that is associated with the topology of vortex lines within the fluid. In superfluids, the vorticity is concentrated along vortex filaments. In this setting, helicity would be expected to acquire its simplest form. However, the lack of a core structure for vortex filaments appears to result in a helicity that does not retain its key attribute as a quadratic invariant. By defining a spanwise vector to the vortex through the use of a Seifert framing, we are able to introduce twist and henceforth recover the key properties of helicity. We present several examples for calculating internal twist to illustrate why the centreline helicity alone will lead to ambiguous results if a twist contribution is not introduced. Our choice of the spanwise vector can be expressed in terms of the tangential component of velocity along the filament. Since the tangential velocity does not alter the configuration of the vortex at later times, we are able to recover a similar equation for the internal twist angle to that of classical vortex tubes. Our results allow us to explain how a quasi-classical limit of helicity emerges from helicity considerations for individual superfluid vortex filaments.

Helicity within the vortex filament model

PubMed Central

Hänninen, R.; Hietala, N.; Salman, H.

2016-01-01

Kinetic helicity is one of the invariants of the Euler equations that is associated with the topology of vortex lines within the fluid. In superfluids, the vorticity is concentrated along vortex filaments. In this setting, helicity would be expected to acquire its simplest form. However, the lack of a core structure for vortex filaments appears to result in a helicity that does not retain its key attribute as a quadratic invariant. By defining a spanwise vector to the vortex through the use of a Seifert framing, we are able to introduce twist and henceforth recover the key properties of helicity. We present several examples for calculating internal twist to illustrate why the centreline helicity alone will lead to ambiguous results if a twist contribution is not introduced. Our choice of the spanwise vector can be expressed in terms of the tangential component of velocity along the filament. Since the tangential velocity does not alter the configuration of the vortex at later times, we are able to recover a similar equation for the internal twist angle to that of classical vortex tubes. Our results allow us to explain how a quasi-classical limit of helicity emerges from helicity considerations for individual superfluid vortex filaments. PMID:27883029

On the Helicity of Open Magnetic Fields

NASA Astrophysics Data System (ADS)

Prior, C.; Yeates, A. R.

2014-06-01

We reconsider the topological interpretation of magnetic helicity for magnetic fields in open domains, and relate this to the relative helicity. Specifically, our domains stretch between two parallel planes, and each of these ends may be magnetically open. It is demonstrated that, while the magnetic helicity is gauge-dependent, its value in any gauge may be physically interpreted as the average winding number among all pairs of field lines with respect to some orthonormal frame field. In fact, the choice of gauge is equivalent to the choice of reference field in the relative helicity, meaning that the magnetic helicity is no less physically meaningful. We prove that a particular gauge always measures the winding with respect to a fixed frame, and propose that this is normally the best choice. For periodic fields, this choice is equivalent to measuring relative helicity with respect to a potential reference field. However, for aperiodic fields, we show that the potential field can be twisted. We prove by construction that there always exists a possible untwisted reference field.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Hongqi; Brandenburg, Axel; Sokoloff, D. D., E-mail: hzhang@bao.ac.cn

We adopt an isotropic representation of the Fourier-transformed two-point correlation tensor of the magnetic field to estimate the magnetic energy and helicity spectra as well as current helicity spectra of two individual active regions (NOAA 11158 and NOAA 11515) and the change of the spectral indices during their development as well as during the solar cycle. The departure of the spectral indices of magnetic energy and current helicity from 5/3 are analyzed, and it is found that it is lower than the spectral index of the magnetic energy spectrum. Furthermore, the fractional magnetic helicity tends to increase when the scale of themore » energy-carrying magnetic structures increases. The magnetic helicity of NOAA 11515 violates the expected hemispheric sign rule, which is interpreted as an effect of enhanced field strengths at scales larger than 30–60 Mm with opposite signs of helicity. This is consistent with the general cycle dependence, which shows that around the solar maximum the magnetic energy and helicity spectra are steeper, emphasizing the large-scale field.« less

Time-dependent behavior in a transport-barrier model for the quasi-single helcity state

NASA Astrophysics Data System (ADS)

Terry, P. W.; Whelan, G. G.

2014-09-01

Time-dependent behavior that follows from a recent theory of the quasi-single-helicity (QSH) state of the reversed field pinch is considered. The theory (Kim and Terry 2012 Phys. Plasmas 19 122304) treats QSH as a core fluctuation structure tied to a tearing mode of the same helicity, and shows that strong magnetic and velocity shears in the structure suppress the nonlinear interaction with other fluctuations. By summing the multiple helicity fluctuation energies over wavenumber, we reduce the theory to a predator-prey model. The suppression of the nonlinear interaction is governed by the single helicity energy, which, for fixed radial structure, controls the magnetic and velocity shearing rates. It is also controlled by plasma current which, in the theory, sets the shearing threshold for suppression. The model shows a limit cycle oscillation in which the system toggles between QSH and multiple helicity states, with the single helicity phase becoming increasingly long-lived relative to the multiple helicity phase as plasma current increases.

Interaction of rotating helical magnetic field with the HIST spherical torus plasmas

NASA Astrophysics Data System (ADS)

Kikuchi, Yusuke; Sugahara, Masato; Yamada, Satoshi; Yoshikawa, Tatsuya; Fukumoto, Naoyuki; Nagata, Masayoshi

2006-10-01

The physical mechanism of current drive by co-axial helicity injection (CHI) has been experimentally investigated on both spheromak and spherical torus (ST) configurations on the HIST device [1]. It has been observed that the n = 1 kink mode rotates toroidally with a frequency of 10-20 kHz in the ExB direction. It seems that the induced toroidal current by CHI strongly relates with the observed rotating kink mode. On the other hand, it is well known that MHD instabilities can be controlled or even suppressed by an externally applied helical magnetic field in tokamak devices. Therefore, we have started to install two sets of external helical coils in order to produce a rotating helical magnetic field on HIST. Mode structures of the generated rotating helical magnetic field and preliminary experimental results of the interaction of the rotating helical magnetic field with the HIST plasmas will be shown in the conference. [1] M. Nagata, et al., Physics of Plasmas 10, 2932 (2003)

The next large helical devices

NASA Astrophysics Data System (ADS)

Iiyoshi, Atsuo; Yamazaki, Kozo

1995-06-01

Helical systems have the strong advantage of inherent steady-state operation for fusion reactors. Two large helical devices with fully superconducting coil systems are presently under design and construction. One is the LHD (Large Helical Device) [Fusion Technol. 17, 169 (1990)] with major radius=3.9 m and magnetic field=3-4 T, that is under construction during 1990-1997 at NIFS (National Institute for Fusion Science), Nagoya/Toki, Japan; it features continuous helical coils and a clean helical divertor focusing on edge configuration optimization. The other one in the W7-X (Wendelstein 7-X) [in Plasma Physics and Controlled Fusion Nuclear Research, 1990, (International Atomic Energy Agency, Vienna, 1991), Vol. 3, p. 525] with major radius=5.5 m and magnetic field=3 T, that is under review at IPP (Max-Planck Institute for Plasma Physics), Garching, Germany; it has adopted a modular coil system after elaborate optimization studies. These two programs are complementary in promoting world helical fusion research and in extending the understanding of toroidal plasmas through comparisons with large tokamaks.

320-Row wide volume CT significantly reduces density heterogeneity observed in the descending aorta: comparisons with 64-row helical CT.

PubMed

Yamashiro, Tsuneo; Miyara, Tetsuhiro; Honda, Osamu; Kamiya, Ayano; Tanaka, Yuko; Murayama, Sadayuki

2014-01-01

The aim of this study was to compare density heterogeneity on wide volume (WV) scans with that on helical CT scans. 22 subjects underwent chest CT using 320-WV and 64-helical modes. Density heterogeneity of the descending aorta was evaluated quantitatively and qualitatively. At qualitative assessment, the heterogeneity was judged to be smaller on WV scans than on helical scans (p<0.0001). Mean changes in aortic density between two contiguous slices were 1.64 HU (3.40%) on WV scans and 2.29 HU (5.19%) on helical scans (p<0.0001). CT density of thoracic organs is more homogeneous and reliable on WV scans than on helical scans. Copyright © 2013 Elsevier Ltd. All rights reserved.

Helicity patterns on the Sun

NASA Astrophysics Data System (ADS)

Pevtsov, A.

Solar magnetic fields exhibit hemispheric preference for negative (pos- itive) helicity in northern (southern) hemisphere. The hemispheric he- licity rule, however, is not very strong, - the patterns of opposite sign helicity were observed on different spatial scales in each hemisphere. For instance, many individual sunspots exhibit patches of opposite he- licity inside the single polarity field. There are also helicity patterns on scales larger than the size of typical active region. Such patterns were observed in distribution of active regions with abnormal (for a give hemisphere) helicity, in large-scale photospheric magnetic fields and coronal flux systems. We will review the observations of large-scale pat- terns of helicity in solar atmosphere and their possible relationship with (sub-)photospheric processes. The emphasis will be on large-scale pho- tospheric magnetic field and solar corona.

Helicity conservation under quantum reconnection of vortex rings.

PubMed

Zuccher, Simone; Ricca, Renzo L

2015-12-01

Here we show that under quantum reconnection, simulated by using the three-dimensional Gross-Pitaevskii equation, self-helicity of a system of two interacting vortex rings remains conserved. By resolving the fine structure of the vortex cores, we demonstrate that the total length of the vortex system reaches a maximum at the reconnection time, while both writhe helicity and twist helicity remain separately unchanged throughout the process. Self-helicity is computed by two independent methods, and topological information is based on the extraction and analysis of geometric quantities such as writhe, total torsion, and intrinsic twist of the reconnecting vortex rings.

Generation of helical gears with new surfaces topology by application of CNC machines

NASA Technical Reports Server (NTRS)

Litvin, F. L.; Chen, N. X.; Hsiao, C. L.; Handschuh, Robert F.

1993-01-01

Analysis of helical involute gears by tooth contact analysis shows that such gears are very sensitive to angular misalignment that leads to edge contact and the potential for high vibration. A new topology of tooth surfaces of helical gears that enables a favorable bearing contact and a reduced level of vibration is described. Methods for grinding of the helical gears with the new topology are proposed. A TCA (tooth contact analysis) program for simulation of meshing and contact of helical gears with the new topology has been developed. Numerical examples that illustrate the proposed ideas are discussed.

Generation of helical gears with new surfaces, topology by application of CNC machines

NASA Technical Reports Server (NTRS)

Litvin, F. L.; Chen, N. X.; Hsiao, C. L.; Handschuh, R. F.

1993-01-01

Analysis of helical involute gears by tooth contact analysis shows that such gears are very sensitive to angular misalignment that leads to edge contact and the potential for high vibration. A new topology of tooth surfaces of helical gears that enables a favorable bearing contact and a reduced level of vibration is described. Methods for grinding of the helical gears with the new topology are proposed. A TCA (tooth contact analysis) program for simulation of meshing and contact of helical gears with the new topology has been developed. Numerical examples that illustrate the proposed ideas are discussed.

Observation of an optical vortex beam from a helical undulator in the XUV region.

PubMed

Kaneyasu, Tatsuo; Hikosaka, Yasumasa; Fujimoto, Masaki; Iwayama, Hiroshi; Hosaka, Masahito; Shigemasa, Eiji; Katoh, Masahiro

2017-09-01

The observation of an optical vortex beam at 60 nm wavelength, produced as the second-harmonic radiation from a helical undulator, is reported. The helical wavefront of the optical vortex beam was verified by measuring the interference pattern between the vortex beam from a helical undulator and a normal beam from another undulator. Although the interference patterns were slightly blurred owing to the relatively large electron beam emittance, it was possible to observe the interference features thanks to the helical wavefront of the vortex beam. The experimental results were well reproduced by simulation.

Small-x asymptotics of the gluon helicity distribution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kovchegov, Yuri V.; Pitonyak, Daniel; Sievert, Matthew D.

2017-10-27

Here, we determine the small-x asymptotics of the gluon helicity distribution in a proton at leading order in perturbative QCD at large N c. To achieve this, we begin by evaluating the dipole gluon helicity TMD at small x. In the process we obtain an interesting new result: in contrast to the unpolarized dipole gluon TMD case, the operator governing the small-x behavior of the dipole gluon helicity TMD is different from the operator corresponding to the polarized dipole scattering amplitude (used in our previous work to determine the small-x asymptotics of the quark helicity distribution).

Determination of magnetic helicity in the solar wind and implications for cosmic ray propagation

NASA Technical Reports Server (NTRS)

Matthaeus, W. H.; Goldstein, M. L.

1981-01-01

The mean value of the correlation between local magnetic field and vector potential, known as the magnetic helicity, is a measure of the lack of mirror reflection symmetry of magnetic covariances in a turbulent medium. A method is presented for extraction of helicity spectra from magnetometer data, and applied to an evaluation of the magnetic helicity of interplanetary magnetic fluctuations.

Biot-Savart helicity versus physical helicity: A topological description of ideal flows

NASA Astrophysics Data System (ADS)

Sahihi, Taliya; Eshraghi, Homayoon

2014-08-01

For an isentropic (thus compressible) flow, fluid trajectories are considered as orbits of a family of one parameter, smooth, orientation-preserving, and nonsingular diffeomorphisms on a compact and smooth-boundary domain in the Euclidian 3-space which necessarily preserve a finite measure, later interpreted as the fluid mass. Under such diffeomorphisms the Biot-Savart helicity of the pushforward of a divergence-free and tangent to the boundary vector field is proved to be conserved and since these circumstances present an isentropic flow, the conservation of the "Biot-Savart helicity" is established for such flows. On the other hand, the well known helicity conservation in ideal flows which here we call it "physical helicity" is found to be an independent constant with respect to the Biot-Savart helicity. The difference between these two helicities reflects some topological features of the domain as well as the velocity and vorticity fields which is discussed and is shown for simply connected domains the two helicities coincide. The energy variation of the vorticity field is shown to be formally the same as for the incompressible flow obtained before. For fluid domains consisting of several disjoint solid tori, at each time, the harmonic knot subspace of smooth vector fields on the fluid domain is found to have two independent base sets with a special type of orthogonality between these two bases by which a topological description of the vortex and velocity fields depending on the helicity difference is achieved since this difference is shown to depend only on the harmonic knot parts of velocity, vorticity, and its Biot-Savart vector field. For an ideal magnetohydrodynamics (MHD) flow three independent constant helicities are reviewed while the helicity of magnetic potential is generalized for non-simply connected domains by inserting a special harmonic knot field in the dynamics of the magnetic potential. It is proved that the harmonic knot part of the vorticity in hydrodynamics and the magnetic field in MHD is presented by constant coefficients (fluxes) when expanded in terms of one of the time dependent base functions.

Frequency-Domain Streak Camera and Tomography for Ultrafast Imaging of Evolving and Channeled Plasma Accelerator Structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li Zhengyan; Zgadzaj, Rafal; Wang Xiaoming

2010-11-04

We demonstrate a prototype Frequency Domain Streak Camera (FDSC) that can capture the picosecond time evolution of the plasma accelerator structure in a single shot. In our prototype Frequency-Domain Streak Camera, a probe pulse propagates obliquely to a sub-picosecond pump pulse that creates an evolving nonlinear index 'bubble' in fused silica glass, supplementing a conventional Frequency Domain Holographic (FDH) probe-reference pair that co-propagates with the 'bubble'. Frequency Domain Tomography (FDT) generalizes Frequency-Domain Streak Camera by probing the 'bubble' from multiple angles and reconstructing its morphology and evolution using algorithms similar to those used in medical CAT scans. Multiplexing methods (Temporalmore » Multiplexing and Angular Multiplexing) improve data storage and processing capability, demonstrating a compact Frequency Domain Tomography system with a single spectrometer.« less

The Writhe of Helical Structures in the Solar Corona

NASA Technical Reports Server (NTRS)

Toeroek, T.; Berger, M. A.; Kliem, B.

2010-01-01

Context. Helicity is a fundamental property of magnetic fields, conserved in ideal MHD. In flux rope topology, it consists of twist and writhe helicity. Despite the common occurrence of helical structures in the solar atmosphere, little is known about how their shape relates to the writhe, which fraction of helicity is contained in writhe, and how much helicity is exchanged between twist and writhe when they erupt. Aims. Here we perform a quantitative investigation of these questions relevant for coronal flux ropes. Methods. The decomposition of the writhe of a curve into local and nonlocal components greatly facilitates its computation. We use it to study the relation between writhe and projected S shape of helical curves and to measure writhe and twist in numerical simulations of flux rope instabilities. The results are discussed with regard to filament eruptions and coronal mass ejections (CMEs). Results. (1) We demonstrate that the relation between writhe and projected S shape is not unique in principle, but that the ambiguity does not affect low-lying structures, thus supporting the established empirical rule which associates stable forward (reverse) S shaped structures low in the corona with positive (negative) helicity. (2) Kink-unstable erupting flux ropes are found to transform a far smaller fraction of their twist helicity into writhe helicity than often assumed. (3) Confined flux rope eruptions tend to show stronger writhe at low heights than ejective eruptions (CMEs). This argues against suggestions that the writhing facilitates the rise of the rope through the overlying field. (4) Erupting filaments which are S shaped already before the eruption and keep the sign of their axis writhe (which is expected if field of one chirality dominates the source volume of the eruption), must reverse their S shape in the course of the rise. Implications for the occurrence of the helical kink instability in such events are discussed.

Use of reconstructed 3D equilibria to determine onset conditions of helical cores in tokamaks for extrapolation to ITER

NASA Astrophysics Data System (ADS)

Wingen, A.; Wilcox, R. S.; Seal, S. K.; Unterberg, E. A.; Cianciosa, M. R.; Delgado-Aparicio, L. F.; Hirshman, S. P.; Lao, L. L.

2018-03-01

Large, spontaneous m/n  =  1/1 helical cores are shown to be expected in tokamaks such as ITER with extended regions of low- or reversed- magnetic shear profiles and q near 1 in the core. The threshold for this spontaneous symmetry breaking is determined using VMEC scans, beginning with reconstructed 3D equilibria from DIII-D and Alcator C-Mod based on observed internal 3D deformations. The helical core is a saturated internal kink mode (Wesson 1986 Plasma Phys. Control. Fusion 28 243); its onset threshold is shown to be proportional to (dp/dρ)/B_t2 around q  =  1. Below the threshold, applied 3D fields can drive a helical core to finite size, as in DIII-D. The helical core size thereby depends on the magnitude of the applied perturbation. Above it, a small, random 3D kick causes a bifurcation from axisymmetry and excites a spontaneous helical core, which is independent of the kick size. Systematic scans of the q-profile show that the onset threshold is very sensitive to the q-shear in the core. Helical cores occur frequently in Alcator C-Mod during ramp-up when slow current penetration results in a reversed shear q-profile, which is favorable for helical core formation. Finally, a comparison of the helical core onset threshold for discharges from DIII-D, Alcator C-Mod and ITER confirms that while DIII-D is marginally stable, Alcator C-Mod and especially ITER are highly susceptible to helical core formation without being driven by an externally applied 3D magnetic field.

Use of reconstructed 3D equilibria to determine onset conditions of helical cores in tokamaks for extrapolation to ITER

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wingen, A.; Wilcox, R. S.; Seal, S. K.

In this paper, large, spontaneous m/n = 1/1 helical cores are shown to be expected in tokamaks such as ITER with extended regions of low- or reversed- magnetic shear profiles and q near 1 in the core. The threshold for this spontaneous symmetry breaking is determined using VMEC scans, beginning with reconstructed 3D equilibria from DIII-D and Alcator C-Mod based on observed internal 3D deformations. The helical core is a saturated internal kink mode (Wesson 1986 Plasma Phys. Control. Fusion 28 243); its onset threshold is shown to be proportional tomore » $$({\\rm d}p/{\\rm d}\\rho)/B_t^2$$ around q = 1. Below the threshold, applied 3D fields can drive a helical core to finite size, as in DIII-D. The helical core size thereby depends on the magnitude of the applied perturbation. Above it, a small, random 3D kick causes a bifurcation from axisymmetry and excites a spontaneous helical core, which is independent of the kick size. Systematic scans of the q-profile show that the onset threshold is very sensitive to the q-shear in the core. Helical cores occur frequently in Alcator C-Mod during ramp-up when slow current penetration results in a reversed shear q-profile, which is favorable for helical core formation. In conclusion, a comparison of the helical core onset threshold for discharges from DIII-D, Alcator C-Mod and ITER confirms that while DIII-D is marginally stable, Alcator C-Mod and especially ITER are highly susceptible to helical core formation without being driven by an externally applied 3D magnetic field.« less

A NEW SIMPLE DYNAMO MODEL FOR STELLAR ACTIVITY CYCLE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yokoi, N.; Hamba, F.; Schmitt, D.

2016-06-20

A new simple dynamo model for stellar activity cycle is proposed. By considering an inhomogeneous flow effect on turbulence, it is shown that turbulent cross helicity (velocity–magnetic-field correlation) enters the expression of turbulent electromotive force as the coupling coefficient for the mean absolute vorticity. This makes the present model different from the current α –Ω-type models in two main ways. First, in addition to the usual helicity ( α ) and turbulent magnetic diffusivity ( β ) effects, we consider the cross-helicity effect as a key ingredient of the dynamo process. Second, the spatiotemporal evolution of cross helicity is solvedmore » simultaneously with the mean magnetic fields. The basic scenario is as follows. In the presence of turbulent cross helicity, the toroidal field is induced by the toroidal rotation. Then, as in usual models, the α effect generates the poloidal field from the toroidal one. This induced poloidal field produces a turbulent cross helicity whose sign is opposite to the original one (negative production). With this cross helicity of the reversed sign, a reversal in field configuration starts. Eigenvalue analyses of the simplest possible model give a butterfly diagram, which confirms the above scenario and the equatorward migrations, the phase relationship between the cross helicity and magnetic fields. These results suggest that the oscillation of the turbulent cross helicity is a key for the activity cycle. The reversal of the cross helicity is not the result of the magnetic-field reversal, but the cause of the latter. This new model is expected to open up the possibility of the mean-field or turbulence closure dynamo approaches.« less

Helicity dynamics in stratified turbulence in the absence of forcing.

PubMed

Rorai, C; Rosenberg, D; Pouquet, A; Mininni, P D

2013-06-01

A numerical study of decaying stably stratified flows is performed. Relatively high stratification (Froude number ≈10(-2)-10(-1)) and moderate Reynolds (Re) numbers (Re≈ 3-6×10(3)) are considered and a particular emphasis is placed on the role of helicity (velocity-vorticity correlations), which is not an invariant of the nondissipative equations. The problem is tackled by integrating the Boussinesq equations in a periodic cubical domain using different initial conditions: a nonhelical Taylor-Green (TG) flow, a fully helical Beltrami [Arnold-Beltrami-Childress (ABC)] flow, and random flows with a tunable helicity. We show that for stratified ABC flows helicity undergoes a substantially slower decay than for unstratified ABC flows. This fact is likely associated to the combined effect of stratification and large-scale coherent structures. Indeed, when the latter are missing, as in random flows, helicity is rapidly destroyed by the onset of gravitational waves. A type of large-scale dissipative "cyclostrophic" balance can be invoked to explain this behavior. No production of helicity is observed, contrary to the case of rotating and stratified flows. When helicity survives in the system, it strongly affects the temporal energy decay and the energy distribution among Fourier modes. We discover in fact that the decay rate of energy for stratified helical flows is much slower than for stratified nonhelical flows and can be considered with a phenomenological model in a way similar to what is done for unstratified rotating flows. We also show that helicity, when strong, has a measurable effect on the Fourier spectra, in particular at scales larger than the buoyancy scale, for which it displays a rather flat scaling associated with vertical shear, as observed in the planetary boundary layer.

Multipinhole SPECT helical scan parameters and imaging volume

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yao, Rutao, E-mail: rutaoyao@buffalo.edu; Deng, Xiao; Wei, Qingyang

Purpose: The authors developed SPECT imaging capability on an animal PET scanner using a multiple-pinhole collimator and step-and-shoot helical data acquisition protocols. The objective of this work was to determine the preferred helical scan parameters, i.e., the angular and axial step sizes, and the imaging volume, that provide optimal imaging performance. Methods: The authors studied nine helical scan protocols formed by permuting three rotational and three axial step sizes. These step sizes were chosen around the reference values analytically calculated from the estimated spatial resolution of the SPECT system and the Nyquist sampling theorem. The nine helical protocols were evaluatedmore » by two figures-of-merit: the sampling completeness percentage (SCP) and the root-mean-square (RMS) resolution. SCP was an analytically calculated numerical index based on projection sampling. RMS resolution was derived from the reconstructed images of a sphere-grid phantom. Results: The RMS resolution results show that (1) the start and end pinhole planes of the helical scheme determine the axial extent of the effective field of view (EFOV), and (2) the diameter of the transverse EFOV is adequately calculated from the geometry of the pinhole opening, since the peripheral region beyond EFOV would introduce projection multiplexing and consequent effects. The RMS resolution results of the nine helical scan schemes show optimal resolution is achieved when the axial step size is the half, and the angular step size is about twice the corresponding values derived from the Nyquist theorem. The SCP results agree in general with that of RMS resolution but are less critical in assessing the effects of helical parameters and EFOV. Conclusions: The authors quantitatively validated the effective FOV of multiple pinhole helical scan protocols and proposed a simple method to calculate optimal helical scan parameters.« less

Use of reconstructed 3D equilibria to determine onset conditions of helical cores in tokamaks for extrapolation to ITER

DOE PAGES

Wingen, A.; Wilcox, R. S.; Seal, S. K.; ...

2018-01-15

In this paper, large, spontaneous m/n = 1/1 helical cores are shown to be expected in tokamaks such as ITER with extended regions of low- or reversed- magnetic shear profiles and q near 1 in the core. The threshold for this spontaneous symmetry breaking is determined using VMEC scans, beginning with reconstructed 3D equilibria from DIII-D and Alcator C-Mod based on observed internal 3D deformations. The helical core is a saturated internal kink mode (Wesson 1986 Plasma Phys. Control. Fusion 28 243); its onset threshold is shown to be proportional tomore » $$({\\rm d}p/{\\rm d}\\rho)/B_t^2$$ around q = 1. Below the threshold, applied 3D fields can drive a helical core to finite size, as in DIII-D. The helical core size thereby depends on the magnitude of the applied perturbation. Above it, a small, random 3D kick causes a bifurcation from axisymmetry and excites a spontaneous helical core, which is independent of the kick size. Systematic scans of the q-profile show that the onset threshold is very sensitive to the q-shear in the core. Helical cores occur frequently in Alcator C-Mod during ramp-up when slow current penetration results in a reversed shear q-profile, which is favorable for helical core formation. In conclusion, a comparison of the helical core onset threshold for discharges from DIII-D, Alcator C-Mod and ITER confirms that while DIII-D is marginally stable, Alcator C-Mod and especially ITER are highly susceptible to helical core formation without being driven by an externally applied 3D magnetic field.« less

Hexagonally Ordered Arrays of α-Helical Bundles Formed from Peptide-Dendron Hybrids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barkley, Deborah A.; Rokhlenko, Yekaterina; Marine, Jeannette E.

Combining monodisperse building blocks that have distinct folding properties serves as a modular strategy for controlling structural complexity in hierarchically organized materials. We combine an α-helical bundle-forming peptide with self-assembling dendrons to better control the arrangement of functional groups within cylindrical nanostructures. Site-specific grafting of dendrons to amino acid residues on the exterior of the α-helical bundle yields monodisperse macromolecules with programmable folding and self-assembly properties. The resulting hybrid biomaterials form thermotropic columnar hexagonal mesophases in which the peptides adopt an α-helical conformation. Bundling of the α-helical peptides accompanies self-assembly of the peptide-dendron hybrids into cylindrical nanostructures. The bundle stoichiometrymore » in the mesophase agrees well with the size found in solution for α-helical bundles of peptides with a similar amino acid sequence.« less

Hierarchical Helical Order in the Twisted Growth of Plant Organs

NASA Astrophysics Data System (ADS)

Wada, Hirofumi

2012-09-01

The molecular and cellular basis of left-right asymmetry in plant morphogenesis is a fundamental issue in biology. A rapidly elongating root or hypocotyl of twisting mutants of Arabidopsis thaliana exhibits a helical growth with a handedness opposite to that of the underlying cortical microtubule arrays in epidermal cells. However, how such a hierarchical helical order emerges is currently unknown. We propose a model for investigating macroscopic chiral asymmetry in Arabidopsis mutants. Our elastic model suggests that the helical pattern observed is a direct consequence of the simultaneous presence of anisotropic growth and tilting of cortical microtubule arrays. We predict that the root helical pitch angle is a function of the microtubule helical angle and elastic moduli of the tissues. The proposed model is versatile and is potentially important for other biological systems ranging from protein fibrous structures to tree trunks.

Helicity in dynamic atmospheric processes

NASA Astrophysics Data System (ADS)

Kurgansky, M. V.

2017-03-01

An overview on the helicity of the velocity field and the role played by this concept in modern research in the field of geophysical fluid dynamics and dynamic meteorology is given. Different (both previously known in the literature and first presented) formulations of the equation of helicity balance in atmospheric motions (including those with allowance for effects of air compressibility and Earth's rotation) are brought together. Equations and relationships are given which are valid in different approximations accepted in dynamic meteorology: Boussinesq approximation, quasi-static approximation, and quasi-geostrophic approximation. Emphasis is placed on the analysis of helicity budget in large-scale quasi-geostrophic systems of motion; a formula for the helicity flux across the upper boundary of the nonlinear Ekman boundary layer is given, and this flux is shown to be exactly compensated for by the helicity destruction inside the Ekman boundary layer.

Helical modes generate antimagnetic rotational spectra in nuclei

NASA Astrophysics Data System (ADS)

Malik, Sham S.

2018-03-01

A systematic analysis of the antimagnetic rotation band using r -helicity formalism is carried out for the first time. The observed octupole correlation in a nucleus is likely to play a role in establishing the antimagnetic spectrum. Such octupole correlations are explained within the helical orbits. In a rotating field, two identical fermions (generally protons) with paired spins generate these helical orbits in such a way that its positive (i.e., up) spin along the axis of quantization refers to one helicity (right-handedness) while negative (down) spin along the same quantization-axis decides another helicity (left-handedness). Since the helicity remains invariant under rotation, therefore, the quantum state of a fermion is represented by definite angular momentum and helicity. These helicity represented states support a pear-shaped structure of a rotating system having z axis as the symmetry axis. A combined operation of parity, time-reversal, and signature symmetries ensures an absence of one of the signature partner band from the observed antimagnetic spectrum. This formalism has also been tested for the recently observed negative parity Δ I =2 antimagnetic spectrum in odd-A 101Pd nucleus and explains nicely its energy spectrum as well as the B (E 2 ) values. Further, this formalism is found to be fully consistent with twin-shears mechanism popularly known for such type of rotational bands. It also provides significant clue for extending these experiments in various mass regions spread over the nuclear chart.

Numerical Simulations of Helicity Condensation in the Solar Corona

NASA Technical Reports Server (NTRS)

Zhao, L.; DeVore, C. R.; Antiochos, S. K.; Zurbuchen, T. H.

2015-01-01

The helicity condensation model has been proposed by Antiochos (2013) to explain the observed smoothness of coronal loops and the observed buildup of magnetic shear at filament channels. The basic hypothesis of the model is that magnetic reconnection in the corona causes the magnetic stress injected by photospheric motions to collect only at those special locations where prominences form. In this work we present the first detailed quantitative MHD simulations of the reconnection evolution proposed by the helicity condensation model. We use the well-known ansatz of modeling the closed corona as an initially uniform field between two horizontal photospheric plates. The system is driven by applying photospheric rotational flows that inject magnetic helicity into the system. The flows are confined to a finite region on the photosphere so as to mimic the finite flux system of, for example, a bipolar active region. The calculations demonstrate that, contrary to common belief, coronal loops having opposite helicity do not reconnect, whereas loops having the same sense of helicity do reconnect. Furthermore, we find that for a given amount of helicity injected into the corona, the evolution of the magnetic shear is insensitive to whether the pattern of driving photospheric motions is fixed or quasi-random. In all cases, the shear propagates via reconnection to the boundary of the flow region while the total magnetic helicity is conserved, as predicted by the model. We discuss the implications of our results for solar observations and for future, more realistic simulations of the helicity condensation process.

Influence of drill helical direction on exit damage development in drilling carbon fiber reinforced plastic

NASA Astrophysics Data System (ADS)

Bai, Y.; Jia, Z. Y.; Wang, F. J.; Fu, R.; Guo, H. B.; Cheng, D.; Zhang, B. Y.

2017-06-01

Drilling is inevitable for CFRP components’ assembling process in the aviation industry. The exit damage frequently occurs and affects the load carrying capacity of components. Consequently, it is of great urgency to enhance drilling exit quality on CFRP components. The article aims to guide the reasonable choice of drill helical direction and effectively reduce exit damage. Exit observation experiments are carried out with left-hand helical, right-hand helical and straight one-shot drill drilling T800S CFRP laminates separately. The development rules of exit damage and delamination factor curves are obtained. Combined with loading conditions and fracture modes of push-out burrs, and thrust force curves, the influence of drill helical direction on exit damage development is derived. It is found that the main fracture modes for left-hand helical, right-hand helical, and straight one-shot drill are mode I, extrusive fracture, mode III respectively. Among them, mode III has the least effect on exit damage development. Meanwhile, the changing rate of thrust force is relative slow for right-hand helical and straight one-shot drill in the thrust force increasing phase of stage II, which is disadvantaged for exit damage development. Therefore, straight one-shot drill’s exit quality is the best.

Design of the Helicity Injected Torus with Steady Inductive Helicity Injection (HIT-SI)

NASA Astrophysics Data System (ADS)

Sieck, P. E.; Gu, P.; Hamp, W. T.; Izzo, V. A.; McCollam, K. J.; Jarboe, T. R.; Nelson, B. A.; Redd, A. J.; Rogers, J. A.; Shumlak, U.

2000-10-01

Steady Inductive Helicity Injection (SIHI) is an inductive current drive method that injects helicity at a nearly constant rate, without open field lines, and without removing any helicity or magnetic energy from the plasma(T.R. Jarboe, Fusion Technology 36), p. 85, 1999. SIHI directly produces a rotating magnetic field structure, and the current profile is nearly time independent in the frame of the rotating field. The Helicity Injected Torus with SIHI (HIT-SI) is a ``bow tie'' spheromak designed to implement SIHI so that the current profile in the rotating frame is optimized. SIHI is accomplished using two inductive helicity injectors that operate 90^o out of phase with each other. Each helicity injector is a 180^o segment of a ZT-P size (a ≈ 8cm, R ≈ 32cm) RFP. The presence of a spheromak equilibrium will be readily apparent on several diagnostics, including the surface magnetic probes. The design of HIT-SI is presented, including the manufacturing techniques and metallurgical processes being used in the construction of the one-meter diameter close-fitting flux conserver. Several small prototype tests have been performed to prove the vacuum seal and electrical insulation capabilities of the design, and a finite element stress analysis of the flux conserver will be presented.

Tubular Crystals and Helical Arrays: Structural Determination of HIV-1 Capsid Assemblies Using Iterative Helical Real-Space Reconstruction

PubMed Central

Zhang, Peijun; Meng, Xin; Zhao, Gongpu

2013-01-01

Helical structures are important in many different life forms and are well-suited for structural studies by cryo-EM. A unique feature of helical objects is that a single projection image contains all the views needed to perform a three-dimensional (3D) crystallographic reconstruction. Here, we use HIV-1 capsid assemblies to illustrate the detailed approaches to obtain 3D density maps from helical objects. Mature HIV-1 particles contain a conical- or tubular-shaped capsid that encloses the viral RNA genome and performs essential functions in the virus life cycle. The capsid is composed of capsid protein (CA) oligomers which are helically arranged on the surface. The N-terminal domain (NTD) of CA is connected to its C-terminal domain (CTD) through a flexible hinge. Structural analysis of two- and three-dimensional crystals provided molecular models of the capsid protein (CA) and its oligomer forms. We determined the 3D density map of helically assembled HIV-1 CA hexamers at 16 Å resolution using an iterative helical real-space reconstruction method. Docking of atomic models of CA-NTD and CA-CTD dimer into the electron density map indicated that the CTD dimer interface is retained in the assembled CA. Furthermore, molecular docking revealed an additional, novel CTD trimer interface. PMID:23132072

Effect of helicity on the correlation time of large scales in turbulent flows

NASA Astrophysics Data System (ADS)

Cameron, Alexandre; Alexakis, Alexandros; Brachet, Marc-Étienne

2017-11-01

Solutions of the forced Navier-Stokes equation have been conjectured to thermalize at scales larger than the forcing scale, similar to an absolute equilibrium obtained for the spectrally truncated Euler equation. Using direct numeric simulations of Taylor-Green flows and general-periodic helical flows, we present results on the probability density function, energy spectrum, autocorrelation function, and correlation time that compare the two systems. In the case of highly helical flows, we derive an analytic expression describing the correlation time for the absolute equilibrium of helical flows that is different from the E-1 /2k-1 scaling law of weakly helical flows. This model predicts a new helicity-based scaling law for the correlation time as τ (k ) ˜H-1 /2k-1 /2 . This scaling law is verified in simulations of the truncated Euler equation. In simulations of the Navier-Stokes equations the large-scale modes of forced Taylor-Green symmetric flows (with zero total helicity and large separation of scales) follow the same properties as absolute equilibrium including a τ (k ) ˜E-1 /2k-1 scaling for the correlation time. General-periodic helical flows also show similarities between the two systems; however, the largest scales of the forced flows deviate from the absolute equilibrium solutions.

Building blocks for subleading helicity operators

DOE PAGES

Kolodrubetz, Daniel W.; Moult, Ian; Stewart, Iain W.

2016-05-24

On-shell helicity methods provide powerful tools for determining scattering amplitudes, which have a one-to-one correspondence with leading power helicity operators in the Soft-Collinear Effective Theory (SCET) away from singular regions of phase space. We show that helicity based operators are also useful for enumerating power suppressed SCET operators, which encode subleading amplitude information about singular limits. In particular, we present a complete set of scalar helicity building blocks that are valid for constructing operators at any order in the SCET power expansion. In conclusion, we also describe an interesting angular momentum selection rule that restricts how these building blocks canmore » be assembled.« less

Modeling the Structure of Helical Assemblies with Experimental Constraints in Rosetta.

PubMed

André, Ingemar

2018-01-01

Determining high-resolution structures of proteins with helical symmetry can be challenging due to limitations in experimental data. In such instances, structure-based protein simulations driven by experimental data can provide a valuable approach for building models of helical assemblies. This chapter describes how the Rosetta macromolecular package can be used to model homomeric protein assemblies with helical symmetry in a range of modeling scenarios including energy refinement, symmetrical docking, comparative modeling, and de novo structure prediction. Data-guided structure modeling of helical assemblies with experimental information from electron density, X-ray fiber diffraction, solid-state NMR, and chemical cross-linking mass spectrometry is also described.

On the helical arrangements of protein molecules.

PubMed

Dauter, Zbigniew; Jaskolski, Mariusz

2018-03-01

Helical structures are prevalent in biology. In the PDB, there are many examples where protein molecules are helically arranged, not only according to strict crystallographic screw axes but also according to approximate noncrystallographic screws. The preponderance of such screws is rather striking as helical arrangements in crystals must preserve an integer number of subunits per turn, while intuition and simple packing arguments would seem to favor fractional helices. The article provides insights into such questions, based on stereochemistry, trigonometry, and topology, and illustrates the findings with concrete PDB structures. Updated statistics of Sohncke space groups in the PDB are also presented. © 2017 The Protein Society.

The alpha dynamo parameter and measurability of helicities in magnetohydrodynamic turbulence

NASA Technical Reports Server (NTRS)

Matthaeus, W. H.; Goldstein, M. L.; Lantz, S. R.

1986-01-01

Alpha, an important parameter in dynamo theory, is shown to be proportional to either the kinetic, current, magnetic, or velocity helicities of the fluctuating magnetic field and fluctuating velocity field. The particular helicity to which alpha is proportional depends on the assumptions used in deriving the first-order smoothed equations that describe the alpha effect. In two cases, viz., when alpha is proportional to either the magnetic helicity or velocity helicity, alpha can be determined experimentally from two-point measurements of the fluctuating fields in incompressible, homogeneous turbulence with arbitrary rotational symmetry. For the other two possibilities, alpha can be determined if the turbulence is isotropic.

Structure determination of a peptide model of the repeated helical domain in Samia cynthia ricini silk fibroin before spinning by a combination of advanced solid-state NMR methods.

PubMed

Nakazawa, Yasumoto; Asakura, Tetsuo

2003-06-18

Fibrous proteins unlike globular proteins, contain repetitive amino acid sequences, giving rise to very regular secondary protein structures. Silk fibroin from a wild silkworm, Samia cynthia ricini, consists of about 100 repeats of alternating polyalanine (poly-Ala) regions of 12-13 residues in length and Gly-rich regions. In this paper, the precise structure of the model peptide, GGAGGGYGGDGG(A)(12)GGAGDGYGAG, which is a typical repeated sequence of the silk fibroin, was determined using a combination of three kinds of solid-state NMR studies; a quantitative use of (13)C CP/MAS NMR chemical shift with conformation-dependent (13)C chemical shift contour plots, 2D spin diffusion (13)C solid-state NMR under off magic angle spinning and rotational echo double resonance. The structure of the model peptide corresponding to the silk fibroin structure before spinning was determined. The torsion angles of the central Ala residue, Ala(19), in the poly-Ala region were determined to be (phi, psi) = (-59 degrees, -48 degrees ) which are values typically associated with alpha-helical structures. However, the torsion angles of the Gly(25) residue adjacent to the C-terminal side of the poly-Ala chain were determined to be (phi, psi) = (-66 degrees, -22 degrees ) and those of Gly(12) and Ala(13) residues at the N-terminal of the poly-Ala chain to be (phi, psi) = (-70 degrees, -30 degrees ). In addition, REDOR experiments indicate that the torsion angles of the two C-terminal Ala residues, Ala(23) and Ala(24), are (phi, psi) = (-66 degrees, -22 degrees ) and those of N-terminal two Ala residues, Ala(13) and Ala(14) are (phi, psi) = (-70 degrees, -30 degrees ). Thus, the local structure of N-terminal and C-terminal residues, and also the neighboring residues of alpha-helical poly-Ala chain in the model peptide is a more strongly wound structure than found in typical alpha-helix structures.

Research on the influence of helical strakes on dynamic response of floating wind turbine platform

NASA Astrophysics Data System (ADS)

Ding, Qin-wei; Li, Chun

2017-04-01

The stability of platform structure is the paramount guarantee of the safe operation of the offshore floating wind turbine. The NREL 5MW floating wind turbine is established based on the OC3-Hywind Spar Buoy platform with the supplement of helical strakes for the purpose to analyze the impact of helical strakes on the dynamic response of the floating wind turbine Spar platform. The dynamic response of floating wind turbine Spar platform under wind, wave and current loading from the impact of number, height and pitch ratio of the helical strakes is analysed by the radiation and diffraction theory, the finite element method and orthogonal design method. The result reveals that the helical strakes can effectively inhibit the dynamic response of the platform but enlarge the wave exciting force; the best parameter combination is two pieces of helical strakes with the height of 15% D ( D is the diameter of the platform) and the pitch ratio of 5; the height of the helical strake and its pitch ratio have significant influence on pitch response.

Magnetic helices as metastable states of finite XY ferromagnetic chains: An analytical study

NASA Astrophysics Data System (ADS)

Popov, Alexander P.; Pini, Maria Gloria

2018-04-01

We investigated a simple but non trivial model, consisting of a chain of N classical XY spins with nearest neighbor ferromagnetic interaction, where each of the two end-point spins is assumed to be exchange-coupled to a fully-pinned fictitious spin. In the mean field approximation, the system might be representative of a soft ferromagnetic film sandwiched between two magnetically hard layers. We show that, while the ground state is ferromagnetic and collinear, the system can attain non-collinear metastable states in the form of magnetic helices. The helical solutions and their stability were studied analytically in the absence of an external magnetic field. There are four possible classes of solutions. Only one class is metastable, and its helical states contain an integer number of turns. Among the remaining unstable classes, there is a class of helices which contain an integer number of turns. Therefore, an integer number of turns in a helical configuration is a necessary, but not a sufficient, condition for metastability. These results may be useful to devise future applications of metastable magnetic helices as energy-storing elements.

Magnetic helicity balance at Taylor relaxed states sustained by AC helicity injection

NASA Astrophysics Data System (ADS)

Hirota, Makoto; Morrison, Philip J.; Horton, Wendell; Hattori, Yuji

2017-10-01

Magnitudes of Taylor relaxed states that are sustained by AC magnetic helicity injection (also known as oscillating field current drive, OFCD) are investigated numerically in a cylindrical geometry. Compared with the amplitude of the oscillating magnetic field at the skin layer (which is normalized to 1), the strength of the axial guide field Bz 0 is shown to be an important parameter. The relaxation process seems to be active only when Bz 0 < 1 . Moreover, in the case of weak guide field Bz 0 < 0.2 , a helically-symmetric relaxed state is self-generated instead of the axisymmetric reversed-field pinch. As a theoretical model, the helicity balance is considered in a similar way to R. G. O'Neill et al., where the helicity injection rate is directly equated with the dissipation rate at the Taylor states. Then, the bifurcation to the helical Taylor state is predicted theoretically and the estimated magnitudes of the relaxed states reasonably agree with numerical results as far as Bz 0 < 1 . This work was supported by JSPS KAKENHI Grant Number 16K05627.

INVESTIGATION OF HELICITY AND ENERGY FLUX TRANSPORT IN THREE EMERGING SOLAR ACTIVE REGIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vemareddy, P., E-mail: vemareddy@iiap.res.in

We report the results of an investigation of helicity and energy flux transport from three emerging solar active regions (ARs). Using time sequence vector magnetic field observations obtained from the Helioseismic Magnetic Imager, the velocity field of plasma flows is derived by the differential affine velocity estimator for vector magnetograms. In three cases, the magnetic fluxes evolve to pump net positive, negative, and mixed-sign helicity flux into the corona. The coronal helicity flux is dominantly coming from the shear term that is related to horizontal flux motions, whereas energy flux is dominantly contributed by the emergence term. The shear helicity fluxmore » has a phase delay of 5–14 hr with respect to absolute magnetic flux. The nonlinear curve of coronal energy versus relative helicity identifies the configuration of coronal magnetic fields, which is approximated by a fit of linear force-free fields. The nature of coronal helicity related to the particular pattern of evolving magnetic fluxes at the photosphere has implications for the generation mechanism of two kinds of observed activity in the ARs.« less

Helicity-dependent single-walled carbon nanotube alignment on graphite for helical angle and handedness recognition

PubMed Central

Chen, Yabin; Shen, Ziyong; Xu, Ziwei; Hu, Yue; Xu, Haitao; Wang, Sheng; Guo, Xiaolei; Zhang, Yanfeng; Peng, Lianmao; Ding, Feng; Liu, Zhongfan; Zhang, Jin

2013-01-01

Aligned single-walled carbon nanotube arrays provide a great potential for the carbon-based nanodevices and circuit integration. Aligning single-walled carbon nanotubes with selected helicities and identifying their helical structures remain a daunting issue. The widely used gas-directed and surface-directed growth modes generally suffer the drawbacks of mixed and unknown helicities of the aligned single-walled carbon nanotubes. Here we develop a rational approach to anchor the single-walled carbon nanotubes on graphite surfaces, on which the orientation of each single-walled carbon nanotube sensitively depends on its helical angle and handedness. This approach can be exploited to conveniently measure both the helical angle and handedness of the single-walled carbon nanotube simultaneously at a low cost. In addition, by combining with the resonant Raman spectroscopy, the (n,m) index of anchored single-walled carbon nanotube can be further determined from the (d,θ) plot, and the assigned (n,m) values by this approach are validated by both the electronic transition energy Eii measurement and nanodevice application. PMID:23892334

Analytic, High-beta Solutions of the Helical Grad-Shafranov Equation

DOE Office of Scientific and Technical Information (OSTI.GOV)

D.R. Smith; A.H. Reiman

We present analytic, high-beta ({beta} {approx} O(1)), helical equilibrium solutions for a class of helical axis configurations having large helical aspect ratio, with the helix assumed to be tightly wound. The solutions develop a narrow boundary layer of strongly compressed flux, similar to that previously found in high beta tokamak equilibrium solutions. The boundary layer is associated with a strong localized current which prevents the equilibrium from having zero net current.

The SSME seal test program: Leakage tests for helically-grooved seals

NASA Technical Reports Server (NTRS)

Childs, D. W.

1983-01-01

Helically grooved annular seal configurations were tested in highly turbulent flow to determine if reduced leakage and enhanced stability would result from the pumping action of the seal. It was found that: (1) leakage of a helically grooved seals decreases with running speed; (2) leakage reduction due to increased running speed is greater at lower values of R sub a; (3) an asymptote for leakage reduction is indicated with increasing running speed; (4) leakage is reduced by reducing the ridge (minimum) and average clearances; (5) leakage increases with increasing pitch angles and with increasing groove depth. Plain seals with smooth rotors and stators will leak more than a helically grooved seal. It was also found that plain seals with a rough rotor and a rough stator leak less than a properly designed helically grooved seal. A properly designed helically grooved seal consumes at least twice as much power as a conventional annular seal.

Structure and interactions of biological helices

NASA Astrophysics Data System (ADS)

Kornyshev, Alexei A.; Lee, Dominic J.; Leikin, Sergey; Wynveen, Aaron

2007-07-01

Helices are essential building blocks of living organisms, be they molecular fragments of proteins ( α -helices), macromolecules (DNA and collagen), or multimolecular assemblies (microtubules and viruses). Their interactions are involved in packing of meters of genetic material within cells and phage heads, recognition of homologous genes in recombination and DNA repair, stability of tissues, and many other processes. Helical molecules form a variety of mesophases in vivo and in vitro. Recent structural studies, direct measurements of intermolecular forces, single-molecule manipulations, and other experiments have accumulated a wealth of information and revealed many puzzling physical phenomena. It is becoming increasingly clear that in many cases the physics of biological helices cannot be described by theories that treat them as simple, unstructured polyelectrolytes. The present article focuses on the most important and interesting aspects of the physics of structured macromolecules, highlighting various manifestations of the helical motif in their structure, elasticity, interactions with counterions, aggregation, and poly- and mesomorphic transitions.

Investigations of electron helicity in optically active molecules using polarized beams of electrons and positrons

NASA Technical Reports Server (NTRS)

Gidley, D. W.; Rich, A.; Van House, J. C.; Zitzewitz, P. W.

1981-01-01

A positronium-formation experiment with a high sensitivity to a possible relation between the helicity of beta particles emitted in nuclear beta decay and the optical asymmetry of biological molecules is presented. The experiment is based on a mechanism in which the electrons in optically active molecules possess a helicity of less than 0.001, too weak to detect in radiolysis experiments, the sign of which depends on the chirality of the isomer. A helicity-dependent asymmetry is sought in the formation of the triplet ground state of positronium when a low-energy beam of polarized positrons of reversible helicity interacts with an optically active substance coating a channel electron multiplier. Asymmetries between positronium decays observed at positive and negative helicities for the same substance can thus be determined with a sensitivity of 0.0001, which represents a factor of 100 improvement over previous positronium experiments.

Cross Helicity and Turbulent Magnetic Diffusivity in the Solar Convection Zone

NASA Astrophysics Data System (ADS)

Rüdiger, G.; Kitchatinov, L. L.; Brandenburg, A.

2011-03-01

In a density-stratified turbulent medium, the cross helicity < u'ṡ B'> is considered as a result of the interaction of the velocity fluctuations and a large-scale magnetic field. By means of a quasilinear theory and by numerical simulations, we find the cross helicity and the mean vertical magnetic field to be anti-correlated. In the high-conductivity limit the ratio of the helicity and the mean magnetic field equals the ratio of the magnetic eddy diffusivity and the (known) density scale height. The result can be used to predict that the cross helicity at the solar surface will exceed the value of 1 gauss km s-1. Its sign is anti-correlated to that of the radial mean magnetic field. Alternatively, we can use our result to determine the value of the turbulent magnetic diffusivity from observations of the cross helicity.

Nuclear reactor safety device

DOEpatents

Hutter, Ernest

1986-01-01

A safety device is disclosed for use in a nuclear reactor for axially repositioning a control rod with respect to the reactor core in the event of an upward thermal excursion. Such safety device comprises a laminated helical ribbon configured as a tube-like helical coil having contiguous helical turns with slidably abutting edges. The helical coil is disclosed as a portion of a drive member connected axially to the control rod. The laminated ribbon is formed of outer and inner laminae. The material of the outer lamina has a greater thermal coefficient of expansion than the material of the inner lamina. In the event of an upward thermal excursion, the laminated helical coil curls inwardly to a smaller diameter. Such inward curling causes the total length of the helical coil to increase by a substantial increment, so that the control rod is axially repositioned by a corresponding amount to reduce the power output of the reactor.

Hierarchically arranged helical fibre actuators driven by solvents and vapours.

PubMed

Chen, Peining; Xu, Yifan; He, Sisi; Sun, Xuemei; Pan, Shaowu; Deng, Jue; Chen, Daoyong; Peng, Huisheng

2015-12-01

Mechanical responsiveness in many plants is produced by helical organizations of cellulose microfibrils. However, simple mimicry of these naturally occurring helical structures does not produce artificial materials with the desired tunable actuations. Here, we show that actuating fibres that respond to solvent and vapour stimuli can be created through the hierarchical and helical assembly of aligned carbon nanotubes. Primary fibres consisting of helical assemblies of multiwalled carbon nanotubes are twisted together to form the helical actuating fibres. The nanoscale gaps between the nanotubes and micrometre-scale gaps among the primary fibres contribute to the rapid response and large actuation stroke of the actuating fibres. The compact coils allow the actuating fibre to rotate reversibly. We show that these fibres, which are lightweight, flexible and strong, are suitable for a variety of applications such as energy-harvesting generators, deformable sensing springs and smart textiles.

Hierarchically arranged helical fibre actuators driven by solvents and vapours

NASA Astrophysics Data System (ADS)

Chen, Peining; Xu, Yifan; He, Sisi; Sun, Xuemei; Pan, Shaowu; Deng, Jue; Chen, Daoyong; Peng, Huisheng

2015-12-01

Mechanical responsiveness in many plants is produced by helical organizations of cellulose microfibrils. However, simple mimicry of these naturally occurring helical structures does not produce artificial materials with the desired tunable actuations. Here, we show that actuating fibres that respond to solvent and vapour stimuli can be created through the hierarchical and helical assembly of aligned carbon nanotubes. Primary fibres consisting of helical assemblies of multiwalled carbon nanotubes are twisted together to form the helical actuating fibres. The nanoscale gaps between the nanotubes and micrometre-scale gaps among the primary fibres contribute to the rapid response and large actuation stroke of the actuating fibres. The compact coils allow the actuating fibre to rotate reversibly. We show that these fibres, which are lightweight, flexible and strong, are suitable for a variety of applications such as energy-harvesting generators, deformable sensing springs and smart textiles.

Conservation law of angular momentum in helicity-dependent Raman and Rayleigh scattering

NASA Astrophysics Data System (ADS)

Tatsumi, Yuki; Kaneko, Tomoaki; Saito, Riichiro

2018-05-01

In first-order Raman scattering, helicity of circularly polarized incident light is either conserved or changed depending on the Raman modes. When the helicity of incident light changes in the scattered light, the angular momentum of a photon is transferred to the material. Here, we present the conservation law of pseudoangular momentum in the helicity-dependent Raman scattering for a N -fold (N =1 -4 ,6 ) rotational symmetry of a crystal. Furthermore, the conservation law of electron-phonon interaction is discussed by considering the vibration direction of a phonon that has the same or lower symmetry than the symmetry of the crystal, which is essential to allow the helicity change in Raman scattering in a highly symmetric material, such as graphene. We also discuss the conservation law of pseudoangular momentum in Rayleigh scattering and show that the helicity change is allowed only in the crystal with one- or twofold rotational symmetry.

Dosimetric study and in-vivo dose verification for conformal avoidance treatment of anal adenocarcinoma using helical tomotherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Han Chunhui; Chen Yijen; Liu An

2007-04-01

This study evaluated the efficacy of using helical tomotherapy for conformal avoidance treatment of anal adenocarcinoma. We retrospectively generated step-and-shoot intensity-modulated radiotherapy (sIMRT) plans and helical tomotherapy plans for two anal cancer patients, one male and one female, who were treated by the sIMRT technique. Dose parameters for the planning target volume (PTV) and the organs-at-risk (OARs) were compared between the sIMRT and the helical tomotherapy plans. The helical tomotherapy plans showed better dose homogeneity in the PTV, better dose conformity around the PTV, and, therefore, better sparing of nearby OARs compared with the sIMRT plans. In-vivo skin dose measurementsmore » were performed during conformal avoidance helical tomotherapy treatment of an anal cancer patient to verify adequate delivery of skin dose and sparing of OARs.« less

Investigations of Escherichia coli promoter sequences with artificial neural networks: New signals discovered upstream of the transcriptional startpoint

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pedersen, A.G.; Engelbrecht, J.

1995-12-31

In this paper we present a novel method for using the learning ability of a neural network as a measure of information in local regions of input data. Using the method to analyze Escherichia coli promoters, we discover all previously described signals, and furthermore find new signals that are regularly spaced along the promoter region. The spacing of all signals correspond to the helical periodicity of DNA, meaning that the signals are all present on the same face of the DNA helix in the promoter region. This is consistent with a model where the RNA polymerase contacts the promoter onmore » one side of the DNA, and suggests that the regions important for promoter recognition may include more positions on the DNA than usually assumed. We furthermore analyze the E.coli promoters by calculating the Kullback Leibler distance, and by constructing sequence logos.« less

Actin as the generator of tension during muscle contraction.

PubMed Central

Schutt, C E; Lindberg, U

1992-01-01

We propose that the key structural feature in the conversion of chemical free energy into mechanical work by actomyosin is a myosin-induced change in the length of the actin filament. As reported earlier, there is evidence that helical actin filaments can untwist into ribbons having an increased intersubunit repeat. Regular patterns of actomyosin interactions arise when ribbons are aligned with myosin thick filaments, because the repeat distance of the myosin lattice (429 A) is an integral multiple of the subunit repeat in the ribbon (35.7 A). This commensurability property of the actomyosin lattice leads to a simple mechanism for controlling the sequence of events in chemical-mechanical transduction. A role for tropomyosin in transmitting the forces developed by actomyosin is proposed. In this paper, we describe how these transduction principles provide the basis for a theory of muscle contraction. Images PMID:1530888

How the folding rates of two- and multistate proteins depend on the amino acid properties.

PubMed

Huang, Jitao T; Huang, Wei; Huang, Shanran R; Li, Xin

2014-10-01

Proteins fold by either two-state or multistate kinetic mechanism. We observe that amino acids play different roles in different mechanism. Many residues that are easy to form regular secondary structures (α helices, β sheets and turns) can promote the two-state folding reactions of small proteins. Most of hydrophilic residues can speed up the multistate folding reactions of large proteins. Folding rates of large proteins are equally responsive to the flexibility of partial amino acids. Other properties of amino acids (including volume, polarity, accessible surface, exposure degree, isoelectric point, and phase transfer energy) have contributed little to folding kinetics of the proteins. Cysteine is a special residue, it triggers two-state folding reaction and but inhibits multistate folding reaction. These findings not only provide a new insight into protein structure prediction, but also could be used to direct the point mutations that can change folding rate. © 2014 Wiley Periodicals, Inc.

NUMERICAL SIMULATIONS OF HELICITY CONDENSATION IN THE SOLAR CORONA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, L.; Zurbuchen, T. H.; DeVore, C. R.

The helicity condensation model has been proposed by Antiochos to explain the observed smoothness of coronal loops and the observed buildup of magnetic shear at filament channels. The basic hypothesis of the model is that magnetic reconnection in the corona causes the magnetic stress injected by photospheric motions to collect only at those special locations where prominences are observed to form. In this work we present the first detailed quantitative MHD simulations of the reconnection evolution proposed by the helicity condensation model. We use the well-known ansatz of modeling the closed corona as an initially uniform field between two horizontalmore » photospheric plates. The system is driven by applying photospheric rotational flows that inject magnetic helicity into the corona. The flows are confined to a finite region on the photosphere so as to mimic the finite flux system of a bipolar active region, for example. The calculations demonstrate that, contrary to common belief, opposite helicity twists do not lead to significant reconnection in such a coronal system, whereas twists with the same sense of helicity do produce substantial reconnection. Furthermore, we find that for a given amount of helicity injected into the corona, the evolution of the magnetic shear is insensitive to whether the pattern of driving photospheric motions is fixed or quasi-random. In all cases, the shear propagates via reconnection to the boundary of the flow region while the total magnetic helicity is conserved, as predicted by the model. We discuss the implications of our results for solar observations and for future, more realistic simulations of the helicity condensation process.« less

Sequence and conformational preferences at termini of α-helices in membrane proteins: role of the helix environment.

PubMed

Shelar, Ashish; Bansal, Manju

2014-12-01

α-Helices are amongst the most common secondary structural elements seen in membrane proteins and are packed in the form of helix bundles. These α-helices encounter varying external environments (hydrophobic, hydrophilic) that may influence the sequence preferences at their N and C-termini. The role of the external environment in stabilization of the helix termini in membrane proteins is still unknown. Here we analyze α-helices in a high-resolution dataset of integral α-helical membrane proteins and establish that their sequence and conformational preferences differ from those in globular proteins. We specifically examine these preferences at the N and C-termini in helices initiating/terminating inside the membrane core as well as in linkers connecting these transmembrane helices. We find that the sequence preferences and structural motifs at capping (Ncap and Ccap) and near-helical (N' and C') positions are influenced by a combination of features including the membrane environment and the innate helix initiation and termination property of residues forming structural motifs. We also find that a large number of helix termini which do not form any particular capping motif are stabilized by formation of hydrogen bonds and hydrophobic interactions contributed from the neighboring helices in the membrane protein. We further validate the sequence preferences obtained from our analysis with data from an ultradeep sequencing study that identifies evolutionarily conserved amino acids in the rat neurotensin receptor. The results from our analysis provide insights for the secondary structure prediction, modeling and design of membrane proteins. © 2014 Wiley Periodicals, Inc.

The Great Solar Active Region NOAA 12192: Helicity Transport, Filament Formation, and Impact on the Polar Field

DOE Office of Scientific and Technical Information (OSTI.GOV)

McMaken, Tyler C.; Petrie, Gordon J. D., E-mail: tmcmaken@gmail.com, E-mail: gpetrie@noao.edu

The solar active region (AR), NOAA 12192, appeared in 2014 October as the largest AR in 24 years. Here we examine the counterintuitive nature of two diffusion-driven processes in the region: the role of helicity buildup in the formation of a major filament, and the relationship between the effects of supergranular diffusion and meridional flow on the AR and on the polar field. Quantitatively, calculations of current helicity and magnetic twist from Helioseismic and Magnetic Imager (HMI) vector magnetograms indicate that, though AR 12192 emerged with negative helicity, positive helicity from subsequent flux emergence, consistent with the hemispheric sign-preference ofmore » helicity, increased over time within large-scale, weak-field regions such as those near the polarity inversion line (PIL). Morphologically, Atmospheric Imaging Assembly observations of filament barbs, sigmoidal patterns, and bases of Fe xii stalks initially exhibited signatures of negative helicity, and the long filament that subsequently formed had a strong positive helicity consistent with the helicity buildup along the PIL. We find from full-disk HMI magnetograms that AR 12192's leading positive flux was initially closer to the equator but, owing either to the region’s magnetic surroundings or to its asymmetric flux density distribution, was transported poleward more quickly on average than its trailing negative flux, contrary to the canonical pattern of bipole flux transport. This behavior caused the AR to have a smaller effect on the polar fields than expected and enabled the formation of the very long neutral line where the filament formed.« less

Origins of the helical wrapping of phenyleneethynylene polymers about single-walled carbon nanotubes.

PubMed

Von Bargen, Christopher D; MacDermaid, Christopher M; Lee, One-Sun; Deria, Pravas; Therien, Michael J; Saven, Jeffery G

2013-10-24

The highly charged, conjugated polymer poly[p-{2,5-bis(3-propoxysulfonicacidsodiumsalt)}phenylene]ethynylene (PPES) has been shown to wrap single-wall carbon nanotubes (SWNTs), adopting a robust helical superstructure. Surprisingly, PPES adopts a helical rather than a linear conformation when adhered to SWNTs. The complexes formed by PPES and related polymers upon helical wrapping of a SWNT are investigated using atomistic molecular dynamics (MD) simulations in the presence and absence of aqueous solvent. In simulations of the PPES/SWNT system in an aqueous environment, PPES spontaneously takes on a helical conformation. A potential of mean force, ΔA(ξ), is calculated as a function of ξ, the component of the end-to-end vector of the polymer chain projected on the SWNT axis; ξ is a monotonic function of the polymer's helical pitch. ΔA(ξ) provides a means to quantify the relative free energies of helical conformations of the polymer when wrapped about the SWNT. The aqueous system possesses a global minimum in ΔA(ξ) at the experimentally observed value of the helical pitch. The presence of this minimum is associated with preferred side chain conformations, where the side chains adopt conformations that provide van der Waals contact between the tubes and the aliphatic components of the side chains, while exposing the anionic sulfonates for aqueous solvation. The simulations provide a free energy estimate of a 0.2 kcal/mol/monomer preference for the helical over the linear conformation of the PPES/SWNT system in an aqueous environment.

Global well-posedness of three-dimensional Navier-Stokes equations with partial viscosity under helical symmetry

NASA Astrophysics Data System (ADS)

Liu, Jitao; Niu, Dongjuan

2017-06-01

In this paper, we investigate the global well-posedness of three-dimensional Navier-Stokes equations with horizontal viscosity under a special symmetric structure: helical symmetry. More precisely, by a revised Ladyzhenskaya-type inequality and utilizing the behavior of helical flows, we prove the global existence and uniqueness of weak and strong solutions to the three-dimensional helical flows. Our result reveals that for the issue of global well-posedness of the viscous helical flows, the horizontal viscosity plays the important role. To some extent, our work can be seen as a generalization of the result by Mahalov et al. (Arch Ration Mech Anal 112(3):193-222, 1990).

Numerical analysis on a passive chaotic micromixer with helical microchannel.

PubMed

Wang, Ruijin; Lin, Jianzhong

2006-01-01

In order to improve the mixing efficiency, the diffusion and mixing of species in the helical micro-mixer are simulated numerically. The results show that the mixing efficiency in the helical micromixer is much higher than that in the straight micro-channel and obviously higher than that in the serpentine micro-channel when Reynolds number is low. At high Reynolds number, even though the mixing efficiency in the helical micro-mixer is still much higher than that in the straight micro-channel, no obvious difference of mixing efficiency in the helical micro-mixer and serpentine micro-channel is found. The conclusions are helpful to optimize the structure of the micro-mixer.

Helicity amplitudes for QCD with massive quarks

NASA Astrophysics Data System (ADS)

Ochirov, Alexander

2018-04-01

The novel massive spinor-helicity formalism of Arkani-Hamed, Huang and Huang provides an elegant way to calculate scattering amplitudes in quantum chromodynamics for arbitrary quark spin projections. In this note we compute two families of tree-level QCD amplitudes with one massive quark pair and n - 2 gluons. The two cases include all gluons with identical helicity and one opposite-helicity gluon being color-adjacent to one of the quarks. Our results naturally incorporate the previously known amplitudes for both quark spins quantized along one of the gluonic momenta. In the all-multiplicity formulae presented here the spin quantization axes can be tuned at will, which includes the case of the definite-helicity quark states.

Magnetic helicity in emerging solar active regions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Y.; Hoeksema, J. T.; Bobra, M.

Using vector magnetic field data from the Helioseismic and Magnetic Imager instrument aboard the Solar Dynamics Observatory, we study magnetic helicity injection into the corona in emerging active regions (ARs) and examine the hemispheric helicity rule. In every region studied, photospheric shearing motion contributes most of the helicity accumulated in the corona. In a sample of 28 emerging ARs, 17 follow the hemisphere rule (61% ± 18% at a 95% confidence interval). Magnetic helicity and twist in 25 ARs (89% ± 11%) have the same sign. The maximum magnetic twist, which depends on the size of an AR, is inferredmore » in a sample of 23 emerging ARs with a bipolar magnetic field configuration.« less

Pyrolysis of Helical Coordination Polymers for Metal-Sulfide-Based Helices with Broadband Chiroptical Activity.

PubMed

Hirai, Kenji; Yeom, Bongjun; Sada, Kazuki

2017-06-27

Fabrication of chiroptical materials with broadband response in the visible light region is vital to fully realize their potential applications. One way to achieve broadband chiroptical activity is to fabricate chiral nanostructures from materials that exhibit broadband absorption in the visible light region. However, the compounds used for chiroptical materials have predominantly been limited to materials with narrowband spectral response. Here, we synthesize Ag 2 S-based nanohelices derived from helical coordination polymers. The right- and left-handed coordination helices used as precursors are prepared from l- and d-glutathione with Ag + and a small amount of Cu 2+ . The pyrolysis of the coordination helices yields right- and left-handed helices of Cu 0.12 Ag 1.94 S/C, which exhibit chiroptical activity spanning the entire visible light region. Finite element method simulations substantiate that the broadband chiroptical activity is attributed to synergistic broadband light absorption and light scattering. Furthermore, another series of Cu 0.10 Ag 1.90 S/C nanohelices are synthesized by choosing the l- or d-Glu-Cys as starting materials. The pitch length of nanohelicies is controlled by changing the peptides, which alters their chiroptical properties. The pyrolysis of coordination helices enables one to fabricate helical Ag 2 S-based materials that enable broadband chiroptical activity but have not been explored owing to the lack of synthetic routes.

The L49F mutation in alpha erythroid spectrin induces local disorder in the tetramer association region: Fluorescence and molecular dynamics studies of free and bound alpha spectrin

PubMed Central

Song, Yuanli; Pipalia, Nina H; Fung, L W-M

2009-01-01

The bundling of the N-terminal, partial domain helix (Helix C′) of human erythroid α-spectrin (αI) with the C-terminal, partial domain helices (Helices A′ and B′) of erythroid β-spectrin (βI) to give a spectrin pseudo structural domain (triple helical bundle A′B′C′) has long been recognized as a crucial step in forming functional spectrin tetramers in erythrocytes. We have used apparent polarity and Stern–Volmer quenching constants of Helix C′ of αI bound to Helices A′ and B′ of βI, along with previous NMR and EPR results, to propose a model for the triple helical bundle. This model was used as the input structure for molecular dynamics simulations for both wild type (WT) and αI mutant L49F. The simulation output structures show a stable helical bundle for WT, but not for L49F. In WT, four critical interactions were identified: two hydrophobic clusters and two salt bridges. However, in L49F, the region downstream of Helix C′ was unable to assume a helical conformation and one critical hydrophobic cluster was disrupted. Other molecular interactions critical to the WT helical bundle were also weakened in L49F, possibly leading to the lower tetramer levels observed in patients with this mutation-induced blood disorder. PMID:19593814

Magnetic Helicity Estimations in Models and Observations of the Solar Magnetic Field. III. Twist Number Method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guo, Y.; Pariat, E.; Moraitis, K.

We study the writhe, twist, and magnetic helicity of different magnetic flux ropes, based on models of the solar coronal magnetic field structure. These include an analytical force-free Titov–Démoulin equilibrium solution, non-force-free magnetohydrodynamic simulations, and nonlinear force-free magnetic field models. The geometrical boundary of the magnetic flux rope is determined by the quasi-separatrix layer and the bottom surface, and the axis curve of the flux rope is determined by its overall orientation. The twist is computed by the Berger–Prior formula, which is suitable for arbitrary geometry and both force-free and non-force-free models. The magnetic helicity is estimated by the twistmore » multiplied by the square of the axial magnetic flux. We compare the obtained values with those derived by a finite volume helicity estimation method. We find that the magnetic helicity obtained with the twist method agrees with the helicity carried by the purely current-carrying part of the field within uncertainties for most test cases. It is also found that the current-carrying part of the model field is relatively significant at the very location of the magnetic flux rope. This qualitatively explains the agreement between the magnetic helicity computed by the twist method and the helicity contributed purely by the current-carrying magnetic field.« less

Results of auricular helical rim reconstruction with post-auricular tube flap.

PubMed

Iljin, Aleksandra; Lewandowicz, Edward; Antoszewski, Bogusław; Zieliński, Tomasz

2016-01-01

The aim of the study was to present our experience with post-auricular tube flap (ptf) and clinical evaluation of the results following auricular helical rim reconstruction with this technique in patients after trauma. We analyzed the results in 12 patients who underwent three-staged auricular helical rim reconstruction with ptf following trauma in the Department of Plastic, Reconstructive and Aesthetic Surgery between 2005-2014. The patients were followed-up for at least 1 year. We evaluated early and long-term results after surgery including plastic surgeon's and patient's opinion. Postoperative results were satisfactory (very good) in 10 cases, both in the opinion of the plastic surgeon and patients. Transient venous congestion of the helix occurred in two cases (16.6%). This complication did not have any influence on estimation of the results after surgery. Delayed wound healing in the poles of the reconstructed helical edge, as well as non-aesthetic helical scars with imperfections of helical rim, were seen in another two patients (16.6%). 1. Post-auricular tube flap reconstructions after helical rim trauma allowed for complete restoration of contour, size and orientation of the helix and the whole operated ear, which confirms the efficiency of the applied technique. 2. Reconstructive surgery with post-auricular tube flap in patients with auricular helical rim defects contributed to postoperative satisfaction in both patients and doctors' estimations.

HELICITY CONSERVATION IN NONLINEAR MEAN-FIELD SOLAR DYNAMO

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pipin, V. V.; Sokoloff, D. D.; Zhang, H.

It is believed that magnetic helicity conservation is an important constraint on large-scale astrophysical dynamos. In this paper, we study a mean-field solar dynamo model that employs two different formulations of the magnetic helicity conservation. In the first approach, the evolution of the averaged small-scale magnetic helicity is largely determined by the local induction effects due to the large-scale magnetic field, turbulent motions, and the turbulent diffusive loss of helicity. In this case, the dynamo model shows that the typical strength of the large-scale magnetic field generated by the dynamo is much smaller than the equipartition value for the magneticmore » Reynolds number 10{sup 6}. This is the so-called catastrophic quenching (CQ) phenomenon. In the literature, this is considered to be typical for various kinds of solar dynamo models, including the distributed-type and the Babcock-Leighton-type dynamos. The problem can be resolved by the second formulation, which is derived from the integral conservation of the total magnetic helicity. In this case, the dynamo model shows that magnetic helicity propagates with the dynamo wave from the bottom of the convection zone to the surface. This prevents CQ because of the local balance between the large-scale and small-scale magnetic helicities. Thus, the solar dynamo can operate in a wide range of magnetic Reynolds numbers up to 10{sup 6}.« less

Dispersion Characteristics of a Helix Loaded Waveguide.

DTIC Science & Technology

1985-09-01

be employed to increase the bandwidth of gyroton amplifiers. The structure consists of helical wires contained concentrially 6. in a cylindrical...bandwidth of gyroton amplifiers. The structure consists of helical wires contained concentrially in a cylindrical conductor. The helical wires are close

Simplified Fabrication of Helical Copper Antennas

NASA Technical Reports Server (NTRS)

Petro, Andrew

2006-01-01

A simplified technique has been devised for fabricating helical antennas for use in experiments on radio-frequency generation and acceleration of plasmas. These antennas are typically made of copper (for electrical conductivity) and must have a specific helical shape and precise diameter.

Magnetic Helicity and the Solar Dynamo

NASA Technical Reports Server (NTRS)

Canfield, Richard C.

1997-01-01

The objective of this investigation is to open a new window into the solar dynamo, convection, and magnetic reconnection through measurement of the helicity density of magnetic fields in the photosphere and tracing of large-scale patterns of magnetic helicity in the corona.

Recognizing asymmetry in pseudo-symmetry; structural insights into the interaction between amphipathic α-helices and X-bundle proteins.

PubMed

Haddad, John Faissal; Yang, Yidai; Yeung, Sylvain; Couture, Jean-François

2017-11-01

An α-helix bundle is a small and compact protein fold always composed of more than 2 α-helices that typically run nearly parallel or antiparallel to each other. The repertoire of arrangements of α-helix bundle is such that these domains bind to a myriad of molecular entities including DNA, RNA, proteins and small molecules. A special instance of α-helical bundle is the X-type in which the arrangement of two α-helices interact at 45° to form an X. Among those, some X-helix bundle proteins bind to the hydrophobic section of an amphipathic α-helix in a seemingly orientation and sequence specific manner. In this review, we will compare the binding mode of amphipathic α-helices to X-helix bundle and α-helical bundle proteins. From these structures, we will highlight potential regulatory paradigms that may control the specific interactions of X-helix bundle proteins to amphipathic α-helices. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. Copyright © 2017 Elsevier B.V. All rights reserved.

Matching into the Helical Bunch Coalescing Channel for a High Luminosity Muon Collider

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sy, Amy; Ankenbrandt, Charles; Derbenev, Yaroslav

2015-09-01

For high luminosity in a muon collider, muon bunches that have been cooled in the six-dimensional helical cooling channel (HCC) must be merged into a single bunch and further cooled in preparation for acceleration and transport to the collider ring. The helical bunch coalescing channel has been previously simulated and provides the most natural match from helical upstream and downstream subsystems. This work focuses on the matching from the exit of the multiple bunch HCC into the start of the helical bunch coalescing channel. The simulated helical matching section simultaneously matches the helical spatial period lambda in addition to providingmore » the necessary acceleration for efficient bunch coalescing. Previous studies assumed that the acceleration of muon bunches from p=209.15 MeV/c to 286.816 MeV/c and matching of lambda from 0.5 m to 1.0 m could be accomplished with zero particle losses and zero emittance growth in the individual bunches. This study demonstrates nonzero values for both particle loss and emittance growth, and provides considerations for reducing these adverse effects to best preserve high luminosity.« less

HIT-SI Injector Voltage Measurements Using Injector Langmuir Probes

NASA Astrophysics Data System (ADS)

Aboul Hosn, Rabih; Smith, Roger; Jarboe, Thomas

2006-10-01

A pair of Langmuir probe arrays have been designed and built to measure floating potentials of the plasma at the injector mouth of the HIT-SI device. The Helicity Injected Torus using Steady Inductive Helicity Injection (HIT-SI) [1,2] is a ``bow tie'' spheromak using an electrodeless formation and sustainment concept. HIT-SI is powered by two inductive helicity injectors operated in quadrature to maintain a constant helicity injection rate. The electric probes consist of an array of four floating potential Langmuir probes measuring the voltage distribution in each injector from the shell to midpoint of the injector mouth. The probe measurements combine to determine the part of the injector loop voltage driving the n = 0 spheromak equilibrium region. Preliminary data suggest the spheromak voltage is the loop voltage minus the nearly constant injector voltage of 150-180 volts. These probe data will be used to calculate the helicity decay time of the spheromak. [1] T. R. Jarboe. Steady inductive helicity injection and its application to a high-beta spheromak. Fusion Technology, 36(1):85--91, July 1999. [2] P.E.Sieck et al., ``Demonstration of Steady Inductive Helicity Injection'', Nuc. Fusion, in press (2006).

Biomimetic Hierarchical Assembly of Helical Supraparticles from Chiral Nanoparticles

DOE PAGES

Zhou, Yunlong; Marson, Ryan L.; van Anders, Greg; ...

2016-02-22

Chiroptical materials found in butterflies, beetles, stomatopod crustaceans, and other creatures are attributed to biocomposites with helical motifs and multiscale hierarchical organization. These structurally sophisticated materials self-assemble from primitive nanoscale building blocks, a process that is simpler and more energy efficient than many top-down methods currently used to produce similarly sized three-dimensional materials. In this paper, we report that molecular-scale chirality of a CdTe nanoparticle surface can be translated to nanoscale helical assemblies, leading to chiroptical activity in the visible electromagnetic range. Chiral CdTe nanoparticles coated with cysteine self-organize around Te cores to produce helical supraparticles. D-/L-Form of the aminomore » acid determines the dominant left/right helicity of the supraparticles. Coarse-grained molecular dynamics simulations with a helical pair-potential confirm the assembly mechanism and the origin of its enantioselectivity, providing a framework for engineering three-dimensional chiral materials by self-assembly. Finally, the helical supraparticles further self-organize into lamellar crystals with liquid crystalline order, demonstrating the possibility of hierarchical organization and with multiple structural motifs and length scales determined by molecular-scale asymmetry of nanoparticle interactions.« less

Self-assembly of hard helices: a rich and unconventional polymorphism.

PubMed

Kolli, Hima Bindu; Frezza, Elisa; Cinacchi, Giorgio; Ferrarini, Alberta; Giacometti, Achille; Hudson, Toby S; De Michele, Cristiano; Sciortino, Francesco

2014-11-07

Hard helices can be regarded as a paradigmatic elementary model for a number of natural and synthetic soft matter systems, all featuring the helix as their basic structural unit, from natural polynucleotides and polypeptides to synthetic helical polymers, and from bacterial flagella to colloidal helices. Here we present an extensive investigation of the phase diagram of hard helices using a variety of methods. Isobaric Monte Carlo numerical simulations are used to trace the phase diagram; on going from the low-density isotropic to the high-density compact phases a rich polymorphism is observed, exhibiting a special chiral screw-like nematic phase and a number of chiral and/or polar smectic phases. We present full characterization of the latter, showing that they have unconventional features, ascribable to the helical shape of the constituent particles. Equal area construction is used to locate the isotropic-to-nematic phase transition, and the results are compared with those stemming from an Onsager-like theory. Density functional theory is also used to study the nematic-to-screw-nematic phase transition; within the simplifying assumption of perfectly parallel helices, we compare different levels of approximation, that is second- and third-virial expansions and a Parsons-Lee correction.

Free-fall dynamics of a pair of rigidly linked disks

NASA Astrophysics Data System (ADS)

Kim, Taehyun; Chang, Jaehyeock; Kim, Daegyoum

2018-03-01

We investigate experimentally the free-fall motion of a pair of identical disks rigidly connected to each other. The three-dimensional coordinates of the pair of falling disks were constructed to quantitatively describe its trajectory, and the flow structure formed by the disk pair was identified by using dye visualization. The rigidly linked disk pair exhibits a novel falling pattern that creates a helical path with a conical configuration in which the lower disk rotates in a wider radius than the upper disk with respect to a vertical axis. The helical motion occurs consistently for the range of disk separation examined in this study. The dye visualization reveals that a strong, noticeable helical vortex core is generated from the outer tip of the lower disk during the helical motion. With an increasing length ratio, which is the ratio of the disk separation to the diameter of the disks, the nutation angle and the rate of change in the precession angle that characterize the combined helical and conical kinematics decrease linearly, whereas the pitch of the helical path increases linearly. Although all disk pairs undergo this helical motion, the horizontal-drift patterns of the disk pair depend on the length ratio.

Dipole Alignment in Rotating MHD Turbulence

NASA Technical Reports Server (NTRS)

Shebalin, John V.; Fu, Terry; Morin, Lee

2012-01-01

We present numerical results from long-term CPU and GPU simulations of rotating, homogeneous, magnetohydrodynamic (MHD) turbulence, and discuss their connection to the spherically bounded case. We compare our numerical results with a statistical theory of geodynamo action that has evolved from the absolute equilibrium ensemble theory of ideal MHD turbulence, which is based on the ideal MHD invariants are energy, cross helicity and magnetic helicity. However, for rotating MHD turbulence, the cross helicity is no longer an exact invariant, although rms cross helicity becomes quasistationary during an ideal MHD simulation. This and the anisotropy imposed by rotation suggests an ansatz in which an effective, nonzero value of cross helicity is assigned to axisymmetric modes and zero cross helicity to non-axisymmetric modes. This hybrid statistics predicts a large-scale quasistationary magnetic field due to broken ergodicity , as well as dipole vector alignment with the rotation axis, both of which are observed numerically. We find that only a relatively small value of effective cross helicity leads to the prediction of a dipole moment vector that is closely aligned (less than 10 degrees) with the rotation axis. We also discuss the effect of initial conditions, dissipation and grid size on the numerical simulations and statistical theory.

Space vehicle electromechanical system and helical antenna winding fixture

DOE Office of Scientific and Technical Information (OSTI.GOV)

Judd, Stephen; Dallmann, Nicholas; Guenther, David

A space vehicle electromechanical system may employ an architecture that enables convenient and practical testing, reset, and retesting of solar panel and antenna deployment on the ground. A helical antenna winding fixture may facilitate winding and binding of the helical antenna.

Magnetic helical micromachines.

PubMed

Peyer, Kathrin E; Tottori, Soichiro; Qiu, Famin; Zhang, Li; Nelson, Bradley J

2013-01-02

Helical microrobots have the potential to be used in a variety of application areas, such as in medical procedures, cell biology, or lab-on-a-chip. They are powered and steered wirelessly using low-strength rotating magnetic fields. The helical shape of the device allows propulsion through numerous types of materials and fluids, from tissue to different types of bodily fluids. Helical propulsion is suitable for pipe flow conditions or for 3D swimming in open fluidic environments. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Pulling helices inside bacteria: imperfect helices and rings

NASA Astrophysics Data System (ADS)

Rutenberg, Andrew; Allard, Jun

2009-03-01

We study steady-state configurations of intrinsically-straight elastic filaments constrained within rod-shaped bacteria that have applied forces distributed along their length. Perfect steady-state helices result from axial or azimuthal forces applied at filament ends, however azimuthal forces are required for the small pitches observed for MreB filaments within bacteria. Helix-like configurations can result from distributed forces, including co-existence between rings and imperfect helices. Levels of expression and/or bundling of the polymeric protein could mediate this co-existence.

Pulling Helices inside Bacteria: Imperfect Helices and Rings

NASA Astrophysics Data System (ADS)

Allard, Jun F.; Rutenberg, Andrew D.

2009-04-01

We study steady-state configurations of intrinsically-straight elastic filaments constrained within rod-shaped bacteria that have applied forces distributed along their length. Perfect steady-state helices result from axial or azimuthal forces applied at filament ends, however azimuthal forces are required for the small pitches observed for MreB filaments within bacteria. Helix-like configurations can result from distributed forces, including coexistence between rings and imperfect helices. Levels of expression and/or bundling of the polymeric protein could mediate this coexistence.

Note on the helicity decomposition of spin and orbital optical currents

NASA Astrophysics Data System (ADS)

Aiello, Andrea; Berry, M. V.

2015-06-01

In the helicity representation, the Poynting vector (current) for a monochromatic optical field, when calculated using either the electric or the magnetic field, separates into right-handed and left-handed contributions, with no cross-helicity contributions. Cross-helicity terms do appear in the orbital and spin contributions to the current. But when the electric and magnetic formulas are averaged (‘electric-magnetic democracy’), these terms cancel, restoring the separation into right-handed and left-handed currents for orbital and spin separately.

Scale Dependence of Magnetic Helicity in the Solar Wind

NASA Technical Reports Server (NTRS)

Brandenburg, Axel; Subramanian, Kandaswamy; Balogh, Andre; Goldstein, Melvyn L.

2011-01-01

We determine the magnetic helicity, along with the magnetic energy, at high latitudes using data from the Ulysses mission. The data set spans the time period from 1993 to 1996. The basic assumption of the analysis is that the solar wind is homogeneous. Because the solar wind speed is high, we follow the approach first pioneered by Matthaeus et al. by which, under the assumption of spatial homogeneity, one can use Fourier transforms of the magnetic field time series to construct one-dimensional spectra of the magnetic energy and magnetic helicity under the assumption that the Taylor frozen-in-flow hypothesis is valid. That is a well-satisfied assumption for the data used in this study. The magnetic helicity derives from the skew-symmetric terms of the three-dimensional magnetic correlation tensor, while the symmetric terms of the tensor are used to determine the magnetic energy spectrum. Our results show a sign change of magnetic helicity at wavenumber k approximately equal to 2AU(sup -1) (or frequency nu approximately equal to 2 microHz) at distances below 2.8AU and at k approximately equal to 30AU(sup -1) (or nu approximately equal to 25 microHz) at larger distances. At small scales the magnetic helicity is positive at northern heliographic latitudes and negative at southern latitudes. The positive magnetic helicity at small scales is argued to be the result of turbulent diffusion reversing the sign relative to what is seen at small scales at the solar surface. Furthermore, the magnetic helicity declines toward solar minimum in 1996. The magnetic helicity flux integrated separately over one hemisphere amounts to about 10(sup 45) Mx(sup 2) cycle(sup -1) at large scales and to a three times lower value at smaller scales.

Contribution of proline to the pre-structuring tendency of transient helical secondary structure elements in intrinsically disordered proteins.

PubMed

Lee, Chewook; Kalmar, Lajos; Xue, Bin; Tompa, Peter; Daughdrill, Gary W; Uversky, Vladimir N; Han, Kyou-Hoon

2014-03-01

IDPs function without relying on three-dimensional structures. No clear rationale for such a behavior is available yet. PreSMos are transient secondary structures observed in the target-free IDPs and serve as the target-binding "active" motifs in IDPs. Prolines are frequently found in the flanking regions of PreSMos. Contribution of prolines to the conformational stability of the helical PreSMos in IDPs is investigated. MD simulations are performed for several IDP segments containing a helical PreSMo and the flanking prolines. To measure the influence of flanking-prolines on the structural content of a helical PreSMo calculations were done for wild type as well as for mutant segments with Pro→Asp, His, Lys, or Ala. The change in the helicity due to removal of a proline was measured both for the PreSMo region and for the flanking regions. The α-helical content in ~70% of the helical PreSMos at the early stage of simulation decreases due to replacement of an N-terminal flanking proline by other residues whereas the helix content in nearly all PreSMos increases when the same replacements occur at the C-terminal flanking region. The helix destabilizing/terminating role of the C-terminal flanking prolines is more pronounced than the helix promoting effect of the N-terminal flanking prolines. This work represents a novel example demonstrating that a proline is encoded in an IDP with a defined purpose. The helical PreSMos presage their target-bound conformations. As they most likely mediate IDP-target binding via conformational selection their helical content can be an important feature for IDP function. Copyright © 2013 Elsevier B.V. All rights reserved.

Decay of helical and nonhelical magnetic knots

NASA Astrophysics Data System (ADS)

Candelaresi, Simon; Brandenburg, Axel

2011-07-01

We present calculations of the relaxation of magnetic field structures that have the shape of particular knots and links. A set of helical magnetic flux configurations is considered, which we call n-foil knots of which the trefoil knot is the most primitive member. We also consider two nonhelical knots; namely, the Borromean rings as well as a single interlocked flux rope that also serves as the logo of the Inter-University Centre for Astronomy and Astrophysics in Pune, India. The field decay characteristics of both configurations is investigated and compared with previous calculations of helical and nonhelical triple-ring configurations. Unlike earlier nonhelical configurations, the present ones cannot trivially be reduced via flux annihilation to a single ring. For the n-foil knots the decay is described by power laws that range form t-2/3 to t-1/3, which can be as slow as the t-1/3 behavior for helical triple-ring structures that were seen in earlier work. The two nonhelical configurations decay like t-1, which is somewhat slower than the previously obtained t-3/2 behavior in the decay of interlocked rings with zero magnetic helicity. We attribute the difference to the creation of local structures that contain magnetic helicity which inhibits the field decay due to the existence of a lower bound imposed by the realizability condition. We show that net magnetic helicity can be produced resistively as a result of a slight imbalance between mutually canceling helical pieces as they are being driven apart. We speculate that higher order topological invariants beyond magnetic helicity may also be responsible for slowing down the decay of the two more complicated nonhelical structures mentioned above.

Spiroplasma swim by a processive change in body helicity.

NASA Astrophysics Data System (ADS)

Shaevitz, Joshua

2006-03-01

Microscopic organisms must rely on very different strategies than their macroscopic counterparts to swim through liquid. To date, the best understood method for prokaryotic swimming employs the rotation of flagella. I will present data that Spiroplasma, tiny helical bacteria that infect plants and insects, use a very different approach. By measuring cell kinematics during free swimming, we find that propulsion is generated by the propagation of kink pairs down the length of the cell body. A processive change in the helicity of the body creates these waves and enables directional movement. Unlike the motion of other helical swimmers such as Spirochetes, Spiroplasma swimming velocity increases with increasing viscosity. In addition, cell morphological parameters such as helical pitch and cell length influence swimming velocity.

Interaction of anesthetic molecules with α-helix and polyproline II extended helix of long-chain poly-L-lysine

NASA Astrophysics Data System (ADS)

Cieślik-Boczula, Katarzyna; Rospenk, Maria

2018-01-01

The effect of halothane, enflurane, sevoflurane, and isoflurane molecules, as volatile anesthetics, on the α-helices and polyproline II extended helices (PPII) of long-chain poly-L-lysine (PLL) were studied using Fourier-transform infrared and vibrational circular dichroism spectroscopy. Uncharged and charged α-helices, as well as charged extended PPII helices, were subjected to anesthetic actions in solvents with different pD values or methanol to water ratios. A crucial factor responsible for hindering the anesthetic-PLL interactions is shown to be the ionization of amino groups of the PLL side chains. The α-helix to β-sheet transition was triggered only for the uncharged α-helical structures of PLL by the nonpolar anesthetics under study.

Taming instability of magnetic field in chiral medium

NASA Astrophysics Data System (ADS)

Tuchin, Kirill

2018-01-01

Magnetic field is unstable in a medium with time-independent chiral conductivity. Owing to the chiral anomaly, the electromagnetic field and the medium exchange helicity which results in time-evolution of the chiral conductivity. Using the fastest growing momentum and helicity state of the vector potential as an ansatz, the time-evolution of the chiral conductivity and magnetic field is solved analytically. The solution for the hot and cold equations of state shows that the magnetic field does not develop an instability due to helicity conservation. Moreover, as a function of time, it develops a peak only if a significant part of the initial helicity is stored in the medium. The initial helicity determines the height and position of the peak.

Multilayer DNA origami packed on hexagonal and hybrid lattices.

PubMed

Ke, Yonggang; Voigt, Niels V; Gothelf, Kurt V; Shih, William M

2012-01-25

"Scaffolded DNA origami" has been proven to be a powerful and efficient approach to construct two-dimensional or three-dimensional objects with great complexity. Multilayer DNA origami has been demonstrated with helices packing along either honeycomb-lattice geometry or square-lattice geometry. Here we report successful folding of multilayer DNA origami with helices arranged on a close-packed hexagonal lattice. This arrangement yields a higher density of helical packing and therefore higher resolution of spatial addressing than has been shown previously. We also demonstrate hybrid multilayer DNA origami with honeycomb-lattice, square-lattice, and hexagonal-lattice packing of helices all in one design. The availability of hexagonal close-packing of helices extends our ability to build complex structures using DNA nanotechnology. © 2011 American Chemical Society

Matter-induced magnetic moment and neutrino helicity rotation in external fields

NASA Astrophysics Data System (ADS)

Ternov, Alexei I.

2016-11-01

The induced magnetic moment that arises due to the propagation of neutrinos in a dispersive medium can affect the dynamics of the neutrino spin in an external electromagnetic field. In particular, it can cause a helicity flip of a massive neutrino in a magnetic field. In some astrophysical media, this helicity transition mechanism could be more effective than a similar process caused by the anomalous magnetic moment of the neutrino. If the neutrino energy is sufficiently high, the two helicity transition mechanisms mentioned above can compensate each other. Then a helicity flip in an external field will not occur. Calculations are carried out using both the methods of relativistic quantum mechanics and the quasiclassical Bargmann-Michel-Telegdi equation.

Enhanced performance of core-shell structured polyaniline at helical carbon nanotube hybrids for ammonia gas sensor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tian, Xin; Wang, Qiang; Chen, Xiangnan

2014-11-17

A core-shell structured hybrid of polyaniline at helical carbon nanotubes was synthesized using in situ polymerization, which the helical carbon nanotubes were uniformly surrounded by a layer of polyaniline nanorods array. More interestingly, repeatable responses were experimentally observed that the sensitivity to ammonia gas of the as-prepared helical shaped core-shell hybrid displays an enhancement of more than two times compared to those of only polyaniline or helical carbon nanotubes sensors because of the peculiar structures with high surface area. This kind of hybrid comprising nanorod arrays of conductive polymers covering carbon nanotubes and related structures provide a potential in sensorsmore » of trace gas detection for environmental monitoring and safety forecasting.« less

Evolution of hydromagnetic turbulence from the electroweak phase transition

NASA Astrophysics Data System (ADS)

Brandenburg, Axel; Kahniashvili, Tina; Mandal, Sayan; Pol, Alberto Roper; Tevzadze, Alexander G.; Vachaspati, Tanmay

2017-12-01

We present new simulations of decaying hydromagnetic turbulence for a relativistic equation of state relevant to the early Universe. We compare helical and nonhelical cases either with kinetically or magnetically dominated initial fields. Both kinetic and magnetic initial helicities lead to maximally helical magnetic fields after some time, but with different temporal decay laws. Both are relevant to the early Universe, although no mechanisms have yet been identified that produce magnetic helicity with strengths comparable to the big bang nucleosynthesis limit at scales comparable to the Hubble horizon at the electroweak phase transition. Nonhelical magnetically dominated fields could still produce picoGauss magnetic fields under most optimistic conditions. Only helical magnetic fields can potentially have nanoGauss strengths at scales up to 30 kpc today.

Orientational preferences of neighboring helices can drive ER insertion of a marginally hydrophobic transmembrane helix

PubMed Central

Öjemalm, Karin; Halling, Katrin K.; Nilsson, IngMarie; von Heijne, Gunnar

2013-01-01

Summary α-helical integral membrane proteins critically depend on the correct insertion of their transmembrane α-helices into the lipid bilayer for proper folding, yet a surprisingly large fraction of the transmembrane α-helices in multispanning integral membrane proteins are not sufficiently hydrophobic to insert into the target membrane by themselves. How can such marginally hydrophobic segments nevertheless form transmembrane helices in the folded structure? Here, we show that a transmembrane helix with a strong orientational preference (Ncyt-Clum or Nlum-Ccyt) can both increase and decrease the hydrophobicity threshold for membrane insertion of a neighboring, marginally hydrophobic helix. This effect helps explain the ‘missing hydrophobicity’ in polytopic membrane proteins. PMID:22281052

Propagation dynamics of Helical Hermite-Gaussian beams

NASA Astrophysics Data System (ADS)

López-Mariscal, Carlos; Gutiérrez-Vega, Julio C.

2007-09-01

We investigate theoretically and experimentally the propagation characteristics of the Helical Hermite-Gauss beams corresponding to the helical Ince-Gauss beams in the limit of infinite ellipticity. Particular attention is paid to the transverse irradiance structure, the orbital angular momentum density, and the vortex distribution.

Implementation of dispersion-free slow acoustic wave propagation and phase engineering with helical-structured metamaterials

PubMed Central

Zhu, Xuefeng; Li, Kun; Zhang, Peng; Zhu, Jie; Zhang, Jintao; Tian, Chao; Liu, Shengchun

2016-01-01

The ability to slow down wave propagation in materials has attracted significant research interest. A successful solution will give rise to manageable enhanced wave–matter interaction, freewheeling phase engineering and spatial compression of wave signals. The existing methods are typically associated with constructing dispersive materials or structures with local resonators, thus resulting in unavoidable distortion of waveforms. Here we show that, with helical-structured acoustic metamaterials, it is now possible to implement dispersion-free sound deceleration. The helical-structured metamaterials present a non-dispersive high effective refractive index that is tunable through adjusting the helicity of structures, while the wavefront revolution plays a dominant role in reducing the group velocity. Finally, we numerically and experimentally demonstrate that the helical-structured metamaterials with designed inhomogeneous unit cells can turn a normally incident plane wave into a self-accelerating beam on the prescribed parabolic trajectory. The helical-structured metamaterials will have profound impact to applications in explorations of slow wave physics. PMID:27198887

Peptide tessellation yields micrometre-scale collagen triple helices

NASA Astrophysics Data System (ADS)

Tanrikulu, I. Caglar; Forticaux, Audrey; Jin, Song; Raines, Ronald T.

2016-11-01

Sticky-ended DNA duplexes can associate spontaneously into long double helices; however, such self-assembly is much less developed with proteins. Collagen is the most prevalent component of the extracellular matrix and a common clinical biomaterial. As for natural DNA, the ~103-residue triple helices (~300 nm) of natural collagen are recalcitrant to chemical synthesis. Here we show how the self-assembly of short collagen-mimetic peptides (CMPs) can enable the fabrication of synthetic collagen triple helices that are nearly a micrometre in length. Inspired by the mathematics of tessellations, we derive rules for the design of single CMPs that self-assemble into long triple helices with perfect symmetry. Sticky ends thus created are uniform across the assembly and drive its growth. Enacting this design yields individual triple helices that, in length, match or exceed those in natural collagen and are remarkably thermostable, despite the absence of higher-order association. The symmetric assembly of CMPs provides an enabling platform for the development of advanced materials for medicine and nanotechnology.

Spin dynamics in helical molecules with nonlinear interactions

NASA Astrophysics Data System (ADS)

Díaz, E.; Albares, P.; Estévez, P. G.; Cerveró, J. M.; Gaul, C.; Diez, E.; Domínguez-Adame, F.

2018-04-01

It is widely admitted that the helical conformation of certain chiral molecules may induce a sizable spin selectivity observed in experiments. Spin selectivity arises as a result of the interplay between a helicity-induced spin–orbit coupling (SOC) and electric dipole fields in the molecule. From the theoretical point of view, different phenomena might affect the spin dynamics in helical molecules, such as quantum dephasing, dissipation and the role of metallic contacts. With a few exceptions, previous studies usually neglect the local deformation of the molecule about the carrier, but this assumption seems unrealistic to describe charge transport in molecular systems. We introduce an effective model describing the electron spin dynamics in a deformable helical molecule with weak SOC. We find that the electron–lattice interaction allows the formation of stable solitons such as bright solitons with well defined spin projection onto the molecule axis. We present a thorough study of these bright solitons and analyze their possible impact on the spin dynamics in deformable helical molecules.

Molecular Structure of a Helical ribbon in a Peptide Self-Assembly

NASA Astrophysics Data System (ADS)

Hwang, Wonmuk; Marini, Davide; Kamm, Roger D.; Zhang, Shuguang

2002-03-01

We have studied the molecular structure of nanometer scale helical ribbons observed during self-assembly of the peptide KFE8 (amino acid sequence: FKFEFKFE) (NanoLetters (2002, in press)). By analyzing the hydrogen bonding patterns between neighboring peptide backbones, we constructed a number of possible β-sheets. Using all possible combinations of these, we built helical ribbons with dimensions close to those found experimentally and performed molecular dynamics simulations to identify the most stable structure. Solvation effects were implemented by the analytic continuum electrostatics (ACE) model developed by Schaefer and Karplus (J. Phys. Chem. 100, 1578 (1996)). By applying electrostatic double layer theory, we incorporated the effect of pH by scaling the amount of charge on the sidechains. Our results suggest that the helical ribbon is comprised of a double β-sheet where the inner and the outer helices have distinct hydrogen bonding patterns. Our approach has general applicability to the study of helices formed by the self-assembly of β-sheet forming peptides with various amino acid sequences.

Helical edge states and fractional quantum Hall effect in a graphene electron-hole bilayer

NASA Astrophysics Data System (ADS)

Sanchez-Yamagishi, Javier D.; Luo, Jason Y.; Young, Andrea F.; Hunt, Benjamin M.; Watanabe, Kenji; Taniguchi, Takashi; Ashoori, Raymond C.; Jarillo-Herrero, Pablo

2017-02-01

Helical 1D electronic systems are a promising route towards realizing circuits of topological quantum states that exhibit non-Abelian statistics. Here, we demonstrate a versatile platform to realize 1D systems made by combining quantum Hall (QH) edge states of opposite chiralities in a graphene electron-hole bilayer at moderate magnetic fields. Using this approach, we engineer helical 1D edge conductors where the counterpropagating modes are localized in separate electron and hole layers by a tunable electric field. These helical conductors exhibit strong non-local transport signals and suppressed backscattering due to the opposite spin polarizations of the counterpropagating modes. Unlike other approaches used for realizing helical states, the graphene electron-hole bilayer can be used to build new 1D systems incorporating fractional edge states. Indeed, we are able to tune the bilayer devices into a regime hosting fractional and integer edge states of opposite chiralities, paving the way towards 1D helical conductors with fractional quantum statistics.

Flexible helical-axis stellarator

DOEpatents

Harris, Jeffrey H.; Hender, Timothy C.; Carreras, Benjamin A.; Cantrell, Jack L.; Morris, Robert N.

1988-01-01

An 1=1 helical winding which spirals about a conventional planar, circular central conductor of a helical-axis stellarator adds a significant degree of flexibility by making it possible to control the rotational transform profile and shear of the magnetic fields confining the plasma in a helical-axis stellarator. The toroidal central conductor links a plurality of toroidal field coils which are separately disposed to follow a helical path around the central conductor in phase with the helical path of the 1=1 winding. This coil configuration produces bean-shaped magnetic flux surfaces which rotate around the central circular conductor in the same manner as the toroidal field generating coils. The additional 1=1 winding provides flexible control of the magnetic field generated by the central conductor to prevent the formation of low-order resonances in the rotational transform profile which can produce break-up of the equilibrium magnetic surfaces. Further, this additional winding can deepen the magnetic well which together with the flexible control provides increased stability.

Fabrication and experimentation of FRP helical spring

NASA Astrophysics Data System (ADS)

Ekanthappa, J.; Shiva Shankar, G. S.; Amith, B. M.; Gagan, M.

2016-09-01

In present scenario, the automobile industry sector is showing increased interest in reducing the unsprung weight of the automobile & hence increasing the fuel Efficiency. One of the feasible sub systems of a vehicle where weight reduction may be attempted is vehicle- suspension system. Usage of composite material is a proven way to lower the component weight without any compromise in strength. The composite materials are having high specific strength, more elastic strain energy storage capacity in comparison with those of steel. Therefore, helical coil spring made of steel is replaceable by composite cylindrical helical coil spring. This research aims at preparing a re-usable mandrel (mould) of Mild steel, developing a setup for fabrication, fabrication of FRP helical spring using continuous glass fibers and Epoxy Resin (Polymer). Experimentation has been conducted on fabricated FRP helical spring to determine its strength parameters & for failure analysis. It is found that spring stiffness (K) of Glass/Epoxy helical-spring is greater than steel-coil spring with reduced weight.

Computation of Relative Magnetic Helicity in Spherical Coordinates

NASA Astrophysics Data System (ADS)

Moraitis, Kostas; Pariat, Étienne; Savcheva, Antonia; Valori, Gherardo

2018-06-01

Magnetic helicity is a quantity of great importance in solar studies because it is conserved in ideal magnetohydrodynamics. While many methods for computing magnetic helicity in Cartesian finite volumes exist, in spherical coordinates, the natural coordinate system for solar applications, helicity is only treated approximately. We present here a method for properly computing the relative magnetic helicity in spherical geometry. The volumes considered are finite, of shell or wedge shape, and the three-dimensional magnetic field is considered to be fully known throughout the studied domain. Testing of the method with well-known, semi-analytic, force-free magnetic-field models reveals that it has excellent accuracy. Further application to a set of nonlinear force-free reconstructions of the magnetic field of solar active regions and comparison with an approximate method used in the past indicates that the proposed method can be significantly more accurate, thus making our method a promising tool in helicity studies that employ spherical geometry. Additionally, we determine and discuss the applicability range of the approximate method.

Induced liquid-crystalline ordering in solutions of stiff and flexible amphiphilic macromolecules: Effect of mixture composition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Glagolev, Mikhail K.; Vasilevskaya, Valentina V., E-mail: vvvas@polly.phys.msu.ru; Khokhlov, Alexei R.

Impact of mixture composition on self-organization in concentrated solutions of stiff helical and flexible macromolecules was studied by means of molecular dynamics simulation. The macromolecules were composed of identical amphiphilic monomer units but a fraction f of macromolecules had stiff helical backbones and the remaining chains were flexible. In poor solvents the compacted flexible macromolecules coexist with bundles or filament clusters from few intertwined stiff helical macromolecules. The increase of relative content f of helical macromolecules leads to increase of the length of helical clusters, to alignment of clusters with each other, and then to liquid-crystalline-like ordering along a singlemore » direction. The formation of filament clusters causes segregation of helical and flexible macromolecules and the alignment of the filaments induces effective liquid-like ordering of flexible macromolecules. A visual analysis and calculation of order parameter relaying the anisotropy of diffraction allow concluding that transition from disordered to liquid-crystalline state proceeds sharply at relatively low content of stiff components.« less

Generalized soldering of {+-}2 helicity states in D=2+1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dalmazi, D.; Mendonca, Elias L.

2009-07-15

The direct sum of a couple of Maxwell-Chern-Simons gauge theories of opposite helicities {+-}1 does not lead to a Proca theory in D=2+1, although both theories share the same spectrum. However, it is known that by adding an interference term between both helicities we can join the complementary pieces together and obtain the physically expected result. A generalized soldering procedure can be defined to generate the missing interference term. Here, we show that the same procedure can be applied to join together {+-}2 helicity states in a full off-shell manner. In particular, by using second-order (in derivatives) self-dual models ofmore » helicities {+-}2 (spin-2 analogues of Maxwell-Chern-Simmons models) the Fierz-Pauli theory is obtained after soldering. Remarkably, if we replace the second-order models by third-order self-dual models (linearized topologically massive gravity) of opposite helicities, after soldering, we end up exactly with the new massive gravity theory of Bergshoeff, Hohm, and Townsend in its linearized approximation.« less

Double Helical Gear Performance Results in High Speed Gear Trains

NASA Technical Reports Server (NTRS)

Handschuh, Robert F.; Ehinger, Ryan; Sinusas, Eric; Kilmain, Charles

2009-01-01

The operation of high speed gearing systems in the transmissions of tiltrotor aircraft has an effect on overall propulsion system efficiency. Recent work has focused on many aspects of high-speed helical gear trains as would be used in tiltrotor aircraft such as operational characteristics, comparison of analytical predictions to experimental data and the affect of superfinishing on transmission performance. Baseline tests of an aerospace quality system have been conducted in the NASA Glenn High-Speed Helical Gear Train Test Facility and have been described in earlier studies. These earlier tests had utilized single helical gears. The results that will be described in this study are those attained using double helical gears. This type of gear mesh can be configured in this facility to either pump the air-oil environment from the center gap between the meshing gears to the outside of tooth ends or in the reverse direction. Tests were conducted with both inward and outward air-oil pumping directions. Results are compared to the earlier baseline results of single helical gears.

Double Helical Gear Performance Results in High Speed Gear Trains

NASA Technical Reports Server (NTRS)

Handschuh, Robert F.; Ehinger, Ryan; Sinusas, Eric; Kilmain, Charles

2010-01-01

The operation of high speed gearing systems in the transmissions of tiltrotor aircraft has an effect on overall propulsion system efficiency. Recent work has focused on many aspects of high-speed helical gear trains as would be used in tiltrotor aircraft such as operational characteristics, comparison of analytical predictions to experimental data and the affect of superfinishing on transmission performance. Baseline tests of an aerospace quality system have been conducted in the NASA Glenn High-Speed Helical Gear Train Test Facility and have been described in earlier studies. These earlier tests had utilized single helical gears. The results that will be described in this study are those attained using double helical gears. This type of gear mesh can be configured in this facility to either pump the air-oil environment from the center gap between the meshing gears to the outside of tooth ends or in the reverse direction. Tests were conducted with both inward and outward air-oil pumping directions. Results are compared to the earlier baseline results of single helical gears.

Increase in furfural tolerance by combinatorial overexpression of NAD salvage pathway enzymes in engineered isobutanol-producing E. coli.

PubMed

Song, Hun-Suk; Jeon, Jong-Min; Kim, Hyun-Joong; Bhatia, Shashi Kant; Sathiyanarayanan, Ganesan; Kim, Junyoung; Won Hong, Ju; Gi Hong, Yoon; Young Choi, Kwon; Kim, Yun-Gon; Kim, Wooseong; Yang, Yung-Hun

2017-12-01

To reduce the furfural toxicity for biochemical production in E. coli, a new strategy was successfully applied by supplying NAD(P)H through the nicotine amide salvage pathway. To alleviate the toxicity, nicotinamide salvage pathway genes were overexpressed in recombinant, isobutanol-producing E. coli. Gene expression of pncB and nadE respectively showed increased tolerance to furfural among these pathways. The combined expression of pncB and nadE was the most effective in increasing the tolerance of the cells to toxic aldehydes. By comparing noxE- and fdh-harbouring strains, the form of NADH, rather than NAD + , was the major effector of furfural tolerance. Overall, this study is the application of the salvage pathway to isobutanol production in the presence of furfural, and this system seems to be applicable to alleviate furfural toxicity in the production of other biochemical. Copyright © 2017 Elsevier Ltd. All rights reserved.

Passport-PeopleSoft integration for HANDI 2000 business management system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilson, D.

The integration between the PeopleSoft applications and Passport modules are accomplished with an off the shelf package developed by lNDUS. The product was updated to the PeopleSoft Release 7.O. The Integration product interacts with data from multiple products within Passport and PeopleSoft. For 10/l/98 the Integration will interlace between the following: (1) PassPort Accounts Payable, Contract Management, Inventory Management, Purchasing; and (2) PeopleSoft General Ledger, Project Costing, Human Resources, Payroll. The current supply systems and financial systems interact with each other via multiple custom interfaces. Data integrity and Y2K issues were some of the driving factors in replacement of thesemore » systems. The new systems allow FDH the opportunity to change the current business processes to go to a best business practice that the commercial off the shelf software was adopted.« less

Helicity in the atmospheric boundary layer

NASA Astrophysics Data System (ADS)

Kurgansky, Michael; Koprov, Boris; Koprov, Victor; Chkhetiani, Otto

2017-04-01

An overview is presented of recent direct field measurements at the Tsimlyansk Scientific Station of A.M. Obukhov Institute of Atmospheric Physics in Moscow of turbulent helicity (and potential vorticity) using four acoustic anemometers positioned, within the atmospheric surface-adjacent boundary layer, in the vertices of a rectangular tetrahedron, with an approximate 5 m distance between the anemometers and a 5.5 m elevation of the tetrahedron base above the ground surface (Koprov, Koprov, Kurgansky and Chkhetiani. Izvestiya, Atmospheric and Oceanic Physics, 2015, Vol.51, 565-575). The same ideology was applied in a later field experiment in Tsimlyansk with the tetrahedron's size of 0.7 m and variable elevation over the ground from 3.5 to 25 m. It is illustrated with examples of the statistical distribution of instantaneous (both positive and negative) turbulent helicity values. A theory is proposed that explains the measured mean turbulent helicity sign, including the sign of contribution to helicity from the horizontal and vertical velocity & vorticity components, respectively, and the sign of helicity buoyant production term. By considering a superposition of the classic Ekman spiral solution and a jet-like wind profile that mimics a shallow breeze circulation over a non-uniformly heated Earth surface, a possible explanation is provided, why the measured mean turbulent helicity sign is negative. The pronounced breeze circulation over the Tsimlyansk polygon which is located nearby the Tsimlyansk Reservoir was, indeed, observed during the measurements period. Whereas, essentially positive helicity is injected into the boundary layer from the free atmosphere in the Northern Hemisphere.

Reverse total shoulder arthroplasty using helical blade to optimize glenoid fixation and bone preservation: preliminary results in thirty five patients with minimum two year follow-up.

PubMed

Zilber, Sebastien; Camana, Eleonora; Lapner, Peter; Haritinian, Emil; Nove Josserand, Laurent

2018-03-26

Glenoid loosening is a common cause of reverse total shoulder arthroplasty (RTSA) failure, and grafting of the glenoid is often required for revision due to bone loss due to the central peg in most glenoid baseplates. Helical blades have been used in the hip to optimize bone fixation in proximal femoral fracture. This study presents the initial results of specifically designed helical blade in the shoulder to optimize glenoid bone fixation and preservation as part of RTSA. Thirty-five patients underwent RTSA with glenoid helical blade fixation. An uncemented glenoid baseplate was used with a central helical blade partially coated with hydroxyapatite and two or three screws. Outcome analysis was performed pre-operatively and at two years. All patients were satisfied with the results and significant improvement was observed in functional outcome scores between baseline and final follow-up. There was a single intra-operative undisplaced glenoid fracture which did not compromise the baseplate fixation. There was no radiographic evidence of loosening or radiolucencies around the helical blade. The helical blade provides a satisfactory primary fixation. Because of its length (21 mm), care should be taken in cases of pre-existing bone loss or sclerotic bone to avoid glenoid fracture or anterior cortical perforation. Helical blade has the potential to facilitate glenoid implant revision by preserving the glenoid bone stock.

Membrane-spanning α-helical barrels as tractable protein-design targets.

PubMed

Niitsu, Ai; Heal, Jack W; Fauland, Kerstin; Thomson, Andrew R; Woolfson, Derek N

2017-08-05

The rational ( de novo ) design of membrane-spanning proteins lags behind that for water-soluble globular proteins. This is due to gaps in our knowledge of membrane-protein structure, and experimental difficulties in studying such proteins compared to water-soluble counterparts. One limiting factor is the small number of experimentally determined three-dimensional structures for transmembrane proteins. By contrast, many tens of thousands of globular protein structures provide a rich source of 'scaffolds' for protein design, and the means to garner sequence-to-structure relationships to guide the design process. The α-helical coiled coil is a protein-structure element found in both globular and membrane proteins, where it cements a variety of helix-helix interactions and helical bundles. Our deep understanding of coiled coils has enabled a large number of successful de novo designs. For one class, the α-helical barrels-that is, symmetric bundles of five or more helices with central accessible channels-there are both water-soluble and membrane-spanning examples. Recent computational designs of water-soluble α-helical barrels with five to seven helices have advanced the design field considerably. Here we identify and classify analogous and more complicated membrane-spanning α-helical barrels from the Protein Data Bank. These provide tantalizing but tractable targets for protein engineering and de novo protein design.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'. © 2017 The Author(s).

Impact of helical boundary conditions in MHD modeling of RFP and tokamak plasmas

NASA Astrophysics Data System (ADS)

Bonfiglio, D.; Cappello, S.; Escande, D. F.; Piovesan, P.; Veranda, M.; Chacón, L.

2012-10-01

Helical boundary conditions imposed by the active control system of the RFX-mod device provide a handle to govern the plasma dynamics in both RFP and Ohmic tokamak discharges [1]. By applying an edge radial magnetic field with proper helicity, it is possible to increase the persistence of the spontaneous helical RFP states at high current,and to stimulate them also at low current or high density. Helical BCs even allow to access helical states with different helicity than the spontaneous one [2]. In Ohmic tokamak operation at q(a)<2, the presence of the 2/1 RWM reduces the sawtoothing activity of the 1/1 internal kink, which takes a stationary snake-like character instead. Many of these features are qualitatively reproduced in 3D nonlinear MHD modeling. We study the impact of helical BCs on the MHD dynamics in both RFP and tokamak with two successfully benchmarked numerical tools, SpeCyl and PIXIE3D [3]. We recover the bifurcation from a sawtooth to a snake solution when imposing a 2/1 BC in the tokamak case and we interpret this as a toroidal/nonlinear coupling effect. We show that the bifurcation is more easily stimulated with a 1/1 BC.[4pt] [1] P. Piovesan, invited talk this meeting[0pt] [2] M. Veranda et al EPS-ICPP Conference (2012) P4.004[0pt] [3] D. Bonfiglio et al Phys. Plasmas (2010)

PI-line-based image reconstruction in helical cone-beam computed tomography with a variable pitch.

PubMed

Zou, Yu; Pan, Xiaochuan; Xia, Dan; Wang, Ge

2005-08-01

Current applications of helical cone-beam computed tomography (CT) involve primarily a constant pitch where the translating speed of the table and the rotation speed of the source-detector remain constant. However, situations do exist where it may be more desirable to use a helical scan with a variable translating speed of the table, leading a variable pitch. One of such applications could arise in helical cone-beam CT fluoroscopy for the determination of vascular structures through real-time imaging of contrast bolus arrival. Most of the existing reconstruction algorithms have been developed only for helical cone-beam CT with constant pitch, including the backprojection-filtration (BPF) and filtered-backprojection (FBP) algorithms that we proposed previously. It is possible to generalize some of these algorithms to reconstruct images exactly for helical cone-beam CT with a variable pitch. In this work, we generalize our BPF and FBP algorithms to reconstruct images directly from data acquired in helical cone-beam CT with a variable pitch. We have also performed a preliminary numerical study to demonstrate and verify the generalization of the two algorithms. The results of the study confirm that our generalized BPF and FBP algorithms can yield exact reconstruction in helical cone-beam CT with a variable pitch. It should be pointed out that our generalized BPF algorithm is the only algorithm that is capable of reconstructing exactly region-of-interest image from data containing transverse truncations.

Structural and Functional Characterization of an Archaeal Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated Complex for Antiviral Defense (CASCADE)*

PubMed Central

Lintner, Nathanael G.; Kerou, Melina; Brumfield, Susan K.; Graham, Shirley; Liu, Huanting; Naismith, James H.; Sdano, Matthew; Peng, Nan; She, Qunxin; Copié, Valérie; Young, Mark J.; White, Malcolm F.; Lawrence, C. Martin

2011-01-01

In response to viral infection, many prokaryotes incorporate fragments of virus-derived DNA into loci called clustered regularly interspaced short palindromic repeats (CRISPRs). The loci are then transcribed, and the processed CRISPR transcripts are used to target invading viral DNA and RNA. The Escherichia coli “CRISPR-associated complex for antiviral defense” (CASCADE) is central in targeting invading DNA. Here we report the structural and functional characterization of an archaeal CASCADE (aCASCADE) from Sulfolobus solfataricus. Tagged Csa2 (Cas7) expressed in S. solfataricus co-purifies with Cas5a-, Cas6-, Csa5-, and Cas6-processed CRISPR-RNA (crRNA). Csa2, the dominant protein in aCASCADE, forms a stable complex with Cas5a. Transmission electron microscopy reveals a helical complex of variable length, perhaps due to substoichiometric amounts of other CASCADE components. A recombinant Csa2-Cas5a complex is sufficient to bind crRNA and complementary ssDNA. The structure of Csa2 reveals a crescent-shaped structure unexpectedly composed of a modified RNA-recognition motif and two additional domains present as insertions in the RNA-recognition motif. Conserved residues indicate potential crRNA- and target DNA-binding sites, and the H160A variant shows significantly reduced affinity for crRNA. We propose a general subunit architecture for CASCADE in other bacteria and Archaea. PMID:21507944

Structural and functional characterization of an archaeal clustered regularly interspaced short palindromic repeat (CRISPR)-associated complex for antiviral defense (CASCADE).

PubMed

Lintner, Nathanael G; Kerou, Melina; Brumfield, Susan K; Graham, Shirley; Liu, Huanting; Naismith, James H; Sdano, Matthew; Peng, Nan; She, Qunxin; Copié, Valérie; Young, Mark J; White, Malcolm F; Lawrence, C Martin

2011-06-17

In response to viral infection, many prokaryotes incorporate fragments of virus-derived DNA into loci called clustered regularly interspaced short palindromic repeats (CRISPRs). The loci are then transcribed, and the processed CRISPR transcripts are used to target invading viral DNA and RNA. The Escherichia coli "CRISPR-associated complex for antiviral defense" (CASCADE) is central in targeting invading DNA. Here we report the structural and functional characterization of an archaeal CASCADE (aCASCADE) from Sulfolobus solfataricus. Tagged Csa2 (Cas7) expressed in S. solfataricus co-purifies with Cas5a-, Cas6-, Csa5-, and Cas6-processed CRISPR-RNA (crRNA). Csa2, the dominant protein in aCASCADE, forms a stable complex with Cas5a. Transmission electron microscopy reveals a helical complex of variable length, perhaps due to substoichiometric amounts of other CASCADE components. A recombinant Csa2-Cas5a complex is sufficient to bind crRNA and complementary ssDNA. The structure of Csa2 reveals a crescent-shaped structure unexpectedly composed of a modified RNA-recognition motif and two additional domains present as insertions in the RNA-recognition motif. Conserved residues indicate potential crRNA- and target DNA-binding sites, and the H160A variant shows significantly reduced affinity for crRNA. We propose a general subunit architecture for CASCADE in other bacteria and Archaea.

Theoretical studies on the electronic structure and spectroscopic properties of transition metals bis(dipyrrinate)s

NASA Astrophysics Data System (ADS)

Ksenofontov, Alexander A.; Guseva, Galina B.; Antina, Elena V.

2016-10-01

Density functional theory (DFT) and Time-dependent density functional theory (TD- DFT) computations have been used to reveal structural, molecular, electronic and spectral-luminescent parameters and features of several homoleptic transition metals bis(dipyrrine) complexes. The influence of complexing agent and ligand nature on the regularities in geometric, spectral-luminescent properties, kinetic and thermal stability changes in the [M2L2] complexes series were studied. Special attention is paid to the influence of the solvating media (PCM/TD-B3LYP/Def2-SVP) on changing spectral-luminescent properties of d-metals bis(dipyrrinate)s. The interpretation of the dependence between spectral-luminescent properties of the complexes and HOMO-LUMO (highest occupied molecular orbital and lowest unoccupied molecular orbital) energy gap's width was given. It was shown that the regularities in changing the helicates' quantum yield depending on the nature of complexing agent, ligand and solvent properties, obtained from quantum-chemical calculations, are in the agreement with our previously obtained experimental data. Thus, structural and spectral-luminescent characteristics of new [M2L2] luminophors can be evaluated with high reliability, and good forecast prospects for their use as fluorescent dyes for optical devices can be made in terms of the results of theoretical studies (B3LYP/Def2-SVP and TD-B3LYP/Def2-SVP).

Noncovalent Interactions in the Asymmetric Synthesis of Rigid, Conjugated Helical Structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miyasaka, Makoto; Pink, Maren; Rajca, Suchada

Tetrakis({beta}-trithiophene) 1 folds into a helical conformation (RRR) that facilitates double ring annelation, with high diastereoselectivity and modest enantioselectivity, to provide bis[7]helicene 2 (MRM). This rigid, helically locked structure has enhanced chiroptical properties similar to the corresponding [15]helicene.

On a Cyclic Variation of the Hemispheric Helicity Rule

NASA Technical Reports Server (NTRS)

Pevtsov, A. A.; Hagyard, M. J.; Blehm, Z.; Smith, J. E.; Canfield, R. C.; Sakurai, T.

2003-01-01

We report the result of a study magnetic helicity in solar active regions during 1980-2000.Using the vector magnetograms four different instruments we calculated the force-free parameter alpha as in Pevtsov et al.(1995). We use alpha as the proxy for current helicity density.

Helical grip for the cable cars of San Francisco

NASA Technical Reports Server (NTRS)

Peyran, R. J.

1979-01-01

A helical cable car grip to minimize high maintenance costs of San Francisco's cable car operation is presented. The grip establishes a rolling contact between the cable and grip to reduce sliding friction and associated cable wear. The design, development, and testing of the helical cable car grip are described.

Experimental investigation of solar powered diaphragm and helical pumps

USDA-ARS?s Scientific Manuscript database

For several years, many types of solar powered water pumping systems were evaluated, and in this paper, diaphragm and helical solar photovoltaic (PV) powered water pumping systems are discussed. Data were collected on diaphragm and helical pumps which were powered by different solar PV arrays at mul...

Gyrokinetic-Vlasov simulations of the ion temperature gradient turbulence in tokamak and helical systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Watanabe, T.-H.; Sugama, H.; Graduate University for Advanced Studies

2006-11-30

Recent progress of the gyrokinetic-Vlasov simulations on the ion temperature gradient (ITG) turbulence in tokamak and helical systems is reported, where the entropy balance is checked as a reference for the numerical accuracy. The tokamak ITG turbulence simulation carried out on the Earth Simulator clearly captures a nonlinear generation process of zonal flows. The tera-flops and tera-bytes scale simulation is also applied to a helical system with the same poloidal and toroidal periodicities of L = 2 and M = 10 as in the Large Helical Device.

Helical Spin Order from Topological Dirac and Weyl Semimetals

DOE PAGES

Sun, Xiao-Qi; Zhang, Shou-Cheng; Wang, Zhong

2015-08-14

In this paper, we study dynamical mass generation and the resultant helical spin orders in topological Dirac and Weyl semimetals, including the edge states of quantum spin Hall insulators, the surface states of weak topological insulators, and the bulk materials of Weyl semimetals. In particular, the helical spin textures of Weyl semimetals manifest the spin-momentum locking of Weyl fermions in a visible manner. Finally, the spin-wave fluctuations of the helical order carry electric charge density; therefore, the spin textures can be electrically controlled in a simple and predictable manner.

Iron(II) supramolecular helicates interfere with the HIV-1 Tat-TAR RNA interaction critical for viral replication.

PubMed

Malina, Jaroslav; Hannon, Michael J; Brabec, Viktor

2016-07-12

The interaction between the HIV-1 transactivator protein Tat and TAR (transactivation responsive region) RNA, plays a critical role in HIV-1 transcription. Iron(II) supramolecular helicates were evaluated for their in vitro activity to inhibit Tat-TAR RNA interaction using UV melting studies, electrophoretic mobility shift assay, and RNase A footprinting. The results demonstrate that iron(II) supramolecular helicates inhibit Tat-TAR interaction at nanomolar concentrations by binding to TAR RNA. These studies provide a new insight into the biological potential of metallosupramolecular helicates.

A Combined Study of Photospheric Magnetic and Current Helicities and Subsurface Kinetic Helicities of Solar Active Regions during 2006-2012

NASA Astrophysics Data System (ADS)

Seligman, Darryl; Petrie, G.; Komm, R.

2014-01-01

We compare the average photospheric current helicity H_c, photospheric twist parameter α (a well-known proxy for the full relative magnetic helicity), and subsurface kinetic helicity K_h for 128 active regions observed between 2006-2012. We use 1436 Hinode photospheric vector magnetograms and subsurface fluid velocity data from GONG Dopplergrams. We find a significant hemispheric bias in all three parameters. The K_h parameter is preferentially positive/negative in the southern/northern hemisphere. The H_c and α parameters have the same bias for strong fields |{B}|>1000 G). We examine the temporal variability of each parameter for each active region and identify a significant subset of regions whose three helicity parameters all exhibit clear increasing or decreasing trends. The temporal profiles of these regions have the same bias: positive/negative helicity in the northern/southern hemisphere. The results are consistent with Longcope et al.'s Σ-effect. This work is carried out through the National Solar Observatory Research Experiences for Undergraduate (REU) site program, which is co-funded by the Department of Defense in partnership with the NSF REU Program. The National Solar Observatory is operated by the Association of Universities for Research in Astronomy, Inc. (AURA) under cooperative agreement with the National Science Foundation.

Biomechanical comparison of straight DCP and helical plates for fixation of transverse and oblique bone fractures.

PubMed

Aksakal, Bunyamin; Gurger, Murat; Say, Yakup; Yilmaz, Erhan

2014-01-01

Biomechanical comparison of straight DCP and helical plates for fixation of transversal and oblique tibial bone fractures were analyzed and compared to each other by axial compression, bending and torsion tests. An in vitro osteosynthesis of transverse (TF) and oblique bone fracture (OF) fixations have been analysed on fresh sheep tibias by using the DCP and helical compression plates (HP). Statistically significant differences were found for both DCP and helical plate fixations under axial compression, bending and torsional loads. The strength of fixation systems was in favor of DC plating with exception of the TF-HP fixation group under compression loads and torsional moments. The transvers fracture (TF) stability was found to be higher than that found in oblique fracture (OF) fixed by helical plates (HP). However, under torsional testing, compared to conventional plating, the helical plate fixations provided a higher torsional resistance and strength. The maximum stiffness at axial compression loading and maximum torsional strength was achieved in torsional testing for the TF-HP fixations. From in vitro biomechanical analysis, fracture type and plate fixation system groups showed different responses under different loadings. Consequently, current biomechanical analyses may encourage the usage of helical HP fixations in near future during clinical practice for transverse bone fractures.

Expanding Non-solenoidal Startup with Local Helicity Injection to Increased Toroidal Field and Helicity Injection Rate

NASA Astrophysics Data System (ADS)

Perry, J. M.; Barr, J. L.; Bodner, G. M.; Bongard, M. W.; Burke, M. G.; Fonck, R. J.; Hinson, E. T.; Lewicki, B. T.; Reusch, J. A.; Schlossberg, D. J.; Winz, G. R.

2015-11-01

Local helicity injection (LHI) is a non-solenoidal startup technique under development on the Pegasus ST. Plasma currents up to 0.18 MA have been initiated by LHI in conjunction with poloidal field induction. A 0-D power balance model has been developed to predict plasma current evolution by balancing helicity input against resistive dissipation. The model is being validated against a set of experimental measurements and magnetic reconstructions with radically varied plasma geometric evolutions. Outstanding physics issues with LHI startup are the scalings of confinement and MHD activity with helicity injection rate and toroidal field strength, as well as injector behavior at high field. Preliminary results from the newly-installed Thomson scattering system suggest core temperatures of a few hundred eV during LHI startup. Measurements are being expanded to multiple spatial points for ongoing confinement studies. A set of larger-area injectors is being installed in the lower divertor region, where increased toroidal field will provide a helicity injection rate over 3 times that of outboard injectors. In this regime helicity injection will be the dominant current drive. Experiments with divertor injectors will permit experimental differentiation of several possible confinement models, and demonstrate the feasibility of LHI startup at high field. Work supported by US DOE grant DE-FG02-96ER54375.

Molecular dynamics of individual alpha-helices of bacteriorhodopsin in dimyristol phosphatidylocholine. I. Structure and dynamics.

PubMed

Woolf, T B

1997-11-01

Understanding the role of the lipid bilayer in membrane protein structure and dynamics is needed for tertiary structure determination methods. However, the molecular details are not well understood. Molecular dynamics computer calculations can provide insight into these molecular details of protein:lipid interactions. This paper reports on 10 simulations of individual alpha-helices in explicit lipid bilayers. The 10 helices were selected from the bacteriorhodopsin structure as representative alpha-helical membrane folding components. The bilayer is constructed of dimyristoyl phosphatidylcholine molecules. The only major difference between simulations is the primary sequence of the alpha-helix. The results show dramatic differences in motional behavior between alpha-helices. For example, helix A has much smaller root-mean-squared deviations than does helix D. This can be understood in terms of the presence of aromatic residues at the interface for helix A that are not present in helix D. Additional motions are possible for the helices that contain proline side chains relative to other amino acids. The results thus provide insight into the types of motion and the average structures possible for helices within the bilayer setting and demonstrate the strength of molecular simulations in providing molecular details that are not directly visualized in experiments.

Characteristics of Helical Flow through Neck Cutoffs

NASA Astrophysics Data System (ADS)

Richards, D.; Konsoer, K. M.; Turnipseed, C.; Willson, C. S.

2017-12-01

Meander cutoffs and oxbows lakes are a ubiquitous feature of riverine landscapes yet there is a paucity of detailed investigations concentrated on the three-dimensional flow structure through evolving neck cutoffs. The purpose of this research is to investigate and characterize helical flow through neck cutoffs with two different planform configurations: elongate meander loops and serpentine loops. Three-dimensional velocity measurements was collected with an acoustic Doppler current profiler for five cutoffs on the White River, Arkansas. Pronounced helical flow was found through all elongate loop cutoff sites, formed from the balance between centrifugal force resulting from the curving of flow through the cutoff channel and pressure gradient force resulting from water surface super-elevation between primary flow and flow at the entrance and exit of the abandoned loop. The sense of motion of the helical flow caused near-surface fluid to travel outward toward the abandoned loop while near-bed fluid was redirected toward the downstream channel. Another characteristic of the helical flow structure for elongate loop cutoffs was the reversal of helical flow over a relatively short distance, causing patterns of secondary circulation that differed from typical patterns observed through curved channels with point bars. Lastly, helical flow was revealed within zones of strong flow recirculation, enhanced by an exchange of streamwise momentum between shear layers.

Spectroscopic studies of bacteriorhodopsin fragments dissolved in organic solution.

PubMed Central

Torres, J; Padrós, E

1995-01-01

Fourier transform infrared and UV fourth-derivative spectroscopies were used to study the secondary structure of bacteriorhodopsin and its chymotryptic and one of the sodium borohydride fragments dissolved in chloroform-methanol (1:1, v/v), 0.1 M LiClO4. The C1 fragment (helices C, D, E, F, and G) showed an alpha-helical content of about 53%, whereas C2 (helices A and B) had about 60%, and B2 (helices F and G) about 65% alpha-helix. The infrared main band indicated differences in alpha-helical properties between these fragments. These techniques were also used to obtain information on the interactions among helices. According to the results obtained from the hydrogen/deuterium exchange kinetics, about 40% of the amide protons of C2 are particularly protected against exchange, whereas for the C1 fragment this process is unexpectedly fast. UV fourth-derivative spectra of these samples were used to obtain information about the environment of Trp side chains. The results showed that the Trp residues of C2 are more shielded from the solvent than those of C1 or B2. The results of this work indicate that the specific interactions existing between the transmembrane segments induce different types of helical conformations in native bacteriorhodopsin. PMID:7612847

FILAMENT CHANNEL FORMATION VIA MAGNETIC HELICITY CONDENSATION

DOE Office of Scientific and Technical Information (OSTI.GOV)

Knizhnik, K. J.; Antiochos, S. K.; DeVore, C. R.

2015-08-20

A major unexplained feature of the solar atmosphere is the accumulation of magnetic shear in the form of filament channels at photospheric polarity inversion lines (PILs). In addition to free energy, this shear represents magnetic helicity, which is conserved under reconnection. In this paper we address the problem of filament channel formation and show how filaments acquire their shear and magnetic helicity. The results of three-dimensional (3D) simulations using the Adaptively Refined Magnetohydrodynamics Solver are presented. Our findings support the model of filament channel formation by magnetic helicity condensation that was developed by Antiochos. We consider the small-scale photospheric twistingmore » of a quasi-potential flux system that is bounded by a PIL and contains a coronal hole (CH). The magnetic helicity injected by the small-scale photospheric motions is shown to inverse cascade up to the largest allowable scales that define the closed flux system: the PIL and the CH. This process produces field lines that are both sheared and smooth, and are sheared in opposite senses at the PIL and the CH. The accumulated helicity and shear flux are shown to be in excellent quantitative agreement with the helicity condensation model. We present a detailed analysis of the simulations, including comparisons of our analytical and numerical results, and discuss their implications for observations.« less

Engineering and Design of the Steady Inductive Helicity Injected Torus (HIT--SI)

NASA Astrophysics Data System (ADS)

Sieck, P. E.; Jarboe, T. R.; Nelson, B. A.; Rogers, J. A.; Shumlak, U.

1999-11-01

Steady Inductive Helicity Injection (SIHI) is an inductive helicity injection method that injects helicity at a nearly constant rate, without open field lines, and without removing any helicity or magnetic energy from the plasma.(T.R. Jarboe, Fusion Technology, 36) (1), p. 85, 1999 SIHI directly produces a rotating magnetic field structure, and in the frame of the rotating field the current profile is nearly time independent. The Steady Inductive Helicity Injected Torus (HIT--SI) is a spheromak designed to implement SIHI so that the current profile in the rotating frame is optimized. The geometry of HIT--SI will be presented, including the manufacturing techniques and metallurgical processes planned for construction of the close-fitting flux conserver. The flux conserver is made of aged chromium copper with 80% the conductivity of pure copper. The detailed electrical insulation requirements in the helicity injector design lead to a complex o-ring seal and a plasma-sprayed alumina insulation coating. This has prompted the construction of an o-ring prototype test fixture having the main features of the o-ring design and the alumina coating. The design and evaluation of this fixture will also be presented with vacuum and voltage test results.

Numerical Analysis of Helical Pile-Soil Interaction under Compressive Loads

NASA Astrophysics Data System (ADS)

Polishchuk, A. I.; Maksimov, F. A.

2017-11-01

The results of the field tests of full-scale steel helical piles in clay soils intended for prefabricated temporary buildings foundations are presented in this article. The finite element modeling was used for the evaluation of stress distribution of the clay soil around helical piles. An approach of modeling of the screw-pile geometry has been proposed through the Finite Element Analysis. Steel helical piles with a length of 2.0 m, shaft diameter of 0.108 m and a blade diameter of 0.3 m were used in the experiments. The experiments have shown the efficiency of double-bladed helical piles in the clay soils compared to single-bladed piles. It has been experimentally established that the introduction of the second blade into the pile shaft provides an increase of the bearing capacity in clay soil up to 30% compared to a single-bladed helical pile with similar geometrical dimensions. The numerical results are compared with the measurements obtained by a large scale test and the bearing capacity has been estimated. It has been found that the model results fit the field results. For a double-bladed helical pile it was revealed that shear stresses upon pile loading are formed along the lateral surface forming a cylindrical failure surface.

The decay of isotropic magnetohydrodynamics turbulence and the effects of cross-helicity

NASA Astrophysics Data System (ADS)

Briard, Antoine; Gomez, Thomas

2018-02-01

Decaying homogeneous and isotropic magnetohydrodynamics (MHD) turbulence is investigated numerically at large Reynolds numbers thanks to the eddy-damped quasi-normal Markovian (EDQNM) approximation. Without any background mean magnetic field, the total energy spectrum scales as -3/2$ in the inertial range as a consequence of the modelling. Moreover, the total energy is shown, both analytically and numerically, to decay at the same rate as kinetic energy in hydrodynamic isotropic turbulence: this differs from a previous prediction, and thus physical arguments are proposed to reconcile both results. Afterwards, the MHD turbulence is made imbalanced by an initial non-zero cross-helicity. A spectral modelling is developed for the velocity-magnetic correlation in a general homogeneous framework, which reveals that cross-helicity can contain subtle anisotropic effects. In the inertial range, as the Reynolds number increases, the slope of the cross-helical spectrum becomes closer to -5/3$ than -2$ . Furthermore, the Elsässer spectra deviate from -3/2$ with cross-helicity at large Reynolds numbers. Regarding the pressure spectrum P$ , its kinetic and magnetic parts are found to scale with -2$ in the inertial range, whereas the part due to cross-helicity rather scales in -7/3$ . Finally, the two rd laws for the total energy and cross-helicity are assessed numerically at large Reynolds numbers.

Influence of helical external driven current on nonlinear resistive tearing mode evolution and saturation in tokamaks

NASA Astrophysics Data System (ADS)

Zhang, W.; Wang, S.; Ma, Z. W.

2017-06-01

The influences of helical driven currents on nonlinear resistive tearing mode evolution and saturation are studied by using a three-dimensional toroidal resistive magnetohydrodynamic code (CLT). We carried out three types of helical driven currents: stationary, time-dependent amplitude, and thickness. It is found that the helical driven current is much more efficient than the Gaussian driven current used in our previous study [S. Wang et al., Phys. Plasmas 23(5), 052503 (2016)]. The stationary helical driven current cannot persistently control tearing mode instabilities. For the time-dependent helical driven current with f c d = 0.01 and δ c d < 0.04 , the island size can be reduced to its saturated level that is about one third of the initial island size. However, if the total driven current increases to about 7% of the total plasma current, tearing mode instabilities will rebound again due to the excitation of the triple tearing mode. For the helical driven current with time dependent strength and thickness, the reduction speed of the radial perturbation component of the magnetic field increases with an increase in the driven current and then saturates at a quite low level. The tearing mode is always controlled even for a large driven current.

Evolution of relative magnetic helicity. New boundary conditions for the vector potential

NASA Astrophysics Data System (ADS)

Yang, Shangbin; Büchner, Jörg; Skála, Jan; Zhang, Hongqi

2018-05-01

Context. For a better understanding of the dynamics of the solar corona, it is important to analyse the evolution of the helicity of the magnetic field. Since the helicity cannot be directly determined by observations, we have recently proposed a method to calculate the relative magnetic helicity in a finite volume for a given magnetic field, which however required the flux to be balanced separately on all the sides of the considered volume. Aims: We developed a scheme to obtain the vector potential in a volume without the above restriction at the boundary. We studied the dissipation and escape of relative magnetic helicity from an active region. Methods: In order to allow finite magnetic fluxes through the boundaries, a Coulomb gauge was constructed that allows for global magnetic flux balance. The property of sinusoidal function was used to obtain the vector potentials at the 12 edges of the considered rectangular volume extending above an active region. We tested and verified our method in a theoretical fore-free magnetic field model. Results: We applied the new method to the former calculation data and found a difference of less than 1.2%. We also applied our method to the magnetic field above active region NOAA 11429 obtained by a new photospheric-data-driven magnetohydrodynamics (MHD) model code GOEMHD3. We analysed the magnetic helicity evolution in the solar corona using our new method. We find that the normalized magnetic helicity (H/Φ2) is equal to -0.038 when fast magnetic reconnection is triggered. This value is comparable to the previous value (-0.029) in the MHD simulations when magnetic reconnection happened and the observed normalized magnetic helicity (-0.036) from the eruption of newly emerging active regions. We find that only 8% of the accumulated magnetic helicity is dissipated after it is injected through the bottom boundary. This is in accordance with the Woltjer conjecture. Only 2% of the magnetic helicity injected from the bottom boundary escapes through the corona. This is consistent with the observation of magnetic clouds, which could take magnetic helicity into the interplanetary space. In the case considered here, several halo coronal mass ejections (CMEs) and two X-class solar flares originate from this active region.

Validation of an Accurate Three-Dimensional Helical Slow-Wave Circuit Model

NASA Technical Reports Server (NTRS)

Kory, Carol L.

1997-01-01

The helical slow-wave circuit embodies a helical coil of rectangular tape supported in a metal barrel by dielectric support rods. Although the helix slow-wave circuit remains the mainstay of the traveling-wave tube (TWT) industry because of its exceptionally wide bandwidth, a full helical circuit, without significant dimensional approximations, has not been successfully modeled until now. Numerous attempts have been made to analyze the helical slow-wave circuit so that the performance could be accurately predicted without actually building it, but because of its complex geometry, many geometrical approximations became necessary rendering the previous models inaccurate. In the course of this research it has been demonstrated that using the simulation code, MAFIA, the helical structure can be modeled with actual tape width and thickness, dielectric support rod geometry and materials. To demonstrate the accuracy of the MAFIA model, the cold-test parameters including dispersion, on-axis interaction impedance and attenuation have been calculated for several helical TWT slow-wave circuits with a variety of support rod geometries including rectangular and T-shaped rods, as well as various support rod materials including isotropic, anisotropic and partially metal coated dielectrics. Compared with experimentally measured results, the agreement is excellent. With the accuracy of the MAFIA helical model validated, the code was used to investigate several conventional geometric approximations in an attempt to obtain the most computationally efficient model. Several simplifications were made to a standard model including replacing the helical tape with filaments, and replacing rectangular support rods with shapes conforming to the cylindrical coordinate system with effective permittivity. The approximate models are compared with the standard model in terms of cold-test characteristics and computational time. The model was also used to determine the sensitivity of various circuit parameters including typical manufacturing dimensional tolerances and support rod permittivity. By varying the circuit parameters of an accurate model using MAFIA, these sensitivities can be computed for manufacturing concerns, and design optimization previous to fabrication, thus eliminating the need for costly experimental iterations. Several variations were made to a standard helical circuit using MAFIA to investigate the effect that variations on helical tape and support rod width, metallized loading height and support rod permittivity, have on TWT cold-test characteristics.

Characteristics of chiral plasma plumes generated in the absence of external magnetic field

NASA Astrophysics Data System (ADS)

Nie, LanLan; Liu, FengWu; Zhou, XinCai; Lu, XinPei; Xian, YuBin

2018-05-01

A chiral plasma plume has recently been generated inside a dielectric tube without the use of an external magnetic field. In this paper, we seek to further study the key properties of such a chiral plume to improve our understanding of how this interesting structure is generated and controlled. The chiral plume is generated by externally mounting a stainless steel helical coil or a ring onto the dielectric tube. By changing the pitch of the helical coil, the pitch of the plasma plume can be controlled, with the shape of the plume following the shape of the helical coil. The addition of the helical coil significantly expands the range of parameters under which the chiral plasma plume appears. When the frequency of the applied voltage increases, additional stable discharge channels appear between the adjacent helices. The addition of two helical coils results in the formation of two chiral plasma plumes, which follow the shape of the helical coils. When a metal ring is placed on the outside of the tube, there is no chiral plasma plume between the high voltage electrode and the ring; however, a chiral plasma plume appears on the right side of the ring if the distance between the ring and the high voltage electrode is small. These findings suggest that the chiral plasma can be effectively modulated and guided using an externally mounted helical coil, which acts as the floating/actual ground to reduce the impedance of the discharge and as such contributes to the emergence of the chiral plasma plume behavior.

Radiographic Review of Helical Blade Versus Lag Screw Fixation for Cephalomedullary Nailing of Low-Energy Peritrochanteric Femur Fractures: There is a Difference in Cutout.

PubMed

Stern, Lorraine C; Gorczyca, John T; Kates, Stephen; Ketz, John; Soles, Gillian; Humphrey, Catherine A

2017-06-01

To compare the rate of cutout of helical blades and lag screws in low-energy peritrochanteric femur fractures treated with a cephalomedullary nail (CMN). Retrospective review. Academic medical center. Overall, this study included 362 patients with an average age of 83 year old, a majority of whom were women, and had sustained a low-energy peritrochanteric femur fracture treated with a CMN. All patients had at least 3 months of clinical and radiographic follow, with an average follow-up of 11 months and a range of 3-88 months follow-up. Cephalomedullary nailing with the use of a helical blade or single lag screw for proximal fixation. Cutout of the helical blade or lag screw. Twenty-two cutouts occurred, 14 (15.1%) of 93 patients with helical blades and 8 (3.0%) of 269 patients with lag screws. Cutout with the helical blade was significantly more frequent than with the lag screw (P = 0.0001). The average tip-apex distance (TAD) was significantly greater for those patients who experienced cutout both for the helical blades (23.5 vs. 19.7 mm; P = 0.0194) and lag screws (24.5 vs. 20.0 mm; P = 0.0197). An absolute TAD predictive of cutout could not be determined. When the helical blade was used, implant cutout occurred at a significantly higher rate compared with lag screw fixation. There was not a threshold TAD that was predictive of cutout for either implant. Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.

ON ASYMMETRY OF MAGNETIC HELICITY IN EMERGING ACTIVE REGIONS: HIGH-RESOLUTION OBSERVATIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tian Lirong; Alexander, David; Zhu Chunming

We employ the DAVE (differential affine velocity estimator) tracking technique on a time series of Michelson Doppler Imager (MDI)/1 minute high spatial resolution line-of-sight magnetograms to measure the photospheric flow velocity for three newly emerging bipolar active regions (ARs). We separately calculate the magnetic helicity injection rate of the leading and following polarities to confirm or refute the magnetic helicity asymmetry, found by Tian and Alexander using MDI/96 minute low spatial resolution magnetograms. Our results demonstrate that the magnetic helicity asymmetry is robust, being present in the three ARs studied, two of which have an observed balance of the magneticmore » flux. The magnetic helicity injection rate measured is found to depend little on the window size selected, but does depend on the time interval used between the two successive magnetograms being tracked. It is found that the measurement of the magnetic helicity injection rate performs well for a window size between 12 x 10 and 18 x 15 pixels and at a time interval {Delta}t = 10 minutes. Moreover, the short-lived magnetic structures, 10-60 minutes, are found to contribute 30%-50% of the magnetic helicity injection rate. Comparing with the results calculated by MDI/96 minute data, we find that the MDI/96 minute data, in general, can outline the main trend of the magnetic properties, but they significantly underestimate the magnetic flux in strong field regions and are not appropriate for quantitative tracking studies, so provide a poor estimate of the amount of magnetic helicity injected into the corona.« less

Ratio of ellipticities between 192 and 208 nm (R1 ): An effective electronic circular dichroism parameter for characterization of the helical components of proteins and peptides.

PubMed

Banerjee, Raja; Sheet, Tridip

2017-11-01

Circular dichroism (CD) spectroscopy represents an important tool for characterization of the peptide and protein secondary structures that mainly arise from the conformational disposition of the peptide backbone in solution. In 1991 Manning and Woody proposed that, in addition to the signal intensity, the ratio between [θ]nπ* and [θ]ππ*ǁ ((R 2 ) ≅ [θ] 222 /[θ] 208 ), along with [θ]ππ*⊥ and [θ]ππ*ǁ ((R 1 ) ≅ [θ] 192 /[θ] 208 ), may be utilized towards identifying the peptide/protein conformation (especially 3 10 - and α-helices). However, till date the use of the ratiometric ellipticity component for helical structure analysis of peptides and proteins has not been reported. We studied a series of temperature dependent CD spectra of a thermally stable, model helical peptide and its related analogs in water as a function of added 2,2,2-trifluoroethanol (TFE) in order to explore their landscape of helicity. For the first time, we have experimentally shown here that the R 1 parameter can characterize better the individual helices, while the other parameter R 2 and the signal intensity do not always converge. We emphasize the use of the R 1 ratio of ellipticities for helical characterization because of the common origin of these two bands (exciton splitting of the amide π→ π* transition in a helical polypeptide). This approach may become worthwhile and timely with the increasing accessibility of CD synchrotron sources. © 2017 Wiley Periodicals, Inc.

Generation of a Large-scale Magnetic Field in a Convective Full-sphere Cross-helicity Dynamo

NASA Astrophysics Data System (ADS)

Pipin, V. V.; Yokoi, N.

2018-05-01

We study the effects of the cross-helicity in the full-sphere large-scale mean-field dynamo models of a 0.3 M ⊙ star rotating with a period of 10 days. In exploring several dynamo scenarios that stem from magnetic field generation by the cross-helicity effect, we found that the cross-helicity provides the natural generation mechanisms for the large-scale scale axisymmetric and nonaxisymmetric magnetic field. Therefore, the rotating stars with convective envelopes can produce a large-scale magnetic field generated solely due to the turbulent cross-helicity effect (we call it γ 2-dynamo). Using mean-field models we compare the properties of the large-scale magnetic field organization that stems from dynamo mechanisms based on the kinetic helicity (associated with the α 2 dynamos) and cross-helicity. For the fully convective stars, both generation mechanisms can maintain large-scale dynamos even for the solid body rotation law inside the star. The nonaxisymmetric magnetic configurations become preferable when the cross-helicity and the α-effect operate independently of each other. This corresponds to situations with purely γ 2 or α 2 dynamos. The combination of these scenarios, i.e., the γ 2 α 2 dynamo, can generate preferably axisymmetric, dipole-like magnetic fields at strengths of several kGs. Thus, we found a new dynamo scenario that is able to generate an axisymmetric magnetic field even in the case of a solid body rotation of the star. We discuss the possible applications of our findings to stellar observations.

Zymographic differentiation of [NiFe]-Hydrogenases 1, 2 and 3 of Escherichia coli K-12

PubMed Central

2012-01-01

Background When grown under anaerobic conditions, Escherichia coli K-12 is able to synthesize three active [NiFe]-hydrogenases (Hyd1-3). Two of these hydrogenases are respiratory enzymes catalysing hydrogen oxidation, whereby Hyd-1 is oxygen-tolerant and Hyd-2 is considered a standard oxygen-sensitive hydrogenase. Hyd-3, together with formate dehydrogenase H (Fdh-H), forms the formate hydrogenlyase (FHL) complex, which is responsible for H2 evolution by intact cells. Hydrogen oxidation activity can be assayed for all three hydrogenases using benzyl viologen (BV; Eo′ = -360 mV) as an artificial electron acceptor; however ascribing activities to specific isoenzymes is not trivial. Previously, an in-gel assay could differentiate Hyd-1 and Hyd-2, while Hyd-3 had long been considered too unstable to be visualized on such native gels. This study identifies conditions allowing differentiation of all three enzymes using simple in-gel zymographic assays. Results Using a modified in-gel assay hydrogen-dependent BV reduction catalyzed by Hyd-3 has been described for the first time. High hydrogen concentrations facilitated visualization of Hyd-3 activity. The activity was membrane-associated and although not essential for visualization of Hyd-3, the activity was maximal in the presence of a functional Fdh-H enzyme. Furthermore, through the use of nitroblue tetrazolium (NBT; Eo′ = -80 mV) it was demonstrated that Hyd-1 reduces this redox dye in a hydrogen-dependent manner, while neither Hyd-2 nor Hyd-3 could couple hydrogen oxidation to NBT reduction. Hydrogen-dependent reduction of NBT was also catalysed by an oxygen-sensitive variant of Hyd-1 that had a supernumerary cysteine residue at position 19 of the small subunit substituted for glycine. This finding suggests that tolerance toward oxygen is not the main determinant that governs electron donation to more redox-positive electron acceptors such as NBT. Conclusions The utilization of particular electron acceptors at different hydrogen concentrations and redox potentials correlates with the known physiological functions of the respective hydrogenase. The ability to rapidly distinguish between oxygen-tolerant and standard [NiFe]-hydrogenases provides a facile new screen for the discovery of novel enzymes. A reliable assay for Hyd-3 will reinvigorate studies on the characterisation of the hydrogen-evolving FHL complex. PMID:22769583

Patterned helical metallic ribbon for continuous edge winding applications

DOEpatents

Liebermann, Howard H.; Frischmann, Peter G.; Rosenberry, Jr., George M.

1983-04-19

Metallic ribbon having cutout patterns therein is provided in continuous helical form. The cutout patterns may be situated to intersect either or both of the ribbon edges or may be situated entirely within the ribbon. The helical ribbon with the cutout patterns may additionally have a nesting, or self-stacking, feature.

75 FR 16753 - Certain Helical Spring Lock Washers From the People's Republic of China: Rescission of...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-02

... DEPARTMENT OF COMMERCE International Trade Administration [A-570-822] Certain Helical Spring Lock... opportunity to request an administrative review of the antidumping duty order on certain helical spring lock... Works Inc., the petitioner, to conduct an administrative review of Hangzhou Spring Washer Co., Ltd...

76 FR 72722 - Helical Spring Lock Washers From China and Taiwan

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-25

... Spring Lock Washers From China and Taiwan Determination On the basis of the record \\1\\ developed in the... antidumping duty orders on helical spring lock washers from China and Taiwan would be likely to lead to... with respect to helical spring lock washers from Taiwan. Background The Commission instituted these...

Pressure dependence of the magnetic ground states in MnP

DOE PAGES

Matsuda, Masaaki; Ye, Feng; Dissanayake, Sachith E.; ...

2016-03-17

MnP, a superconductor under pressure, exhibits a ferromagnetic order below TC~290 K followed by a helical order with the spins lying in the ab plane and the helical rotation propagating along the c axis below Ts~50 K at ambient pressure. We performed single-crystal neutron diffraction experiments to determine the magnetic ground states under pressure. Both TC and Ts are gradually suppressed with increasing pressure and the helical order disappears at ~1.2 GPa. At intermediate pressures of 1.8 and 2.0 GPa, the ferromagnetic order first develops and changes to a conical or two-phase (ferromagnetic and helical) structure with the propagation alongmore » the b axis below a characteristic temperature. At 3.8 GPa, a helical magnetic order appears below 208 K, which hosts the spins in the ac plane and the propagation along the b axis. The period of this b axis modulation is shorter than that at 1.8 GPa. Here, our results indicate that the magnetic phase in the vicinity of the superconducting phase may have a helical magnetic correlation along the b axis.« less

Pseudo-invariants contributing to inverse energy cascades in three-dimensional turbulence

NASA Astrophysics Data System (ADS)

Rathmann, Nicholas M.; Ditlevsen, Peter D.

2017-05-01

Three-dimensional (3D) turbulence is characterized by a dual forward cascade of both kinetic energy and helicity, a second inviscid flow invariant besides energy, from the integral scale of motion to the viscous dissipative scale. In helical flows, however, such as strongly rotating flows with broken mirror symmetry, an inverse (reversed) energy cascade can be observed analogous to that of two-dimensional turbulence (2D) where enstrophy, a second positive-definite flow invariant, unlike helicity in 3D, effectively blocks the forward cascade of energy. In the spectral-helical decomposition of the Navier-Stokes equation, it has previously been shown that a subset of three-wave (triad) interactions conserve helicity in 3D in a fashion similar to enstrophy in 2D, thus leading to a 2D-like inverse energy cascade in 3D. In this work, we show, both theoretically and numerically, that an additional subset of interactions exist, conserving a new pseudo-invariant in addition to energy and helicity, which contributes either to a forward or an inverse energy cascade depending on the specific triad interaction geometry.

Small-scale anisotropy induced by spectral forcing and by rotation in non-helical and helical turbulence

NASA Astrophysics Data System (ADS)

Vallefuoco, Donato; Naso, Aurore; Godeferd, Fabien S.

2018-02-01

We study the effect of large-scale spectral forcing on the scale-dependent anisotropy of the velocity field in direct numerical simulations of homogeneous turbulence. ABC-type forcing and helical or non-helical Euler-type forcing are considered. We propose a scale-dependent characterisation of anisotropy based on a modal decomposition of the two-point velocity tensor spectrum. This produces direction-dependent spectra of energy, helicity and polarisation. We examine the conditions that allow anisotropy to develop in the small scales due to forcing and we show that the theoretically expected isotropy is not exactly obtained, even in the smallest scales, for ABC and helical Euler forcings. When adding rotation, the anisotropy level in ABC-forced simulations is similar to that of lower Rossby number Euler-forced runs. Moreover, even at low rotation rate, the natural anisotropy induced by the Coriolis force is visible at all scales, and two distinct wavenumber ranges appear from our fine-grained characterisation, not separated by the Zeman scale but by a scale where rotation and dissipation are balanced.

Disentangling the triadic interactions in Navier-Stokes equations.

PubMed

Sahoo, Ganapati; Biferale, Luca

2015-10-01

We study the role of helicity in the dynamics of energy transfer in a modified version of the Navier-Stokes equations with explicit breaking of the mirror symmetry. We select different set of triads participating in the dynamics on the basis of their helicity content. In particular, we remove the negative helically polarized Fourier modes at all wave numbers except for those falling on a localized shell of wave number, |k| ~ k(m). Changing k(m) to be above or below the forcing scale, k(f), we are able to assess the energy transfer of triads belonging to different interaction classes. We observe that when the negative helical modes are present only at a wave number smaller than the forced wave numbers, an inverse energy cascade develops with an accumulation of energy on a stationary helical condensate. Vice versa, when negative helical modes are present only at a wave number larger than the forced wave numbers, a transition from backward to forward energy transfer is observed in the regime when the minority modes become energetic enough.

Molecular dynamics simulations of membrane deformation induced by amphiphilic helices of Epsin, Sar1p, and Arf1

NASA Astrophysics Data System (ADS)

Li, Zhen-Lu

2018-03-01

The N-terminal amphiphilic helices of proteins Epsin, Sar1p, and Arf1 play a critical role in initiating membrane deformation. The interactions of these amphiphilic helices with the lipid membranes are investigated in this study by combining the all-atom and coarse-grained simulations. In the all-atom simulations, the amphiphilic helices of Epsin and Sar1p are found to have a shallower insertion depth into the membrane than the amphiphilic helix of Arf1, but remarkably, the amphiphilic helices of Epsin and Sar1p induce higher asymmetry in the lipid packing between the two monolayers of the membrane. The insertion depth of amphiphilic helix into the membrane is determined not only by the overall hydrophobicity but also by the specific distributions of polar and non-polar residues along the helix. To directly compare their ability to deform the membrane, the coarse-grained simulations are performed to investigate the membrane deformation under the insertion of multiple helices. Project supported by the National Natural Science Foundation of China (Grant Nos. 91427302 and 11474155).

Deformation of a soft helical filament in an axial flow at low Reynolds number.

PubMed

Jawed, Mohammad K; Reis, Pedro M

2016-02-14

We perform a numerical investigation of the deformation of a rotating helical filament subjected to an axial flow, under low Reynolds number conditions, motivated by the propulsion of bacteria using helical flagella. Given its slenderness, the helical rod is intrinsically soft and deforms due to the interplay between elastic forces and hydrodynamic loading. We make use of a previously developed and experimentally validated computational tool framework that models the elasticity of the filament using the discrete elastic rod method and the fluid forces are treated using Lighthill's slender body theory. Under axial flow, and in the absence of rotation, the initially helical rod is extended. Above a critical flow speed its configuration comprises a straight portion connected to a localized helix near the free end. When the rod is also rotated about its helical axis, propulsion is only possible in a finite range of angular velocity, with an upper bound that is limited by buckling of the soft helix arising due to viscous stresses. A systematic exploration of the parameter space allows us to quantify regimes for successful propulsion for a number of specific bacteria.

Fabrication of CA/TPU Helical Nanofibers and its Mechanism Analysis

NASA Astrophysics Data System (ADS)

Wu, Huihui; Zhao, Shihang; Han, Lei

2018-04-01

To explore the mechanism of cellulose acetate (CA)/thermoplastic polyurethane (TPU) on the fabrication of helical nanofibers, a series of experiments were conducted to find the optimum spinning conditions. The experimental results show that the CA (14 wt%, DMAc/acetone, 1/2 volume ratio)/TPU2 (18 wt%, DMAc/acetone, 3/1 volume ratio) system can fabricate helical nanofibers effectively via co-electrospinning. We focus on the interfacial interaction between the polymer components induced by the polymer structure and intrinsic properties, including solution properties, hydrogen bonding, and miscibility behavior of the two solutions. Differential scanning calorimetry (DSC) and Fourier transform infrared spectroscopy (FTIR) are employed to investigate the interfacial interaction between the two phases of the polymer system. The analysis results provide the explanation of the experimental results that the CA/TPU system has the potential for producing helical nanofibers effectively. This study based on the interfacial interaction between polymer components provides an insight into the mechanism of CA/TPU helical fiber formation and introduces a richer choice of materials for the application of helical fibers.

Biomechanical comparison of straight and helical compression plates for fixation of transverse and oblique bone fractures: Modeling and experiments.

PubMed

Sezek, Sinan; Aksakal, Bunyamin; Gürger, Murat; Malkoc, Melih; Say, Y

2016-08-12

Total deformation and stability of straight and helical compression plates were studied by means of the finite element method (FEM) and in vitro biomechanical experiments. Fixations of transverse (TF) and oblique (45°) bone (OF) fractures have been analyzed on sheep tibias by designing the straight compression (SP) and Helical Compression Plate (HP) models. The effects of axial compression, bending and torsion loads on both plating systems were analyzed in terms of total displacements. Numerical models and experimental models suggested that under compression loadings, bone fracture gap closures for both fracture types were found to be in the favor of helical plate designs. The helical plate (HP) fixations provided maximum torsional resistance compared to the (SP) fixations. The fracture gap closure and stability of helical plate fixation for transverse fractures was determined to be higher than that found for the oblique fractures. The comparison of average compression stress, bending and torsion moments showed that the FEM and experimental results are in good agreement and such designs are likely to have a positive impact in future bone fracture fixation designs.

Controllable rotational inversion in nanostructures with dual chirality.

PubMed

Dai, Lu; Zhu, Ka-Di; Shen, Wenzhong; Huang, Xiaojiang; Zhang, Li; Goriely, Alain

2018-04-05

Chiral structures play an important role in natural sciences due to their great variety and potential applications. A perversion connecting two helices with opposite chirality creates a dual-chirality helical structure. In this paper, we develop a novel model to explore quantitatively the mechanical behavior of normal, binormal and transversely isotropic helical structures with dual chirality and apply these ideas to known nanostructures. It is found that both direction and amplitude of rotation can be finely controlled by designing the cross-sectional shape. A peculiar rotational inversion of overwinding followed by unwinding, observed in some gourd and cucumber tendril perversions, not only exists in transversely isotropic dual-chirality helical nanobelts, but also in the binormal/normal ones when the cross-sectional aspect ratio is close to 1. Beyond this rotational inversion region, the binormal and normal dual-chirality helical nanobelts exhibit a fixed directional rotation of unwinding and overwinding, respectively. Moreover, in the binormal case, the rotation of these helical nanobelts is nearly linear, which is promising as a possible design for linear-to-rotary motion converters. The present work suggests new designs for nanoscale devices.

Reduced bispectrum seeded by helical primordial magnetic fields

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hortúa, Héctor Javier; Castañeda, Leonardo, E-mail: hjhortuao@unal.edu.co, E-mail: lcastanedac@unal.edu.co

In this paper, we investigate the effects of helical primordial magnetic fields (PMFs) on the cosmic microwave background (CMB) reduced bispectrum. We derive the full three-point statistics of helical magnetic fields and numerically calculate the even contribution in the collinear configuration. We then numerically compute the CMB reduced bispectrum induced by passive and compensated PMF modes on large angular scales. There is a negative signal on the bispectrum due to the helical terms of the fields and we also observe that the biggest contribution to the bispectrum comes from the non-zero IR cut-off for causal fields, unlike the two-point correlationmore » case. For negative spectral indices, the reduced bispectrum is enhanced by the passive modes. This gives a lower value of the upper limit for the mean amplitude of the magnetic field on a given characteristic scale. However, high values of IR cut-off in the bispectrum, and the helical terms of the magnetic field relaxes this bound. This demonstrates the importance of the IR cut-off and helicity in the study of the nature of PMFs from CMB observations.« less

Controllable helical deformations on printed anisotropic composite soft actuators

NASA Astrophysics Data System (ADS)

Wang, Dong; Li, Ling; Serjouei, Ahmad; Dong, Longteng; Weeger, Oliver; Gu, Guoying; Ge, Qi

2018-04-01

Helical shapes are ubiquitous in both nature and engineering. However, the development of soft actuators and robots that mimic helical motions has been hindered primarily due to the lack of efficient modeling approaches that take into account the material anisotropy and the directional change of the external loading point. In this work, we present a theoretical framework for modeling controllable helical deformations of cable-driven, anisotropic, soft composite actuators. The framework is based on the minimum potential energy method, and its model predictions are validated by experiments, where the microarchitectures of the soft composite actuators can be precisely defined by 3D printing. We use the developed framework to investigate the effects of material and geometric parameters on helical deformations. The results show that material stiffness, volume fraction, layer thickness, and fiber orientation can be used to control the helical deformation of a soft actuator. In particular, we found that a critical fiber orientation angle exists at which the twist of the actuator changes the direction. Thus, this work can be of great importance for the design and fabrication of soft actuators with tailored deformation behavior.

Structure-activity relationship study of Aib-containing amphipathic helical peptide-cyclic RGD conjugates as carriers for siRNA delivery.

PubMed

Wada, Shun-Ichi; Takesada, Anna; Nagamura, Yurie; Sogabe, Eri; Ohki, Rieko; Hayashi, Junsuke; Urata, Hidehito

2017-12-15

The conjugation of Aib-containing amphipathic helical peptide with cyclo(-Arg-Gly-Asp-d-Phe-Cys-) (cRGDfC) at the C-terminus of the helix peptide (PI) has been reported to be useful for constructing a carrier for targeted siRNA delivery into cells. In order to explore structure-activity relationships for the development of potential carriers for siRNA delivery, we synthesized conjugates of Aib-containing amphipathic helical peptide with cRGDfC at the N-terminus (PII) and both the N- and C-termini (PIII) of the helical peptide. Furthermore, to examine the influence of PI helical chain length on siRNA delivery, truncated peptides containing 16 (PIV), 12 (PV), and 8 (PVI) amino acid residues at the N-terminus of the helical chain were synthesized. PII and PIII, as well as PI, could deliver anti-luciferase siRNA into cells to induce the knockdown of luciferase stably expressed in cells. In contrast, all of the truncated peptides were unlikely to transport siRNA into cells. Copyright © 2017 Elsevier Ltd. All rights reserved.

Iron(II) supramolecular helicates condense plasmid DNA and inhibit vital DNA-related enzymatic activities.

PubMed

Malina, Jaroslav; Hannon, Michael J; Brabec, Viktor

2015-07-27

The dinuclear iron(II) supramolecular helicates [Fe2 L3 ]Cl4 (L=C25 H20 N4 ) bind to DNA through noncovalent (i.e., hydrogen-bonding, electrostatic) interactions and exhibit antimicrobial and anticancer effects. In this study, we show that the helicates condense plasmid DNA with a much higher potency than conventional DNA-condensing agents. Notably, molecules of DNA in the presence of the M enantiomer of [Fe2 L3 ]Cl4 do not form intermolecular aggregates typically formed by other condensing agents, such as spermidine or spermine. The helicates inhibit the activity of several DNA-processing enzymes, such as RNA polymerase, DNA topoisomerase I, deoxyribonuclease I, and site-specific restriction endonucleases. However, the results also indicate that the DNA condensation induced by the helicates does not play a crucial role in these inhibition reactions. The mechanisms for the inhibitory effects of [Fe2 L3 ]Cl4 helicates on DNA-related enzymatic activities have been proposed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Magnetic structure in Mn1 -xCoxGe compounds

NASA Astrophysics Data System (ADS)

Altynbaev, E.; Siegfried, S.-A.; Strauß, P.; Menzel, D.; Heinemann, A.; Fomicheva, L.; Tsvyashchenko, A.; Grigoriev, S.

2018-04-01

The magnetic system of the pseudobinary compound Mn1 -xCoxGe has been studied using small-angle neutron scattering and susceptibility measurements. It is found that Mn1 -xCoxGe orders magnetically at low temperatures in the whole concentration range of x ∈[0 /0.9 ] . Four different states of the magnetic structure have been found at low temperatures: the long-range-ordered (LRO) short-period helical magnetic structure at x

Extracting 3D Parametric Curves from 2D Images of Helical Objects.

PubMed

Willcocks, Chris G; Jackson, Philip T G; Nelson, Carl J; Obara, Boguslaw

2017-09-01

Helical objects occur in medicine, biology, cosmetics, nanotechnology, and engineering. Extracting a 3D parametric curve from a 2D image of a helical object has many practical applications, in particular being able to extract metrics such as tortuosity, frequency, and pitch. We present a method that is able to straighten the image object and derive a robust 3D helical curve from peaks in the object boundary. The algorithm has a small number of stable parameters that require little tuning, and the curve is validated against both synthetic and real-world data. The results show that the extracted 3D curve comes within close Hausdorff distance to the ground truth, and has near identical tortuosity for helical objects with a circular profile. Parameter insensitivity and robustness against high levels of image noise are demonstrated thoroughly and quantitatively.

Passive micromixers with dual helical channels

NASA Astrophysics Data System (ADS)

Liu, Keyin; Yang, Qing; Chen, Feng; Zhao, Yulong; Meng, Xiangwei; Shan, Chao; Li, Yanyang

2015-02-01

In this study, a three-dimensional (3D) micromixer with cross-linked double helical microchannels is studied to achieve rapid mixing of fluids at low Reynolds numbers (Re). The 3D micromixer takes full advantages of the chaotic advection model with helical microchannels; meanwhile, the proposed crossing structure of double helical microchannels enables two flow patterns of repelling flow and straight flow in the fluids to promote the agitation effect. The complex 3D micromixer is realized by an improved femtosecond laser wet etching (FLWE) technology embedded in fused silica. The mixing results show that cross-linked double helical microchannels can achieve excellent mixing within 3 cycles (300 μm) over a wide range of low Re (1.5×10-3~600), which compare well with the conventional passive micromixers. This highly-effective micromixer is hoped to contribute to the integration of microfluidic systems.

Computational design of water-soluble α-helical barrels.

PubMed

Thomson, Andrew R; Wood, Christopher W; Burton, Antony J; Bartlett, Gail J; Sessions, Richard B; Brady, R Leo; Woolfson, Derek N

2014-10-24

The design of protein sequences that fold into prescribed de novo structures is challenging. General solutions to this problem require geometric descriptions of protein folds and methods to fit sequences to these. The α-helical coiled coils present a promising class of protein for this and offer considerable scope for exploring hitherto unseen structures. For α-helical barrels, which have more than four helices and accessible central channels, many of the possible structures remain unobserved. Here, we combine geometrical considerations, knowledge-based scoring, and atomistic modeling to facilitate the design of new channel-containing α-helical barrels. X-ray crystal structures of the resulting designs match predicted in silico models. Furthermore, the observed channels are chemically defined and have diameters related to oligomer state, which present routes to design protein function. Copyright © 2014, American Association for the Advancement of Science.

Effect of the amyloid β hairpin's structure on the handedness of helices formed by its aggregates

DOE PAGES

GhattyVenkataKrishna, Pavan K.; Uberbacher, Edward C.; Cheng, Xiaolin

2013-07-08

Various structural models for amyloid β fibrils have been derived from a variety of experimental techniques. However, these models cannot differentiate between the relative position of the two arms of the β hairpin called the stagger. Amyloid fibrils of various hierarchical levels form left-handed helices composed of β sheets. However it is unclear if positive, negative and zero staggers all form the macroscopic left-handed helices. To address this issue we have conducted extensive molecular dynamics simulations of amyloid β sheets of various staggers and shown that only negative staggers lead to the experimentally observed left-handed helices while positive staggers generatemore » the incorrect right-handed helices. In conclusion, this result suggests that the negative staggers are physiologically relevant structure of the amyloid β fibrils.« less

Control of Helical Chirality of Ferrocene-Dipeptide Conjugates by the Secondary Structure of Dipeptide Chains.

PubMed

Moriuchi, Toshiyuki; Nishiyama, Taiki; Nobu, Masaki; Hirao, Toshikazu

2017-09-18

Controlling helical chirality and creating protein secondary structures in cyclic/acyclic ferrocene-dipeptide bioorganometallic conjugates were achieved by adjusting the conformational flexibility of the dipeptide chains. In systems reported to date, the helical chirality of a conjugate was determined by the absolute configuration of the adjacent amino acid reside. In contrast, it was possible to induce both M- and P-helical chirality, even when the configuration of the adjacent amino acid was the same. It is particularly interesting to note that M-helical chirality was produced in a cyclic ferrocene-dipeptide conjugate composed of the l-Ala-d-Pro-cystamine-d-Pro-l-Ala dipeptide sequence (1), in which a type II β-turn-like secondary structure was established. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Modified Involute Helical Gears: Computerized Design, Simulation of Meshing, and Stress Analysis

NASA Technical Reports Server (NTRS)

Handschuh, Robert (Technical Monitor); Litvin, Faydor L.; Gonzalez-Perez, Ignacio; Carnevali, Luca; Kawasaki, Kazumasa; Fuentes-Aznar, Alfonso

2003-01-01

The computerized design, methods for generation, simulation of meshing, and enhanced stress analysis of modified involute helical gears is presented. The approaches proposed for modification of conventional involute helical gears are based on conjugation of double-crowned pinion with a conventional helical involute gear. Double-crowning of the pinion means deviation of cross-profile from an involute one and deviation in longitudinal direction from a helicoid surface. Using the method developed, the pinion-gear tooth surfaces are in point-contact, the bearing contact is localized and oriented longitudinally, and edge contact is avoided. Also, the influence of errors of aligment on the shift of bearing contact, vibration, and noise are reduced substantially. The theory developed is illustrated with numerical examples that confirm the advantages of the gear drives of the modified geometry in comparison with conventional helical involute gears.

Scaling laws in decaying helical hydromagnetic turbulence

NASA Astrophysics Data System (ADS)

Christensson, M.; Hindmarsh, M.; Brandenburg, A.

2005-07-01

We study the evolution of growth and decay laws for the magnetic field coherence length ξ, energy E_M and magnetic helicity H in freely decaying 3D MHD turbulence. We show that with certain assumptions, self-similarity of the magnetic power spectrum alone implies that ξ σm t1/2. This in turn implies that magnetic helicity decays as Hσm t-2s, where s=(ξ_diff/ξH)2, in terms of ξ_diff, the diffusion length scale, and ξ_H, a length scale defined from the helicity power spectrum. The relative magnetic helicity remains constant, implying that the magnetic energy decays as E_M σm t-1/2-2s. The parameter s is inversely proportional to the magnetic Reynolds number Re_M, which is constant in the self-similar regime.

Helicity charging and eruption of magnetic flux from the Sun

NASA Technical Reports Server (NTRS)

Rust, David M.; Kumar, A.

1994-01-01

The ejection of helical toroidal fields from the solar atmosphere and their detection in interplanetary space are described. The discovery that solar magnetic fields are twisted and that they are segregated by hemisphere according to their chirality has important implications for the escape process. The roles played by erupting prominences, coronal mass ejections (CME's) and active region (AR) loops in expressing the escape of magnetic flux and helicity are discussed. Sporadic flux escape associated with filament eruptions accounts for less than one-tenth the flux loss. Azimuthal flux loss by CME's could account for more, but the major contributor to flux escape may be AR loop expansion. It is shown how the transfer of magnetic helicity from the sun's interior into emerged loops ('helicity charging') could be the effective driver of solar eruptions and of flux loss from the sun.

Modified Involute Helical Gears: Computerized Design, Simulation of Meshing and Stress Analysis

NASA Technical Reports Server (NTRS)

2003-01-01

The computerized design, methods for generation, simulation of meshing, and enhanced stress analysis of modified involute helical gears is presented. The approaches proposed for modification of conventional involute helical gears are based on conjugation of double-crowned pinion with a conventional helical involute gear. Double-crowning of the pinion means deviation of cross-profile from an involute one and deviation in longitudinal direction from a helicoid surface. Using the method developed, the pinion-gear tooth surfaces are in point-contact, the bearing contact is localized and oriented longitudinally, and edge contact is avoided. Also, the influence of errors of alignment on the shift of bearing contact, vibration, and noise are reduced substantially. The theory developed is illustrated with numerical examples that confirm the advantages of the gear drives of the modified geometry in comparison with conventional helical involute gears.

An Evolutionarily Conserved Family of Virion Tail Needles Related to Bacteriophage P22 gp26: Correlation between Structural Stability and Length of the -Helical Trimeric Coiled Coil

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhardwaj, A.; Walker-Kopp, N; Casjens, S

2009-01-01

Bacteriophages of the Podoviridae family use short noncontractile tails to inject their genetic material into Gram-negative bacteria. In phage P22, the tail contains a thin needle, encoded by the phage gene 26, which is essential both for stabilization and for ejection of the packaged viral genome. Bioinformatic analysis of the N-terminal domain of gp26 (residues 1-60) led us to identify a family of genes encoding putative homologues of the tail needle gp26. To validate this idea experimentally and to explore their diversity, we cloned the gp26-like gene from phages HK620, Sf6 and HS1, and characterized these gene products in solution.more » All gp26-like factors contain an elongated {alpha}-helical coiled-coil core consisting of repeating, adjacent trimerization heptads and form trimeric fibers with length ranging between about 240 to 300 {angstrom}. gp26 tail needles display a high level of structural stability in solution, with Tm (temperature of melting) between 85 and 95 C. To determine how the structural stability of these phage fibers correlates with the length of the {alpha}-helical core, we investigated the effect of insertions and deletions in the helical core. In the P22 tail needle, we identified an 85-residue-long helical domain, termed MiCRU (minimal coiled-coil repeat unit), that can be inserted in-frame inside the gp26 helical core, preserving the straight morphology of the fiber. Likewise, we were able to remove three quarters of the helical core of the HS1 tail needle, minimally decreasing the stability of the fiber. We conclude that in the gp26 family of tail needles, structural stability increases nonlinearly with the length of the {alpha}-helical core. Thus, the overall stability of these bacteriophage fibers is not solely dependent on the number of trimerization repeats in the {alpha}-helical core.« less

SU-E-T-197: Helical Cranial-Spinal Treatments with a Linear Accelerator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anderson, J; Bernard, D; Liao, Y

2014-06-01

Purpose: Craniospinal irradiation (CSI) of systemic disease requires a high level of beam intensity modulation to reduce dose to bone marrow and other critical structures. Current helical delivery machines can take 30 minutes or more of beam-on time to complete these treatments. This pilot study aims to test the feasibility of performing helical treatments with a conventional linear accelerator using longitudinal couch travel during multiple gantry revolutions. Methods: The VMAT optimization package of the Eclipse 10.0 treatment planning system was used to optimize pseudo-helical CSI plans of 5 clinical patient scans. Each gantry revolution was divided into three 120° arcsmore » with each isocenter shifted longitudinally. Treatments requiring more than the maximum 10 arcs used multiple plans with each plan after the first being optimized including the dose of the others (Figure 1). The beam pitch was varied between 0.2 and 0.9 (couch speed 5- 20cm/revolution and field width of 22cm) and dose-volume histograms of critical organs were compared to tomotherapy plans. Results: Viable pseudo-helical plans were achieved using Eclipse. Decreasing the pitch from 0.9 to 0.2 lowered the maximum lens dose by 40%, the mean bone marrow dose by 2.1% and the maximum esophagus dose by 17.5%. (Figure 2). Linac-based helical plans showed dose results comparable to tomotherapy delivery for both target coverage and critical organ sparing, with the D50 of bone marrow and esophagus respectively 12% and 31% lower in the helical linear accelerator plan (Figure 3). Total mean beam-on time for the linear accelerator plan was 8.3 minutes, 54% faster than the tomotherapy average for the same plans. Conclusions: This pilot study has demonstrated the feasibility of planning pseudo-helical treatments for CSI targets using a conventional linac and dynamic couch movement, and supports the ongoing development of true helical optimization and delivery.« less

Helicity Transformation under the Collision and Merging of Magnetic Flux Ropes

NASA Astrophysics Data System (ADS)

Dehaas, Timothy

2016-10-01

A magnetic flux rope is a tube-like, current carrying plasma embedded in an external magnetic field. The magnetic field lines resemble threads in a rope, which vary in pitch according to radius. Flux ropes are ubiquitous in astrophysical plasmas, and bundles of these structures play an important role in the dynamics of the space environment. They are observed in the solar atmosphere and near-earth environment where they are seen to twist, merge, tear, and writhe. In this MHD context, their global dynamics are bound by rules of magnetic helicity conservation, unless, under a non-ideal process, helicity is transformed through magnetic reconnection, turbulence, or localized instabilities. These processes are tested under experimental conditions in the Large Plasma Device (LAPD). The device is a twenty-meter long, one-meter diameter, cylindrical vacuum vessel designed to generate a highly reproducible, magnetized plasma. Reliable shot-to-shot repetition of plasma parameters and over four hundred diagnostic ports enable the collection of volumetric datasets (measurements of ne, Te, Vp, B, J, E, uflow) as two kink-unstable flux ropes form, move, collide, and merge. Similar experiments on the LAPD have utilized these volumetric datasets, visualizing magnetic reconnection through a topological quasi-separatrix layer, or QSL. This QSL is shown to be spatially coincident with the reconnection rate, ∫ E . dl , and oscillates (although out of phase) with global helicity. Magnetic helicity is observed to have a negative sign and its counterpart, cross helicity, a positive one. These quantities oscillate 8% peak-to-peak, and the changes in helicity are visualized as 1) the transport of helicity (ϕB + E × A) and 2) the dissipation of the helicity - 2 E . B . This work is supported by LANL-UC research Grant and done at the Basic Plasma Science Facility, which is funded by DOE and NSF.

Mechanical and structural characteristics of the new BONE-LOK cortical-cancellous internal fixation device.

PubMed

Cachia, Victor V; Culbert, Brad; Warren, Chris; Oka, Richard; Mahar, Andrew

2003-01-01

The purpose of this study was to evaluate the structural and mechanical characteristics of a new and unique titanium cortical-cancellous helical compression anchor with BONE-LOK (Triage Medical, Inc., Irvine, CA) technology for compressive internal fixation of fractures and osteotomies. This device provides fixation through the use of a distal helical anchor and a proximal retentive collar that are united by an axially movable pin (U.S. and international patents issued and pending). The helical compression anchor (2.7-mm diameter) was compared with 3.0-mm diameter titanium cancellous screws (Synthes, Paoli, PA) for pullout strength and compression in 7# and 12# synthetic rigid polyurethane foam (simulated bone matrix), and for 3-point bending stiffness. The following results (mean +/- standard deviation) were obtained: foam block pullout strength in 12# foam: 2.7-mm helical compression anchor 70 +/- 2.0 N and 3.0-mm titanium cancellous screws 37 +/- 11 N; in 7# foam: 2.7-mm helical compression anchor 33 +/- 3 N and 3.0-mm titanium cancellous screws 31 +/- 12 N. Three-point bending stiffness, 2.7-mm helical compression anchor 988 +/- 68 N/mm and 3.0-mm titanium cancellous screws 845 +/- 88 N/mm. Compression strength testing in 12# foam: 2.7-mm helical compression anchor 70.8 +/- 4.8 N and 3.0-mm titanium cancellous screws 23.0 +/- 3.1 N, in 7# foam: 2.7-mm helical compression anchor 42.6 +/- 3.2 N and 3.0-mm titanium cancellous screws 10.4 +/- 0.9 N. Results showed greater pullout strength, 3-point bending stiffness, and compression strength for the 2.7-mm helical compression anchor as compared with the 3.0-mm titanium cancellous screws in these testing models. This difference represents a distinct advantage in the new device that warrants further in vivo testing.

New mode of operating a magnetized coaxial plasma gun for injecting magnetic helicity into a spheromak.

PubMed

Woodruff, S; Hill, D N; Stallard, B W; Bulmer, R; Cohen, B; Holcomb, C T; Hooper, E B; McLean, H S; Moller, J; Wood, R D

2003-03-07

By operating a magnetized coaxial plasma gun continuously with just sufficient current to enable plasma ejection, large gun-voltage spikes (approximately 1 kV) are produced, giving the highest sustained voltage approximately 500 V and highest sustained helicity injection rate observed in the Sustained Spheromak Physics Experiment. The spheromak magnetic field increases monotonically with time, exhibiting the lowest fluctuation levels observed during formation of any spheromak (B/B>/=2%). The results suggest an important mechanism for field generation by helicity injection, namely, the merging of helicity-carrying filaments.

Polymorphic transformation of helical flagella of bacteria

NASA Astrophysics Data System (ADS)

Lim, Sookkyung; Howard Berg Collaboration; William Ko Collaboration; Yongsam Kim Collaboration; Wanho Lee Collaboration; Charles Peskin Collaboration

2016-11-01

Bacteria such as E. coli swim in an aqueous environment by utilizing the rotation of flagellar motors and alternate two modes of motility, runs and tumbles. Runs are steady forward swimming driven by bundles of flagellar filaments whose motors are turning CCW; tumbles involve a reorientation of the direction of swimming triggered by motor reversals. During tumbling, the helical flagellum undergoes polymorphic transformations, which is a local change in helical pitch, helical radius, and handedness. In this work, we investigate the underlying mechanism of structural conformation and how this polymorphic transition plays a role in bacterial swimming. National Science Foundation.

Can a pure vector gravitational wave mimic a pure tensor one?

NASA Astrophysics Data System (ADS)

Allen, Bruce

2018-06-01

In the general theory of relativity, gravitational waves have two possible polarizations, which are transverse and traceless with helicity ±2 . Some alternative theories contain additional helicity 0 and helicity ±1 polarization modes. Here, we consider a hypothetical "pure vector" theory in which gravitational waves have only two possible polarizations, with helicity ±1 . We show that if these polarizations are allowed to rotate as the wave propagates, then for certain source locations on the sky, the strain outputs of three ideal interferometric gravitational wave detectors can exactly reproduce the strain outputs predicted by general relativity.

Improved particle confinement in transition from multiple-helicity to quasi-single-helicity regimes of a reversed-field pinch.

PubMed

Frassinetti, L; Predebon, I; Koguchi, H; Yagi, Y; Hirano, Y; Sakakita, H; Spizzo, G; White, R B

2006-10-27

The quasi-single-helicity (QSH) state of a reversed-field pinch (RFP) plasma is a regime in which the RFP configuration can be sustained by a dynamo produced mainly by a single tearing mode and in which a helical structure with well-defined magnetic flux surfaces arises. In this Letter, we show that spontaneous transitions to the QSH regime enhance the particle confinement. This improvement is originated by the simultaneous and cooperative action of the increase of the magnetic island and the reduction of the magnetic stochasticity.

Iron(II) supramolecular helicates interfere with the HIV-1 Tat–TAR RNA interaction critical for viral replication

PubMed Central

Malina, Jaroslav; Hannon, Michael J.; Brabec, Viktor

2016-01-01

The interaction between the HIV-1 transactivator protein Tat and TAR (transactivation responsive region) RNA, plays a critical role in HIV-1 transcription. Iron(II) supramolecular helicates were evaluated for their in vitro activity to inhibit Tat–TAR RNA interaction using UV melting studies, electrophoretic mobility shift assay, and RNase A footprinting. The results demonstrate that iron(II) supramolecular helicates inhibit Tat-TAR interaction at nanomolar concentrations by binding to TAR RNA. These studies provide a new insight into the biological potential of metallosupramolecular helicates. PMID:27405089

Measurements of the canonical helicity evolution of a gyrating kinked plasma column

NASA Astrophysics Data System (ADS)

von der Linden, Jens; Sears, Jason; Intrator, Thomas; You, Setthivoine

2017-10-01

Conversions between kinetic and magnetic energy occur over a wide range of plasma scales as exhibited in astrophysical and solar dynamos, and reconnection in the solar corona and laboratory experiments. Canonical flux tubes present the distinct advantage of reconciling all plasma regimes - e.g. kinetic, two-fluid, and MHD - with the topological concept of helicity: twists, writhes, and linkages. This poster presents the first visualization and analysis of the 3D dynamics of canonical flux tubes and their relative helicity evolution from experimental measurements. Ion and electron canonical flux tubes are visualized from Mach, triple, and Ḃ probe measurements at over 10,000 spatial locations of a gyrating kinked plasma column. The flux tubes co-gyrate with the peak density and electron temperature in and out of a measurement volume. The electron and ion canonical flux tubes twist with opposite handedness and the ion flux tube writhes around the electron flux tube. The relative cross helicity between the magnetic and ion flow vorticity flux tubes dominates the relative ion canonical helicity and is anticorrelated with the relative magnetic helicity. The 3D nature of the kink and a reverse eddy current affect the helicity evolution. This work is supported by DOE Grant DE-SC0010340 and the DOE Office of Science Graduate Student Research Program and prepared in part by LLNL under Contract DE-AC52-07NA27344. LLNL-ABS-734669.

Helical wire stress analysis of unbonded flexible riser under irregular response

NASA Astrophysics Data System (ADS)

Wang, Kunpeng; Ji, Chunyan

2017-06-01

A helical wire is a critical component of an unbonded flexible riser prone to fatigue failure. The helical wire has been the focus of much research work in recent years because of the complex multilayer construction of the flexible riser. The present study establishes an analytical model for the axisymmetric and bending analyses of an unbonded flexible riser. The interlayer contact under axisymmetric loads in this model is modeled by setting radial dummy springs between adjacent layers. The contact pressure is constant during the bending response and applied to determine the slipping friction force per unit helical wire. The model tracks the axial stress around the angular position at each time step to calculate the axial force gradient, then compares the axial force gradient with the slipping friction force to judge the helical wire slipping region, which would be applied to determine the bending stiffness for the next time step. The proposed model is verified against the experimental data in the literature. The bending moment-curvature relationship under irregular response is also qualitatively discussed. The stress at the critical point of the helical wire is investigated based on the model by considering the local flexure. The results indicate that the present model can well simulate the bending stiffness variation during irregular response, which has significant effect on the stress of helical wire.

Towards a Predictive Capability for Local Helicity Injection Startup

NASA Astrophysics Data System (ADS)

Barr, J. L.; Bongard, M. W.; Burke, M. G.; Fonck, R. J.; Hinson, E. T.; Lewicki, B. T.; Perry, J. M.; Redd, A. J.; Schlossberg, D. J.

2014-10-01

Local helicity injection (LHI) is a non-solenoidal tokamak startup technique under development on the Pegasus ST. New designs of the injector cathode geometry and plasma-facing shield rings support high-voltage operation up to 1.5 kV. This leads to reduced requirements in injector area for a given helicity input rate. Near-term experiments in Pegasus are testing the gain in Ip obtained with a 1 . 5 × increase in the helicity input rate and the efficacy of helicity injection in the lower divertor region. A predictive model for LHI is needed to project scalable scenarios for larger devices. A lumped-parameter circuit model using power and helicity balance is being developed for LHI on Pegasus-U and NSTX-U. The model indicates that MA-class startup on NSTX-U will require operating in a regime where the drive from LHI dominates the inductive effects arising from dynamically evolving plasma geometry. The physics of this new regime can be tested in Pegasus-U at Ip ~ 0 . 3 MA. The LHI systems on the proposed Pegasus-U will be expanded to provide 3 - 4 × helicity injection rate and the toroidal field doubled to reach this regime. Predictive models to be validated on Pegasus-U include the 0-D power balance model, NIMROD, and TSC. Work supported by US DOE Grants DE-FG02-96ER54375 and DE-SC0006928.

Flow through triple helical microchannel

NASA Astrophysics Data System (ADS)

Rajbanshi, Pravat; Ghatak, Animangsu

2018-02-01

Flow through helical tubes and channels have been examined in different contexts, for facilitating heat and mass transfer at low Reynolds number flow, for generating plug flow to minimize reactor volume for many reactions. The curvature and torsion of the helices have been shown to engender secondary flow in addition to the primary axial flow, which enhances passive in-plane mixing between different fluid streams. Most of these studies, however, involve a single spiral with circular cross-section, which in essence is symmetric. It is not known, however, how the coupled effect of asymmetry of cross-section and the curvature and torsion of channel would affect the flow profile inside such tubes or channels. In this context, we have presented here the analysis of fluid flow at low Reynolds number inside a novel triple helical channel that consists of three helical flow paths joined along their contour length forming a single channel. We have carried out both microparticle image velocimetry (micro-PIV) and 3D simulation in FLUENT of flow of a Newtonian fluid through such channels. Our analysis shows that whereas in conventional single helices, the secondary flow is characterized by two counter-rotating vortices, in the case of triple helical channels, number of such vortices increases with the helix angle. Such flow profile is expected to enhance possibility of mixing between the liquids, yet diminish the pressure drop.

Ribbons characterize magnetohydrodynamic magnetic fields better than lines: a lesson from dynamo theory

NASA Astrophysics Data System (ADS)

Blackman, Eric G.; Hubbard, Alexander

2014-08-01

Blackman and Brandenburg argued that magnetic helicity conservation in dynamo theory can in principle be captured by diagrams of mean field dynamos when the magnetic fields are represented by ribbons or tubes, but not by lines. Here, we present such a schematic ribbon diagram for the α2 dynamo that tracks magnetic helicity and provides distinct scales of large-scale magnetic helicity, small-scale magnetic helicity, and kinetic helicity involved in the process. This also motivates our construction of a new `2.5 scale' minimalist generalization of the helicity-evolving equations for the α2 dynamo that separately allows for these three distinct length-scales while keeping only two dynamical equations. We solve these equations and, as in previous studies, find that the large-scale field first grows at a rate independent of the magnetic Reynolds number RM before quenching to an RM-dependent regime. But we also show that the larger the ratio of the wavenumber where the small-scale current helicity resides to that of the forcing scale, the earlier the non-linear dynamo quenching occurs, and the weaker the large-scale field is at the turnoff from linear growth. The harmony between the theory and the schematic diagram exemplifies a general lesson that magnetic fields in magnetohydrodynamic are better visualized as two-dimensional ribbons (or pairs of lines) rather than single lines.

Improving cell penetration of helical peptides stabilized by N-terminal crosslinked aspartic acids.

PubMed

Zhao, Hui; Jiang, Yanhong; Tian, Yuan; Yang, Dan; Qin, Xuan; Li, Zigang

2017-01-04

Cell penetration and nucleus translocation efficiency are important for the cellular activities of peptide therapeutics. For helical peptides stabilized by N-terminal crosslinked aspartic acid, correlations between their penetration efficiency/nucleus translocation and physicochemical properties were studied. An increase in hydrophobicity and isoelectric point will promote cellular uptake and nucleus translocation of stabilized helices.

Free Energy and Structure of Helix-forming Peptides: A Theoretical Investigation

NASA Astrophysics Data System (ADS)

Karpusenka, Vadzim

This thesis focuses on the structure and free energy of helical secondary structures of short peptides in a variety of experimental settings. Specifically, the formation of alpha-, pi- and 310-helices was investigated using large-scale classical molecular dynamics simulations with state-of-the-art force fields. In addition, the recently developed Adaptively Biased Molecular Dynamics (ABMD) and Steered Molecular Dynamics (SMD) methods were used to calculate the corresponding free energies. The most important results are as follows. For the examined peptide homopolymers, the observed minima on the free energy landscapes (based on suitable collective variables such as the radius of gyration, number of hydrogen bonds, and handedness) were associated with alpha-helices and "globular" or "knot-like" configurations only. No evidence was found to indicate that 310- or pi-helices represent equilibrium structures for these systems. In addition, the free energy landscape of short peptide chains formed by mixing two different amino acids were also examined. These results too indicate that the alpha-helix is only equilibrium helical secondary structure, and that the mixing of different amino acids does not result in the introduction of any significant new minima into the free energy landscapes. These results are in agreement with experimental observations insofar as these indicate that helical structural motifs are primary based on alpha-helices, with 310- and pi-helices being observed only rarely. Although pi- and 310-helices represent nonequilibrium structures, we were still able to estimate their free energies by means of SMD simulations. The helical secondary structure of the examined polypeptide chains is due to the formation of hydrogen bonds. However, there are other mechanisms that may allow for the additional stabilization of these structures. Specifically, in the so-called AK-(4,7) protein, the possible presence of disulfide bonds connecting cysteine residues may significantly alter the free energy landscapes and therefore the stability of different helical structures. We therefore examined this issue with ABMD simulations. However, our results show that while the free energy landscapes are indeed significantly altered only the formation of alpha-helices is favored as a secondary structural motif. Since all the results indicate that alpha-helix formation dominates, it is natural to think in terms of an alpha-helix forming propensity for different amino acids. To address this question, we carried out an extensive residue-by-residue population analysis of different amino acid guests in an alanine-based host setting. Such an analysis allows us to rank the different amino acid guests based on whether they increased or decreased the population in the alpha-helix region of the corresponding Ramachandran plots. Our ranking of the different guest amino acids is in reasonable correspondence with the experimental results, although some differences are observed. Finally, using a four-beads coarse-grained model were have investigated the stability of GA88 and GB88 proteins, which are quite similar in terms of their amino acid sequence, by means of 10mus simulations. The results indicate that while the three alpha-helix bundle of the GA88 protein remains stable, the 2beta--alpha--2beta configuration of the GB88 protein does not: the latter rapidly converts to a structure consisting mostly of helices similar to the GA88 protein design. These results indicate that this particular four-bead coarse-grained model is not able to properly grasp the dynamics of the beta-sheet secondary structure and overstabilizes the corresponding helical content.

Magnetic helicity of the global field in solar cycles 23 and 24

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pipin, V. V.; Pevtsov, A. A.

2014-07-01

For the first time we reconstruct the magnetic helicity density of the global axisymmetric field of the Sun using the method proposed by Brandenburg et al. and Pipin et al. To determine the components of the vector potential, we apply a gauge which is typically employed in mean-field dynamo models. This allows for a direct comparison of the reconstructed helicity with the predictions from the mean-field dynamo models. We apply this method to two different data sets: the synoptic maps of the line-of-sight magnetic field from the Michelson Doppler Imager (MDI) on board the Solar and Heliospheric Observatory (SOHO) andmore » vector magnetic field measurements from the Vector Spectromagnetograph (VSM) on the Synoptic Optical Long-term Investigations of the Sun (SOLIS) system. Based on the analysis of the MDI/SOHO data, we find that in solar cycle 23 the global magnetic field had positive (negative) magnetic helicity in the northern (southern) hemisphere. This hemispheric sign asymmetry is opposite to the helicity of the solar active regions, but it is in agreement with the predictions of mean-field dynamo models. The data also suggest that the hemispheric helicity rule may have reversed its sign during the early and late phases of cycle 23. Furthermore, the data indicate an imbalance in magnetic helicity between the northern and southern hemispheres. This imbalance seems to correlate with the total level of activity in each hemisphere in cycle 23. The magnetic helicity for the rising phase of cycle 24 is derived from SOLIS/VSM data, and qualitatively its latitudinal pattern is similar to the pattern derived from SOHO/MDI data for cycle 23.« less

INTERPRETING ERUPTIVE BEHAVIOR IN NOAA AR 11158 VIA THE REGION'S MAGNETIC ENERGY AND RELATIVE-HELICITY BUDGETS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tziotziou, Kostas; Georgoulis, Manolis K.; Liu Yang

In previous works, we introduced a nonlinear force-free method that self-consistently calculates the instantaneous budgets of free magnetic energy and relative magnetic helicity in solar active regions (ARs). Calculation is expedient and practical, using only a single vector magnetogram per computation. We apply this method to a time series of 600 high-cadence vector magnetograms of the eruptive NOAA AR 11158 acquired by the Helioseismic and Magnetic Imager on board the Solar Dynamics Observatory over a five-day observing interval. Besides testing our method extensively, we use it to interpret the dynamical evolution in the AR, including eruptions. We find that themore » AR builds large budgets of both free magnetic energy and relative magnetic helicity, sufficient to power many more eruptions than the ones it gave within the interval of interest. For each of these major eruptions, we find eruption-related decreases and subsequent free-energy and helicity budgets that are consistent with the observed eruption (flare and coronal mass ejection (CME)) sizes. In addition, we find that (1) evolution in the AR is consistent with the recently proposed (free) energy-(relative) helicity diagram of solar ARs, (2) eruption-related decreases occur before the flare and the projected CME-launch times, suggesting that CME progenitors precede flares, and (3) self terms of free energy and relative helicity most likely originate from respective mutual terms, following a progressive mutual-to-self conversion pattern that most likely stems from magnetic reconnection. This results in the non-ideal formation of increasingly helical pre-eruption structures and instigates further research on the triggering of solar eruptions with magnetic helicity firmly placed in the eruption cadre.« less

The Role of Magnetic Helicity in Structuring the Solar Corona

NASA Technical Reports Server (NTRS)

Knizhnik, K. J.; Antiochos, S. K.; DeVore, C. R.

2017-01-01

Two of the most widely observed and striking features of the Suns magnetic field are coronal loops, which are smooth and laminar, and prominences or filaments, which are strongly sheared. Loops are puzzling because they show little evidence of tangling or braiding, at least on the quiet Sun, despite the chaotic nature of the solar surface convection. Prominences are mysterious because the origin of their underlying magnetic structure filament channels is poorly understood at best. These two types of features would seem to be quite unrelated and wholly distinct. We argue that, on the contrary, they are inextricably linked and result from a single process: the injection of magnetic helicity into the corona by photospheric motions and the subsequent evolution of this helicity by coronal reconnection. In this paper, we present numerical simulations of the response of a Parker (1972) corona to photospheric driving motions that have varying degrees of helicity preference. We obtain four main conclusions: (1) in agreement with the helicity condensation model of Antiochos (2013), the inverse cascade of helicity by magnetic reconnection in the corona results in the formation of filament channels localized about polarity inversion lines; (2) this same process removes most complex fine structure from the rest of the corona, resulting in smooth and laminar coronal loops; (3) the amount of remnant tangling in coronal loops is inversely dependent on the net helicity injected by the driving motions; and (4) the structure of the solar corona depends only on the helicity preference of the driving motions and not on their detailed time dependence. We discuss the implications of our results for high-resolution observations of the corona.

THE ROLE OF MAGNETIC HELICITY IN STRUCTURING THE SOLAR CORONA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Knizhnik, K. J.; Antiochos, S. K.; DeVore, C. R.

Two of the most widely observed and striking features of the Sun's magnetic field are coronal loops, which are smooth and laminar, and prominences or filaments, which are strongly sheared. Loops are puzzling because they show little evidence of tangling or braiding, at least on the quiet Sun, despite the chaotic nature of the solar surface convection. Prominences are mysterious because the origin of their underlying magnetic structure—filament channels—is poorly understood at best. These two types of features would seem to be quite unrelated and wholly distinct. We argue that, on the contrary, they are inextricably linked and result frommore » a single process: the injection of magnetic helicity into the corona by photospheric motions and the subsequent evolution of this helicity by coronal reconnection. In this paper, we present numerical simulations of the response of a Parker (1972) corona to photospheric driving motions that have varying degrees of helicity preference. We obtain four main conclusions: (1) in agreement with the helicity condensation model of Antiochos (2013), the inverse cascade of helicity by magnetic reconnection in the corona results in the formation of filament channels localized about polarity inversion lines; (2) this same process removes most complex fine structure from the rest of the corona, resulting in smooth and laminar coronal loops; (3) the amount of remnant tangling in coronal loops is inversely dependent on the net helicity injected by the driving motions; and (4) the structure of the solar corona depends only on the helicity preference of the driving motions and not on their detailed time dependence. We discuss the implications of our results for high-resolution observations of the corona.« less

A Sun-to-Earth Analysis of Magnetic Helicity of the 2013 March 17–18 Interplanetary Coronal Mass Ejection

NASA Astrophysics Data System (ADS)

Pal, Sanchita; Gopalswamy, Nat; Nandy, Dibyendu; Akiyama, Sachiko; Yashiro, Seiji; Makela, Pertti; Xie, Hong

2017-12-01

We compare the magnetic helicity in the 2013 March 17–18 interplanetary coronal mass ejection (ICME) flux rope at 1 au and in its solar counterpart. The progenitor coronal mass ejection (CME) erupted on 2013 March 15 from NOAA active region 11692 and is associated with an M1.1 flare. We derive the source region reconnection flux using the post-eruption arcade (PEA) method that uses the photospheric magnetogram and the area under the PEA. The geometrical properties of the near-Sun flux rope is obtained by forward-modeling of white-light CME observations. Combining the geometrical properties and the reconnection flux, we extract the magnetic properties of the CME flux rope. We derive the magnetic helicity of the flux rope using its magnetic and geometric properties obtained near the Sun and at 1 au. We use a constant-α force-free cylindrical flux rope model fit to the in situ observations in order to derive the magnetic and geometric information of the 1 au ICME. We find a good correspondence in both amplitude and sign of the helicity between the ICME and the CME, assuming a semi-circular (half torus) ICME flux rope with a length of π au. We find that about 83% of the total flux rope helicity at 1 au is injected by the magnetic reconnection in the low corona. We discuss the effect of assuming flux rope length in the derived value of the magnetic helicity. This study connecting the helicity of magnetic flux ropes through the Sun–Earth system has important implications for the origin of helicity in the interplanetary medium and the topology of ICME flux ropes at 1 au and hence their space weather consequences.

Using Magnetic Helicity Diagnostics to Determine the Nature of Solar Active-Region Formation

NASA Astrophysics Data System (ADS)

Georgoulis, Manolis K.

Employing a novel nonlinear force-free (NLFF) method that self-consistently infers instantaneous free magnetic-energy and relative magnetic-helicity budgets from single photospheric vector magnetograms, we recently constructed the magnetic energy-helicity (EH) diagram of solar active regions. The EH diagram implies dominant relative helicities of left-handed or right-handed chiralities for the great majority of active regions. The amplitude (budget) of these helicities scales monotonically with the free magnetic energy. This constructive, strongly preferential accumulation of a certain sense of magnetic helicity seems to disqualify recently proposed mechanisms relying on a largely random near-surface convection for the formation of the great majority of active regions. The existing qualitative formation mechanism for these regions remains the conventional Omega-loop emergence following a buoyant ascension from the bottom of the convection zone. However, exceptions to this rule include even eruptive active regions: NOAA AR 11283 is an obvious outlier to the EH diagram, involving significant free magnetic energy with a small relative magnetic helicity. Relying on a timeseries of vector magnetograms of this region, our methodology shows nearly canceling amounts of both senses of helicity and an overall course from a weakly left-handed to a weakly right-handed structure, in the course of which a major eruption occurs. For this and similarly behaving active regions the latest near-surface formation scenario might conceivably be employed successfully. Research partially supported by the EU Seventh Framework Programme under grant agreement No. PIRG07-GA-2010-268245 and by the European Union Social Fund (ESF) and Greek national funds through the Operational Program "Education and Lifelong Learning" of the National Strategic Reference Framework (NSRF) - Research Funding Program: Thales. Investing in knowledge society through the European Social Fund.

Aortic Valve Stenosis Increases Helical Flow and Flow Complexity: A Study of Intra-Operative Cardiac Vector Flow Imaging.

PubMed

Hansen, Kristoffer Lindskov; Møller-Sørensen, Hasse; Kjaergaard, Jesper; Jensen, Maiken Brit; Jensen, Jørgen Arendt; Nielsen, Michael Bachmann

2017-08-01

Aortic valve stenosis alters blood flow in the ascending aorta. Using intra-operative vector flow imaging on the ascending aorta, secondary helical flow during peak systole and diastole, as well as flow complexity of primary flow during systole, were investigated in patients with normal, stenotic and replaced aortic valves. Peak systolic helical flow, diastolic helical flow and flow complexity during systole differed between the groups (p < 0.0001), and correlated to peak systolic velocity (R = 0.94, 0.87 and 0.88, respectively). The study indicates that aortic valve stenosis increases helical flow and flow complexity, which are measurable with vector flow imaging. For assessment of aortic stenosis and optimization of valve surgery, vector flow imaging may be useful. Copyright © 2017 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

Helicity multiplexed broadband metasurface holograms.

PubMed

Wen, Dandan; Yue, Fuyong; Li, Guixin; Zheng, Guoxing; Chan, Kinlong; Chen, Shumei; Chen, Ming; Li, King Fai; Wong, Polis Wing Han; Cheah, Kok Wai; Pun, Edwin Yue Bun; Zhang, Shuang; Chen, Xianzhong

2015-09-10

Metasurfaces are engineered interfaces that contain a thin layer of plasmonic or dielectric nanostructures capable of manipulating light in a desirable manner. Advances in metasurfaces have led to various practical applications ranging from lensing to holography. Metasurface holograms that can be switched by the polarization state of incident light have been demonstrated for achieving polarization multiplexed functionalities. However, practical application of these devices has been limited by their capability for achieving high efficiency and high image quality. Here we experimentally demonstrate a helicity multiplexed metasurface hologram with high efficiency and good image fidelity over a broad range of frequencies. The metasurface hologram features the combination of two sets of hologram patterns operating with opposite incident helicities. Two symmetrically distributed off-axis images are interchangeable by controlling the helicity of the input light. The demonstrated helicity multiplexed metasurface hologram with its high performance opens avenues for future applications with functionality switchable optical devices.

Asymmetric supercapacitors with high energy density based on helical hierarchical porous Na x MnO2 and MoO2.

PubMed

Lu, Xue-Feng; Huang, Zhi-Xiang; Tong, Ye-Xiang; Li, Gao-Ren

2016-01-01

Helical hierarchical porous Na x MnO 2 /CC and MoO 2 /CC, which are assembled from nanosheets and nanoparticles, respectively, are fabricated using a simple electrodeposition method. These unique helical porous structures enable electrodes to have a high capacitance and an outstanding cycling performance. Based on the helical Na x MnO 2 /CC as the positive electrodes and helical MoO 2 /CC as the negative electrodes, high performance Na x MnO 2 /CC//MoO 2 /CC asymmetric supercapacitors (ASCs) are successfully assembled, and they achieve a maximum volume C sp of 2.04 F cm -3 and a maximum energy density of 0.92 mW h cm -3 for the whole device and an excellent cycling stability with 97.22% C sp retention after 6000 cycles.

Measurement of the W boson helicity in t$$\\bar{t}$$ decays

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schmitt, Christian

2005-06-01

The subject of this thesis is the measurement of the helicity of the W boson produced in the decay of the top quark. The standard model predicts the helicity of these W bosons to be either negative or zero, but not positive. In case the top quark sector is already influenced by effects from new physics, the weak charged current, responsible for the decay of the top quark, can be altered from a pure V=A charged current interaction to a pure V+A interaction or a mixture between these two scenarios. This would decrease the fraction of W bosons with negativemore » helicity and W bosons with positive helicity would appear. A change would then be visible in the distribution of the decay angle θ between the lepton and the (negative) b quark direction in the rest frame of the W boson.« less

Non-solenoidal startup and low-β operations in Pegasus

NASA Astrophysics Data System (ADS)

Schlossberg, D. J.; Battaglia, D. J.; Bongard, M. W.; Fonck, R. J.; Redd, A. J.

2009-11-01

Non-solenoidal startup using point-source DC helicity injectors (plasma guns) has been achieved in the Pegasus Toroidal Experiment for plasmas with Ip in excess of 100 kA using Iinj<4,A. The maximum achieved Ip tentatively scales as √ITFIinj/w, where w is the radial thickness of the gun-driven edge. The Ip limits appear to conform to a simple stationary model involving helicity conservation and Taylor relaxation. However, observed MHD activity reveals the additional dynamics of the relaxation process, evidenced by intermittent bursts of n=1 activity correlated with rapid redistribution of the current channel. Recent upgrades to the gun system provide higher helicity injection rates, smaller w, a more constrained gun current path, and more precise diagnostics. Experimental goals include extending parametric scaling studies, determining the conditions where parallel conduction losses dominate the helicity dissipation, and building the physics understanding of helicity injection to confidently design gun systems for larger, future tokamaks.

Observation of enhanced radial transport of energetic ion due to energetic particle mode destabilized by helically-trapped energetic ion in the Large Helical Device

NASA Astrophysics Data System (ADS)

Ogawa, K.; Isobe, M.; Kawase, H.; Nishitani, T.; Seki, R.; Osakabe, M.; LHD Experiment Group

2018-04-01

A deuterium experiment was initiated to achieve higher-temperature and higher-density plasmas in March 2017 in the Large Helical Device (LHD). The central ion temperature notably increases compared with that in hydrogen experiments. However, an energetic particle mode called the helically-trapped energetic-ion-driven resistive interchange (EIC) mode is often excited by intensive perpendicular neutral beam injections on high ion-temperature discharges. The mode leads to significant decrease of the ion temperature or to limiting the sustainment of the high ion-temperature state. To understand the effect of EIC on the energetic ion confinement, the radial transport of energetic ions is studied by means of the neutron flux monitor and vertical neutron camera newly installed on the LHD. Decreases of the line-integrated neutron profile in core channels show that helically-trapped energetic ions are lost from the plasma.

Helical vortices: viscous dynamics and instability

NASA Astrophysics Data System (ADS)

Rossi, Maurice; Selcuk, Can; Delbende, Ivan; Ijlra-Upmc Team; Limsi-Cnrs Team

2014-11-01

Understanding the dynamical properties of helical vortices is of great importance for numerous applications such as wind turbines, helicopter rotors, ship propellers. Locally these flows often display a helical symmetry: fields are invariant through combined axial translation of distance Δz and rotation of angle θ = Δz / L around the same z-axis, where 2 πL denotes the helix pitch. A DNS code with built-in helical symmetry has been developed in order to compute viscous quasi-steady basic states with one or multiple vortices. These states will be characterized (core structure, ellipticity, ...) as a function of the pitch, without or with an axial flow component. The instability modes growing in the above base flows and their growth rates are investigated by a linearized version of the DNS code coupled to an Arnoldi procedure. This analysis is complemented by a helical thin-cored vortex filaments model. ANR HELIX.

Helicity multiplexed broadband metasurface holograms

PubMed Central

Wen, Dandan; Yue, Fuyong; Li, Guixin; Zheng, Guoxing; Chan, Kinlong; Chen, Shumei; Chen, Ming; Li, King Fai; Wong, Polis Wing Han; Cheah, Kok Wai; Yue Bun Pun, Edwin; Zhang, Shuang; Chen, Xianzhong

2015-01-01

Metasurfaces are engineered interfaces that contain a thin layer of plasmonic or dielectric nanostructures capable of manipulating light in a desirable manner. Advances in metasurfaces have led to various practical applications ranging from lensing to holography. Metasurface holograms that can be switched by the polarization state of incident light have been demonstrated for achieving polarization multiplexed functionalities. However, practical application of these devices has been limited by their capability for achieving high efficiency and high image quality. Here we experimentally demonstrate a helicity multiplexed metasurface hologram with high efficiency and good image fidelity over a broad range of frequencies. The metasurface hologram features the combination of two sets of hologram patterns operating with opposite incident helicities. Two symmetrically distributed off-axis images are interchangeable by controlling the helicity of the input light. The demonstrated helicity multiplexed metasurface hologram with its high performance opens avenues for future applications with functionality switchable optical devices. PMID:26354497

Macroscopic ordering of helical pores for arraying guest molecules noncentrosymmetrically

PubMed Central

Li, Chunji; Cho, Joonil; Yamada, Kuniyo; Hashizume, Daisuke; Araoka, Fumito; Takezoe, Hideo; Aida, Takuzo; Ishida, Yasuhiro

2015-01-01

Helical nanostructures have attracted continuous attention, not only as media for chiral recognition and synthesis, but also as motifs for studying intriguing physical phenomena that never occur in centrosymmetric systems. To improve the quality of signals from these phenomena, which is a key issue for their further exploration, the most straightforward is the macroscopic orientation of helices. Here as a versatile scaffold to rationally construct this hardly accessible structure, we report a polymer framework with helical pores that unidirectionally orient over a large area (∼10 cm2). The framework, prepared by crosslinking a supramolecular liquid crystal preorganized in a magnetic field, is chemically robust, functionalized with carboxyl groups and capable of incorporating various basic or cationic guest molecules. When a nonlinear optical chromophore is incorporated in the framework, the resultant complex displays a markedly efficient nonlinear optical output, owing to the coherence of signals ensured by the macroscopically oriented helical structure. PMID:26416086

On the Conservation of Cross Helicity and Wave Action in Solar-wind Models with Non-WKB Alfvén Wave Reflection

NASA Astrophysics Data System (ADS)

Chandran, Benjamin D. G.; Perez, Jean C.; Verscharen, Daniel; Klein, Kristopher G.; Mallet, Alfred

2015-09-01

The interaction between Alfvén-wave turbulence and the background solar wind affects the cross helicity (\\int {d}3x {\\boldsymbol{v}}\\cdot {\\boldsymbol{B}}) in two ways. Non-WKB reflection converts outward-propagating Alfvén waves into inward-propagating Alfvén waves and vice versa, and the turbulence transfers momentum to the background flow. When both effects are accounted for, the total cross helicity is conserved. In the special case that the background density and flow speed are independent of time, the equations of cross-helicity conservation and total-energy conservation can be combined to recover a well-known equation derived by Heinemann and Olbert that has been interpreted as a non-WKB generalization of wave-action conservation. This latter equation (in contrast to cross-helicity and energy conservation) does not hold when the background varies in time.

Helical Structure Determines Different Susceptibilities of dsDNA, dsRNA, and tsDNA to Counterion-Induced Condensation

PubMed Central

Kornyshev, Alexei A.; Leikin, Sergey

2013-01-01

Recent studies of counterion-induced condensation of nucleic acid helices into aggregates produced several puzzling observations. For instance, trivalent cobalt hexamine ions condensed double-stranded (ds) DNA oligomers but not their more highly charged dsRNA counterparts. Divalent alkaline earth metal ions condensed triple-stranded (ts) DNA oligomers but not dsDNA. Here we show that these counterintuitive experimental results can be rationalized within the electrostatic zipper model of interactions between molecules with helical charge motifs. We report statistical mechanical calculations that reveal dramatic and nontrivial interplay between the effects of helical structure and thermal fluctuations on electrostatic interaction between oligomeric nucleic acids. Combining predictions for oligomeric and much longer helices, we also interpret recent experimental studies of the role of counterion charge, structure, and chemistry. We argue that an electrostatic zipper attraction might be a major or even dominant force in nucleic acid condensation. PMID:23663846

Energy and helicity of magnetic torus knots and braids

NASA Astrophysics Data System (ADS)

Oberti, Chiara; Ricca, Renzo L.

2018-02-01

By considering steady magnetic fields in the shape of torus knots and unknots in ideal magnetohydrodynamics, we compute some fundamental geometric and physical properties to provide estimates for magnetic energy and helicity. By making use of an appropriate parametrization, we show that knots with dominant toroidal coils that are a good model for solar coronal loops have negligible total torsion contribution to magnetic helicity while writhing number provides a good proxy. Hence, by the algebraic definition of writhe based on crossing numbers, we show that the estimated values of writhe based on image analysis provide reliable information for the exact values of helicity. We also show that magnetic energy is linearly related to helicity, and the effect of the confinement of magnetic field can be expressed in terms of geometric information. These results can find useful application in solar and plasma physics, where braided structures are often present.

Signatures of unfolding in the early stages of protein denaturation

NASA Astrophysics Data System (ADS)

Gray, Harry B.; Winkler, Jay R.; Kozak, John J.

2012-04-01

A comparative study of the early stages of unfolding of five proteins: cyt c, c-b 562, cyt c‧, azurin, and lysozyme is reported. From crystallographic data, helical regions and intervening non-helical (or 'turning') regions are identified in each. Exploiting a previously introduced geometrical model, the paper describes quantitatively the stepwise extension of a polypeptide chain subject to the geometrical constraint that the spatial relationship among the residues of each triplet is fixed by native-state crystallographic data. Despite differences among the above-cited proteins, remarkable universality of behavior is found in the early stages of unfolding. At the very earliest stages, internal residues in each helical region have a common unfolding history; the terminal residues, however, are extraordinarily sensitive to structural perturbations. Residues in non-helical sections of the polypeptide unfold after residues in the internal helical regions, but with increasing steric perturbation playing a dominant role in advancing denaturation.

Bidirectional helical motility of cytoplasmic dynein around microtubules

PubMed Central

Can, Sinan; Dewitt, Mark A; Yildiz, Ahmet

2014-01-01

Cytoplasmic dynein is a molecular motor responsible for minus-end-directed cargo transport along microtubules (MTs). Dynein motility has previously been studied on surface-immobilized MTs in vitro, which constrains the motors to move in two dimensions. In this study, we explored dynein motility in three dimensions using an MT bridge assay. We found that dynein moves in a helical trajectory around the MT, demonstrating that it generates torque during cargo transport. Unlike other cytoskeletal motors that produce torque in a specific direction, dynein generates torque in either direction, resulting in bidirectional helical motility. Dynein has a net preference to move along a right-handed helical path, suggesting that the heads tend to bind to the closest tubulin binding site in the forward direction when taking sideways steps. This bidirectional helical motility may allow dynein to avoid roadblocks in dense cytoplasmic environments during cargo transport. DOI: http://dx.doi.org/10.7554/eLife.03205.001 PMID:25069614

Plant tendrils: Nature's hygroscopic springs

NASA Astrophysics Data System (ADS)

Gerbode, Sharon; Puzey, Joshua; McCormick, Andrew; Mahadevan, L.

2012-02-01

Plant tendrils are specialized climbing organs that have fascinated biologists and physicists alike for centuries. Initially straight tendrils attach at the tip to an elevated rigid support and then winch the plant upward by coiling into a helical morphology characterized by two helices of opposite handedness connected by a helical perversion. In his renowned treatise on twining and tendril-bearing plants, Charles Darwin surmised that coiled tendrils serve as soft, springy attachments for the climbing plant. Yet, the true effect of the perverted helical shape of a coiled plant tendril has not been fully revealed. Using a combination of experiments on Cucurbitaceae tendrils, physical models constructed from strained rubber sheets, and numerical models of helical perversions, we have uncovered that tendril coiling occurs via anisotropic shrinkage of a strip of specialized cells in the interior of the tendril. Furthermore, variations in the mechanical behavior of tendrils as they become drier and ``woodier'' adds a new twist to the story of tendril coiling.

Conformation of chromatin oligomers. A new argument for a change with the hexanucleosome.

PubMed

Marion, C; Bezot, P; Hesse-Bezot, C; Roux, B; Bernengo, J C

1981-11-01

Quasielastic laser light scattering measurements have been made on chromatin oligomers to obtain information on the transition in their electrooptical properties, previously observed for the hexameric structures [Marion, C. and Roux, B. (1978) Nucleic Acids Res. 5, 4431-4449]. Translational diffusion coefficients were determined for mononucleosomes to octanucleosomes containing histone H1 over a range of ionic strength. At high ionic strength, oligomers show a linear dependence of the logarithm of diffusion coefficient upon the logarithm of number of nucleosomes. At low ionic strength a change occurs between hexamer and heptamer. Our results agree well with the recent sedimentation data of Osipova et al. [Eur. J. Biochem. (1980) 113, 183-188] and of Butler and Thomas [J. Mol. Biol. (1980) 140, 505-529] showing a change in stability with hexamer. Various models for the arrangements of nucleosomes in the superstructure of chromatin are discussed. All calculations clearly indicate a conformational change with the hexanucleosome and the results suggest that, at low ionic strength, the chromatin adopts a loosely helical structure of 28-nm diameter and 22-nm pitch. These results are also consistent with a discontinuity every sixth nucleosome, corresponding to a turn of the helix. This discontinuity may explain the recent electric dichroism data of Lee et al. [Biochemistry (1981) 20, 1438-1445]. The hexanucleosome structure which we have previously suggested, with the faces of nucleosomes arranged radially to the helical axis has been recently confirmed by Mc Ghee et al. [Cell (1980) 22, 87-96]. With an increase of ionic strength, the helix becomes more regular and compact with a slightly reduced outer diameter and a decreased pitch, the dimensions resembling those proposed for solenoid models.

Enantiomeric excesses induced in amino acids by ultraviolet circularly polarized light irradiation of extraterrestrial ice analogs: A possible source of asymmetry for prebiotic chemistry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Modica, Paola; De Marcellus, Pierre; D'Hendecourt, Louis Le Sergeant

2014-06-10

The discovery of meteoritic amino acids with enantiomeric excesses of the L-form (ee {sub L}) has suggested that extraterrestrial organic materials may have contributed to prebiotic chemistry and directed the initial occurrence of the ee {sub L} that further led to homochirality of amino acids on Earth. A proposed mechanism for the origin of ee {sub L} in meteorites involves an asymmetric photochemistry of extraterrestrial ices by UV circularly polarized light (CPL). We have performed the asymmetric synthesis of amino acids on achiral extraterrestrial ice analogs by VUV CPL, investigating the chiral asymmetry transfer at two different evolutionary stages atmore » which the analogs were irradiated (regular ices and/or organic residues) and at two different photon energies (6.6 and 10.2 eV). We identify 16 distinct amino acids and precisely measure the L-enantiomeric excesses using the enantioselective GC × GC-TOFMS technique in five of them: α-alanine, 2,3-diaminopropionic acid, 2-aminobutyric acid, valine, and norvaline, with values ranging from ee {sub L} = –0.20% ± 0.14% to ee {sub L} = –2.54% ± 0.28%. The sign of the induced ee {sub L} depends on the helicity and the energy of CPL, but not on the evolutionary stage of the samples, and is the same for all five considered amino acids. Our results support an astrophysical scenario in which the solar system was formed in a high-mass star-forming region where icy grains were irradiated during the protoplanetary phase by an external source of CPL of a given helicity and a dominant energy, inducing a stereo-specific photochemistry.« less

Sarcomere-length dependence of myosin filament structure in skeletal muscle fibres of the frog.

PubMed

Reconditi, Massimo; Brunello, Elisabetta; Fusi, Luca; Linari, Marco; Martinez, Manuel Fernandez; Lombardi, Vincenzo; Irving, Malcolm; Piazzesi, Gabriella

2014-03-01

X-ray diffraction patterns were recorded at beamline ID02 of the European Synchrotron Radiation Facility from small bundles of skeletal muscle fibres from Rana esculenta at sarcomere lengths between 2.1 and 3.5 μm at 4°C. The intensities of the X-ray reflections from resting fibres associated with the quasi-helical order of the myosin heads and myosin binding protein C (MyBP-C) decreased in the sarcomere length range 2.6-3.0 μm but were constant outside it, suggesting that an OFF conformation of the thick filament is maintained by an interaction between MyBP-C and the thin filaments. During active isometric contraction the intensity of the M3 reflection from the regular repeat of the myosin heads along the filaments decreased in proportion to the overlap between thick and thin filaments, with no change in its interference fine structure. Thus, myosin heads in the regions of the thick filaments that do not overlap with thin filaments are highly disordered during isometric contraction, in contrast to their quasi-helical order at rest. Heads in the overlap region that belong to two-headed myosin molecules that are fully detached from actin are also highly disordered, in contrast to the detached partners of actin-attached heads. These results provide strong support for the concept of a regulatory structural transition in the thick filament involving changes in both the organisation of the myosin heads on its surface and the axial periodicity of the myosin tails in its backbone, mediated by an interaction between MyBP-C and the thin filaments.

Enantiomeric Excesses Induced in Amino Acids by Ultraviolet Circularly Polarized Light Irradiation of Extraterrestrial Ice Analogs: A Possible Source of Asymmetry for Prebiotic Chemistry

NASA Astrophysics Data System (ADS)

Modica, Paola; Meinert, Cornelia; de Marcellus, Pierre; Nahon, Laurent; Meierhenrich, Uwe J.; Le Sergeant d'Hendecourt, Louis

2014-06-01

The discovery of meteoritic amino acids with enantiomeric excesses of the L-form (ee L) has suggested that extraterrestrial organic materials may have contributed to prebiotic chemistry and directed the initial occurrence of the ee L that further led to homochirality of amino acids on Earth. A proposed mechanism for the origin of ee L in meteorites involves an asymmetric photochemistry of extraterrestrial ices by UV circularly polarized light (CPL). We have performed the asymmetric synthesis of amino acids on achiral extraterrestrial ice analogs by VUV CPL, investigating the chiral asymmetry transfer at two different evolutionary stages at which the analogs were irradiated (regular ices and/or organic residues) and at two different photon energies (6.6 and 10.2 eV). We identify 16 distinct amino acids and precisely measure the L-enantiomeric excesses using the enantioselective GC × GC-TOFMS technique in five of them: α-alanine, 2,3-diaminopropionic acid, 2-aminobutyric acid, valine, and norvaline, with values ranging from ee L = -0.20% ± 0.14% to ee L = -2.54% ± 0.28%. The sign of the induced ee L depends on the helicity and the energy of CPL, but not on the evolutionary stage of the samples, and is the same for all five considered amino acids. Our results support an astrophysical scenario in which the solar system was formed in a high-mass star-forming region where icy grains were irradiated during the protoplanetary phase by an external source of CPL of a given helicity and a dominant energy, inducing a stereo-specific photochemistry.

Insights into the folding pathway of the Engrailed Homeodomain protein using replica exchange molecular dynamics simulations.

PubMed

Koulgi, Shruti; Sonavane, Uddhavesh; Joshi, Rajendra

2010-11-01

Protein folding studies were carried out by performing microsecond time scale simulations on the ultrafast/fast folding protein Engrailed Homeodomain (EnHD) from Drosophila melanogaster. It is a three-helix bundle protein consisting of 54 residues (PDB ID: 1ENH). The positions of the helices are 8-20 (Helix I), 26-36 (Helix II) and 40-53 (Helix III). The second and third helices together form a Helix-Turn-Helix (HTH) motif which belongs to the family of DNA binding proteins. The molecular dynamics (MD) simulations were performed using replica exchange molecular dynamics (REMD). REMD is a method that involves simulating a protein at different temperatures and performing exchanges at regular time intervals. These exchanges were accepted or rejected based on the Metropolis criterion. REMD was performed using the AMBER FF03 force field with the generalised Born solvation model for the temperature range 286-373 K involving 30 replicas. The extended conformation of the protein was used as the starting structure. A simulation of 600 ns per replica was performed resulting in an overall simulation time of 18 μs. The protein was seen to fold close to the native state with backbone root mean square deviation (RMSD) of 3.16 Å. In this low RMSD structure, the Helix I was partially formed with a backbone RMSD of 3.37 Å while HTH motif had an RMSD of 1.81 Å. Analysis suggests that EnHD folds to its native structure via an intermediate in which the HTH motif is formed. The secondary structure development occurs first followed by tertiary packing. The results were in good agreement with the experimental findings. Copyright © 2010 Elsevier Inc. All rights reserved.

Sarcomere-length dependence of myosin filament structure in skeletal muscle fibres of the frog

PubMed Central

Reconditi, Massimo; Brunello, Elisabetta; Fusi, Luca; Linari, Marco; Martinez, Manuel Fernandez; Lombardi, Vincenzo; Irving, Malcolm; Piazzesi, Gabriella

2014-01-01

X-ray diffraction patterns were recorded at beamline ID02 of the European Synchrotron Radiation Facility from small bundles of skeletal muscle fibres from Rana esculenta at sarcomere lengths between 2.1 and 3.5 μm at 4°C. The intensities of the X-ray reflections from resting fibres associated with the quasi-helical order of the myosin heads and myosin binding protein C (MyBP-C) decreased in the sarcomere length range 2.6–3.0 μm but were constant outside it, suggesting that an OFF conformation of the thick filament is maintained by an interaction between MyBP-C and the thin filaments. During active isometric contraction the intensity of the M3 reflection from the regular repeat of the myosin heads along the filaments decreased in proportion to the overlap between thick and thin filaments, with no change in its interference fine structure. Thus, myosin heads in the regions of the thick filaments that do not overlap with thin filaments are highly disordered during isometric contraction, in contrast to their quasi-helical order at rest. Heads in the overlap region that belong to two-headed myosin molecules that are fully detached from actin are also highly disordered, in contrast to the detached partners of actin-attached heads. These results provide strong support for the concept of a regulatory structural transition in the thick filament involving changes in both the organisation of the myosin heads on its surface and the axial periodicity of the myosin tails in its backbone, mediated by an interaction between MyBP-C and the thin filaments. PMID:24344169

The lobular transposition flap: a useful adjunct to reconstruct helical defects.

PubMed

Saleh, D B; Tan, J; Mohammed, P; Majumder, S

2012-07-01

We detail our adjunct to Antia and Buch's chondrocutaneous advancement flap for helical reconstruction. It is simple, reliable and negates the need for transfer of the defect to the lobule and/or V-Y advancement of the helical crus. Copyright © 2011 British Association of Plastic, Reconstructive and Aesthetic Surgeons. Published by Elsevier Ltd. All rights reserved.

Topological characteristics of helical repeat proteins.

PubMed

Groves, M R; Barford, D

1999-06-01

The recent elucidation of protein structures based upon repeating amino acid motifs, including the armadillo motif, the HEAT motif and tetratricopeptide repeats, reveals that they belong to the class of helical repeat proteins. These proteins share the common property of being assembled from tandem repeats of an alpha-helical structural unit, creating extended superhelical structures that are ideally suited to create a protein recognition interface.

Tokamak startup using point-source dc helicity injection.

PubMed

Battaglia, D J; Bongard, M W; Fonck, R J; Redd, A J; Sontag, A C

2009-06-05

Startup of a 0.1 MA tokamak plasma is demonstrated on the ultralow aspect ratio Pegasus Toroidal Experiment using three localized, high-current density sources mounted near the outboard midplane. The injected open field current relaxes via helicity-conserving magnetic turbulence into a tokamaklike magnetic topology where the maximum sustained plasma current is determined by helicity balance and the requirements for magnetic relaxation.

75 FR 29720 - Certain Helical Spring Lock Washers From the People's Republic of China: Final Results of...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-27

...) provide a hardened bearing surface. The scope does not include internal or external tooth washers, nor... helical spring lock washers of carbon steel, of carbon alloy steel, or of stainless steel, heat- treated or non-heat-treated, plated or non-plated, with ends that are off-line. Helical spring lock washers...

Alternating phenylene and furan/pyrrole/thiophene units-based oligomers: A computational study of the structures and optoelectronic properties

NASA Astrophysics Data System (ADS)

Sahu, Harikrishna; Shukla, Rishabh; Goswami, Juri; Gaur, Priyank; Panda, Aditya N.

2018-01-01

Structural and optoelectronic properties of phenylene-furan, phenylene-pyrrole and phenylene-thiophene oligomers are reported using density functional theory methods. Studies reveal that stabilities of conformers change with increasing chain length, and helical conformers are energetically feasible for large oligomers of the studied systems, due to stacking interactions between adjacent helical turns. Absorption spectra of helices are dominated by multiple number of electronic transitions other than the S0 →S1 , involving orbitals other than the HOMO/LUMO. All studied helices are optically active having similar pattern of negative and positive peaks in the CD spectra.

Advanced Face Gear Surface Durability Evaluations

NASA Technical Reports Server (NTRS)

Lewicki, David G.; Heath, Gregory F.

2016-01-01

The surface durability life of helical face gears and isotropic super-finished (ISF) face gears was investigated. Experimental fatigue tests were performed at the NASA Glenn Research Center. Endurance tests were performed on 10 sets of helical face gears in mesh with tapered involute helical pinions, and 10 sets of ISF-enhanced straight face gears in mesh with tapered involute spur pinions. The results were compared to previous tests on straight face gears. The life of the ISF configuration was slightly less than that of previous tests on straight face gears. The life of the ISF configuration was slightly greater than that of the helical configuration.

Extragalactic magnetic fields unlikely generated at the electroweak phase transition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wagstaff, Jacques M.; Banerjee, Robi, E-mail: jwagstaff@hs.uni-hamburg.de, E-mail: banerjee@hs.uni-hamburg.de

2016-01-01

In this paper we show that magnetic fields generated at the electroweak phase transition are most likely too weak to explain the void magnetic fields apparently observed today unless they have considerable helicity. We show that, in the simplest estimates, the helicity naturally produced in conjunction with the baryon asymmetry is too small to explain observations, which require a helicity fraction at least of order 10{sup −14}–10{sup −10} depending on the void fields constraint used. Therefore new mechanisms to generate primordial helicity are required if magnetic fields generated during the electroweak phase transition should explain the extragalactic fields.

Chiral Sulfoxide-Induced Single Turn Peptide α-Helicity

PubMed Central

Zhang, Qingzhou; Jiang, Fan; Zhao, Bingchuan; Lin, Huacan; Tian, Yuan; Xie, Mingsheng; Bai, Guoyun; Gilbert, Adam M.; Goetz, Gilles H.; Liras, Spiros; Mathiowetz, Alan A.; Price, David A.; Song, Kun; Tu, Meihua; Wu, Yujie; Wang, Tao; Flanagan, Mark E.; Wu, Yun-Dong; Li, Zigang

2016-01-01

Inducing α-helicity through side-chain cross-linking is a strategy that has been pursued to improve peptide conformational rigidity and bio-availability. Here we describe the preparation of small peptides tethered to chiral sulfoxide-containing macrocyclic rings. Furthermore, a study of structure-activity relationships (SARs) disclosed properties with respect to ring size, sulfur position, oxidation state, and stereochemistry that show a propensity to induce α-helicity. Supporting data include circular dichroism spectroscopy (CD), NMR spectroscopy, and a single crystal X-ray structure for one such stabilized peptide. Finally, theoretical studies are presented to elucidate the effect of chiral sulfoxides in inducing backbone α-helicity. PMID:27934919

Computational Investigation of Helical Traveling Wave Tube Transverse RF Field Forces

NASA Technical Reports Server (NTRS)

Kory, Carol L.; Dayton, James A.

1998-01-01

In a previous study using a fully three-dimensional (3D) helical slow-wave circuit cold- test model it was found, contrary to classical helical circuit analyses, that transverse FF electric fields have significant amplitudes compared with the longitudinal component. The RF fields obtained using this helical cold-test model have been scaled to correspond to those of an actual TWT. At the output of the tube, RF field forces reach 61%, 26% and 132% for radial, azimuthal and longitudinal components, respectively, compared to radial space charge forces indicating the importance of considering them in the design of electron beam focusing.

Does Hooke's law work in helical nanosprings?

PubMed

Ben, Sudong; Zhao, Junhua; Rabczuk, Timon

2015-08-28

Hooke's law is a principle of physics that states that the force needed to extend a spring by some distance is proportional to that distance. The law is always valid for an initial portion of the elastic range for nearly all helical macrosprings. Here we report the sharp nonlinear force-displacement relation of tightly wound helical carbon nanotubes at even small displacement via a molecular mechanics model. We demonstrate that the van der Waals (vdW) interaction between the intertube walls dominates the nonlinear relation based on our analytical expressions. This study provides physical insights into the origin of huge nonlinearity of the helical nanosprings.

Point-source helicity injection for ST plasma startup in Pegasus

NASA Astrophysics Data System (ADS)

Redd, A. J.; Battaglia, D. J.; Bongard, M. W.; Fonck, R. J.; Schlossberg, D. J.

2009-11-01

Plasma current guns are used as point-source DC helicity injectors for forming non-solenoidal tokamak plasmas in the Pegasus Toroidal Experiment. Discharges driven by this injection scheme have achieved Ip>= 100 kA using Iinj<= 4 kA. They form at the outboard midplane, transition to a tokamak-like equilibrium, and continue to grow inward as Ip increases due to helicity injection and outer- PF induction. The maximum Ip is determined by helicity balance (injection rate vs resistive dissipation) and a Taylor relaxation limit, in which Ip√ITF Iinj/w, where w is the radial thickness of the gun-driven edge. Preliminary experiments tentatively confirm these scalings with ITF, Iinj, and w, increasing confidence in this simple relaxation model. Adding solenoidal inductive drive during helicity injection can push Ip up to, but not beyond, the predicted relaxation limit, demonstrating that this is a hard performance limit. Present experiments are focused on increasing the injection voltage (i.e., helicity injection rate) and reducing w. Near-term goals are to further test scalings predicted by the simple relaxation model and to study in detail the observed bursty n=1 activity correlated with rapid increases in Ip.

The influence of the aortic valve angle on the hemodynamic features of the thoracic aorta

NASA Astrophysics Data System (ADS)

Ha, Hojin; Kim, Guk Bae; Kweon, Jihoon; Lee, Sang Joon; Kim, Young-Hak; Kim, Namkug; Yang, Dong Hyun

2016-08-01

Since the first observation of a helical flow pattern in aortic blood flow, the existence of helical blood flow has been found to be associated with various pathological conditions such as bicuspid aortic valve, aortic stenosis, and aortic dilatation. However, an understanding of the development of helical blood flow and its clinical implications are still lacking. In our present study, we hypothesized that the direction and angle of aortic inflow can influence helical flow patterns and related hemodynamic features in the thoracic aorta. Therefore, we investigated the hemodynamic features in the thoracic aorta and various aortic inflow angles using patient-specific vascular phantoms that were generated using a 3D printer and time-resolved, 3D, phase-contrast magnetic resonance imaging (PC-MRI). The results show that the rotational direction and strength of helical blood flow in the thoracic aorta largely vary according to the inflow direction of the aorta, and a higher helical velocity results in higher wall shear stress distributions. In addition, right-handed rotational flow conditions with higher rotational velocities imply a larger total kinetic energy than left-handed rotational flow conditions with lower rotational velocities.

The influence of the aortic valve angle on the hemodynamic features of the thoracic aorta.

PubMed

Ha, Hojin; Kim, Guk Bae; Kweon, Jihoon; Lee, Sang Joon; Kim, Young-Hak; Kim, Namkug; Yang, Dong Hyun

2016-08-26

Since the first observation of a helical flow pattern in aortic blood flow, the existence of helical blood flow has been found to be associated with various pathological conditions such as bicuspid aortic valve, aortic stenosis, and aortic dilatation. However, an understanding of the development of helical blood flow and its clinical implications are still lacking. In our present study, we hypothesized that the direction and angle of aortic inflow can influence helical flow patterns and related hemodynamic features in the thoracic aorta. Therefore, we investigated the hemodynamic features in the thoracic aorta and various aortic inflow angles using patient-specific vascular phantoms that were generated using a 3D printer and time-resolved, 3D, phase-contrast magnetic resonance imaging (PC-MRI). The results show that the rotational direction and strength of helical blood flow in the thoracic aorta largely vary according to the inflow direction of the aorta, and a higher helical velocity results in higher wall shear stress distributions. In addition, right-handed rotational flow conditions with higher rotational velocities imply a larger total kinetic energy than left-handed rotational flow conditions with lower rotational velocities.

Robust integer and fractional helical modes in the quantum Hall effect

NASA Astrophysics Data System (ADS)

Ronen, Yuval; Cohen, Yonatan; Banitt, Daniel; Heiblum, Moty; Umansky, Vladimir

2018-04-01

Electronic systems harboring one-dimensional helical modes, where spin and momentum are locked, have lately become an important field of their own. When coupled to a conventional superconductor, such systems are expected to manifest topological superconductivity; a unique phase hosting exotic Majorana zero modes. Even more interesting are fractional helical modes, yet to be observed, which open the route for realizing generalized parafermions. Possessing non-Abelian exchange statistics, these quasiparticles may serve as building blocks in topological quantum computing. Here, we present a new approach to form protected one-dimensional helical edge modes in the quantum Hall regime. The novel platform is based on a carefully designed double-quantum-well structure in a GaAs-based system hosting two electronic sub-bands; each tuned to the quantum Hall effect regime. By electrostatic gating of different areas of the structure, counter-propagating integer, as well as fractional, edge modes with opposite spins are formed. We demonstrate that, due to spin protection, these helical modes remain ballistic over large distances. In addition to the formation of helical modes, this platform can serve as a rich playground for artificial induction of compounded fractional edge modes, and for construction of edge-mode-based interferometers.

The influence of the aortic valve angle on the hemodynamic features of the thoracic aorta

PubMed Central

Ha, Hojin; Kim, Guk Bae; Kweon, Jihoon; Lee, Sang Joon; Kim, Young-Hak; Kim, Namkug; Yang, Dong Hyun

2016-01-01

Since the first observation of a helical flow pattern in aortic blood flow, the existence of helical blood flow has been found to be associated with various pathological conditions such as bicuspid aortic valve, aortic stenosis, and aortic dilatation. However, an understanding of the development of helical blood flow and its clinical implications are still lacking. In our present study, we hypothesized that the direction and angle of aortic inflow can influence helical flow patterns and related hemodynamic features in the thoracic aorta. Therefore, we investigated the hemodynamic features in the thoracic aorta and various aortic inflow angles using patient-specific vascular phantoms that were generated using a 3D printer and time-resolved, 3D, phase-contrast magnetic resonance imaging (PC-MRI). The results show that the rotational direction and strength of helical blood flow in the thoracic aorta largely vary according to the inflow direction of the aorta, and a higher helical velocity results in higher wall shear stress distributions. In addition, right-handed rotational flow conditions with higher rotational velocities imply a larger total kinetic energy than left-handed rotational flow conditions with lower rotational velocities. PMID:27561388

Spontaneous formation of non-uniform double helices for elastic rods under torsion

NASA Astrophysics Data System (ADS)

Li, Hongyuan; Zhao, Shumin; Xia, Minggang; He, Siyu; Yang, Qifan; Yan, Yuming; Zhao, Hanqiao

2017-02-01

The spontaneous formation of double helices for filaments under torsion is common and significant. For example, the research on the supercoiling of DNA is helpful for understanding the replication and transcription of DNA. Similar double helices can appear in carbon nanotube yarns, cables, telephone wires and so forth. We noticed that non-uniform double helices can be produced due to the surface friction induced by the self-contact. Therefore an ideal model was presented to investigate the formation of double helices for elastic rods under torque. A general equilibrium condition which is valid for both the smooth surface and the rough surface situations is derived by using the variational method. By adding further constraints, the smooth and rough surface situations are investigated in detail respectively. Additionally, the model showed that the specific process of how to twist and slack the rod can determine the surface friction and hence influence the configuration of the double helix formed by rods with rough surfaces. Based on this principle, a method of manufacturing double helices with designed configurations was proposed and demonstrated. Finally, experiments were performed to verify the model and the results agreed well with the theory.

On the resonance amplification of magnetic perturbations near the threshold of tearing instability in a tokamak

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arsenin, V. V., E-mail: arsenin-vv@nrcki.ru; Skovoroda, A. A., E-mail: skovoroda-aa@nrcki.ru

2015-12-15

Using a cylindrical model, a relatively simple description is presented of how a magnetic field perturbation stimulated by a low external helical current or a small helical distortion of the boundary and generating magnetic islands penetrates into a plasma column with a magnetic surface q=m/n to which tearing instability is attached. Linear analysis of the classical instability with an aperiodic growth of the perturbation in time shows that the perturbation amplitude in plasma increases in a resonant manner as the discharge parameters approach the threshold of tearing instability. In a stationary case, under the assumption on the helical character ofmore » equilibrium, which can be found from the two-dimensional nonlinear equation for the helical flux, there is no requirement for the small size of the island. Examples of calculations in which magnetic islands are large near the threshold of tearing instability are presented. The bifurcation of equilibrium near the threshold of tearing instability in plasma with a cylindrical boundary, i.e., the existence of helical equilibrium (along with cylindrical equilibrium) with large islands, is described. Moreover, helical equilibrium can also exist in the absence of instability.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lello, Louis; Boyanovsky, Daniel; Pisarski, Robert D.

Here, in the standard model extended with a seesaw mass matrix, we study the production of sterile neutrinos from the decay of vector bosons at temperatures near the masses of the electroweak bosons. We derive a general quantum kinetic equation for the production of sterile neutrinos and their effective mixing angles, which is applicable over a wide range of temperature, to all orders in interactions of the standard model and to leading order in a small mixing angle for the neutrinos. We emphasize the relation between the production rate and Landau damping at one-loop order and show that production rates and effective mixing angles depend sensitively upon the neutrino’s helicity. Sterile neutrinos with positive helicity interact more weakly with the medium than those with negative helicity, and their effective mixing angle is not modified significantly. Negative helicity states couple more strongly to the vector bosons, but their mixing angle is strongly suppressed by the medium. Consequently, if the mass of the sterile neutrino is ≲ 8.35 MeV , there are fewer states with negative helicity produced than those with positive helicity. There is an Mikheyev-Smirnov-Wolfenstein-type resonance in the absence of lepton asymmetry, but due to screening by the damping rate, the production rate is not enhanced. Sterile neutrinos with negative helicity freeze out at Tmore » $$-\\atop{f}$$ ≃ 5 GeV , whereas positive helicity neutrinos freeze out at T$$+\\atop{f}$$≃ 8 GeV , with both distributions far from thermal. As the temperature decreases, due to competition between a decreasing production rate and an increasing mixing angle, the distribution function for states with negative helicity is broader in momentum and hotter than that for those with positive helicity. Sterile neutrinos produced via vector boson decay do not satisfy the abundance, lifetime, and cosmological constraints to be the sole dark matter component in the Universe. Massive sterile neutrinos produced via vector boson decay might solve the 7Li problem, albeit at the very edge of the possible parameter space. A heavy sterile neutrino with a mass of a few MeV could decay into light sterile neutrinos, of a few keV in mass, that contribute to warm dark matter. In conclusion, we argue that heavy sterile neutrinos with lifetime ≤1/H 0 reach local thermodynamic equilibrium.« less

Production of heavy sterile neutrinos from vector boson decay at electroweak temperatures

NASA Astrophysics Data System (ADS)

Lello, Louis; Boyanovsky, Daniel; Pisarski, Robert D.

2017-02-01

In the standard model extended with a seesaw mass matrix, we study the production of sterile neutrinos from the decay of vector bosons at temperatures near the masses of the electroweak bosons. We derive a general quantum kinetic equation for the production of sterile neutrinos and their effective mixing angles, which is applicable over a wide range of temperature, to all orders in interactions of the standard model and to leading order in a small mixing angle for the neutrinos. We emphasize the relation between the production rate and Landau damping at one-loop order and show that production rates and effective mixing angles depend sensitively upon the neutrino's helicity. Sterile neutrinos with positive helicity interact more weakly with the medium than those with negative helicity, and their effective mixing angle is not modified significantly. Negative helicity states couple more strongly to the vector bosons, but their mixing angle is strongly suppressed by the medium. Consequently, if the mass of the sterile neutrino is ≲8.35 MeV , there are fewer states with negative helicity produced than those with positive helicity. There is an Mikheyev-Smirnov-Wolfenstein-type resonance in the absence of lepton asymmetry, but due to screening by the damping rate, the production rate is not enhanced. Sterile neutrinos with negative helicity freeze out at Tf-≃5 GeV , whereas positive helicity neutrinos freeze out at Tf+≃8 GeV , with both distributions far from thermal. As the temperature decreases, due to competition between a decreasing production rate and an increasing mixing angle, the distribution function for states with negative helicity is broader in momentum and hotter than that for those with positive helicity. Sterile neutrinos produced via vector boson decay do not satisfy the abundance, lifetime, and cosmological constraints to be the sole dark matter component in the Universe. Massive sterile neutrinos produced via vector boson decay might solve the 7Li problem, albeit at the very edge of the possible parameter space. A heavy sterile neutrino with a mass of a few MeV could decay into light sterile neutrinos, of a few keV in mass, that contribute to warm dark matter. We argue that heavy sterile neutrinos with lifetime ≤1 /H0 reach local thermodynamic equilibrium.

Production of heavy sterile neutrinos from vector boson decay at electroweak temperatures

DOE PAGES

Lello, Louis; Boyanovsky, Daniel; Pisarski, Robert D.

2017-02-22

Here, in the standard model extended with a seesaw mass matrix, we study the production of sterile neutrinos from the decay of vector bosons at temperatures near the masses of the electroweak bosons. We derive a general quantum kinetic equation for the production of sterile neutrinos and their effective mixing angles, which is applicable over a wide range of temperature, to all orders in interactions of the standard model and to leading order in a small mixing angle for the neutrinos. We emphasize the relation between the production rate and Landau damping at one-loop order and show that production rates and effective mixing angles depend sensitively upon the neutrino’s helicity. Sterile neutrinos with positive helicity interact more weakly with the medium than those with negative helicity, and their effective mixing angle is not modified significantly. Negative helicity states couple more strongly to the vector bosons, but their mixing angle is strongly suppressed by the medium. Consequently, if the mass of the sterile neutrino is ≲ 8.35 MeV , there are fewer states with negative helicity produced than those with positive helicity. There is an Mikheyev-Smirnov-Wolfenstein-type resonance in the absence of lepton asymmetry, but due to screening by the damping rate, the production rate is not enhanced. Sterile neutrinos with negative helicity freeze out at Tmore » $$-\\atop{f}$$ ≃ 5 GeV , whereas positive helicity neutrinos freeze out at T$$+\\atop{f}$$≃ 8 GeV , with both distributions far from thermal. As the temperature decreases, due to competition between a decreasing production rate and an increasing mixing angle, the distribution function for states with negative helicity is broader in momentum and hotter than that for those with positive helicity. Sterile neutrinos produced via vector boson decay do not satisfy the abundance, lifetime, and cosmological constraints to be the sole dark matter component in the Universe. Massive sterile neutrinos produced via vector boson decay might solve the 7Li problem, albeit at the very edge of the possible parameter space. A heavy sterile neutrino with a mass of a few MeV could decay into light sterile neutrinos, of a few keV in mass, that contribute to warm dark matter. In conclusion, we argue that heavy sterile neutrinos with lifetime ≤1/H 0 reach local thermodynamic equilibrium.« less

Structure and Dynamics of Helical Protein Fragments Investigated by Theory and Experiment

NASA Astrophysics Data System (ADS)

Karimi, Afshin

This work addresses the conformation and dynamics of model peptides using spectroscopy and molecular dynamics simulations. Experimentally, we investigate the structure and dynamics of peptide fragments taken from coiled coil and three helical bundle motifs of bacterial coat proteins. Theoretically, we use molecular dynamics simulations of isolated helices with explicit water molecules to derive trajectories which reveal features about picosecond dynamics and local unfolding events. The assignment of the ^1H, ^{15}N, and ^ {13}C resonances, secondary structure, backbone dynamics, hydration and other biophysical parameters of a 30 residue recombinant peptide corresponding to an immunogenic site on the coiled coil region of Streptococcus pyogenes 24M protein are reported. Our results suggest that this peptide is a symmetric parallel dimeric alpha-helical coiled coil with local defects within the helix and fraying at the termini. The ^1H and ^ {15}N assignments, the hydration, the overall fold, and other biophysical parameters of a recombinant B domain of Staphylococcal protein A (FB) are reported. Our results indicate FB is a highly stable monomeric three helical bundle. A symmetric two domain construct was used to probe the modular assembly of two B domains. Here, spectroscopic results suggest weak interactions between the two domains. The folding pathway of FB was investigated using amide exchange data of the native protein and peptide models. We propose that the helical hairpin consisting of helices II and III is an on-pathway intermediate in the folding of FB. Two 1 ns molecular dynamics simulations (MD) on two mainly helical peptides--an 18 residue peptide corresponding to a portion of the H helix of myoglobin (MBH) and a 14 residue analogue of the C-peptide of ribonuclease A (CRNA) --were carried out in water using the united atom AMBER/OPLS force-field. In the case of MBH, the initial helical conformation progressively frays to a more disordered structure. A common motif in the unfolding mechanism involves the formation of transient turn structures involving several water molecules. In contrast to the MBH simulation, the CRNA trajectory was characterized by the presence of fairly stable i ... i+4 (alpha-helical) hydrogen bonds throughout the simulation, except at the N-terminus where some fraying was observed.

Consortium for Osteogenesis Imperfecta Mutations in the Helical Domain of Type I Collagen: Regions Rich in Lethal Mutations Align With Collagen Binding Sites for Integrins and Proteoglycans

PubMed Central

Marini, Joan C.; Forlino, Antonella; Cabral, Wayne A.; Barnes, Aileen M.; San Antonio, James D.; Milgrom, Sarah; Hyland, James C.; Körkkö, Jarmo; Prockop, Darwin J.; De Paepe, Anne; Coucke, Paul; Symoens, Sofie; Glorieux, Francis H.; Roughley, Peter J.; Lund, Alan M.; Kuurila-Svahn, Kaija; Hartikka, Heini; Cohn, Daniel H.; Krakow, Deborah; Mottes, Monica; Schwarze, Ulrike; Chen, Diana; Yang, Kathleen; Kuslich, Christine; Troendle, James; Dalgleish, Raymond; Byers, Peter H.

2014-01-01

Osteogenesis imperfecta (OI) is a generalized disorder of connective tissue characterized by fragile bones and easy susceptibility to fracture. Most cases of OI are caused by mutations in type I collagen. We have identified and assembled structural mutations in type I collagen genes (COL1A1 and COL1A2, encoding the proα1(I) and proα2(I) chains, respectively) that result in OI. Quantitative defects causing type I OI were not included. Of these 832 independent mutations, 682 result in substitution for glycine residues in the triple helical domain of the encoded protein and 150 alter splice sites. Distinct genotype–phenotype relationships emerge for each chain. One-third of the mutations that result in glycine substitutions in α1(I) are lethal, especially when the substituting residues are charged or have a branched side chain. Substitutions in the first 200 residues are nonlethal and have variable outcome thereafter, unrelated to folding or helix stability domains. Two exclusively lethal regions (helix positions 691–823 and 910–964) align with major ligand binding regions (MLBRs), suggesting crucial interactions of collagen monomers or fibrils with integrins, matrix metalloproteinases (MMPs), fibronectin, and cartilage oligomeric matrix protein (COMP). Mutations in COL1A2 are predominantly nonlethal (80%). Lethal substitutions are located in eight regularly spaced clusters along the chain, supporting a regional model. The lethal regions align with proteoglycan binding sites along the fibril, suggesting a role in fibril–matrix interactions. Recurrences at the same site in α2(I) are generally concordant for outcome, unlike α1(I). Splice site mutations comprise 20% of helical mutations identified in OI patients, and may lead to exon skipping, intron inclusion, or the activation of cryptic splice sites. Splice site mutations in COL1A1 are rarely lethal; they often lead to frameshifts and the mild type I phenotype. In α2(I), lethal exon skipping events are located in the carboxyl half of the chain. Our data on genotype–phenotype relationships indicate that the two collagen chains play very different roles in matrix integrity and that phenotype depends on intracellular and extracellular events. PMID:17078022

SU-F-J-76: Evaluation of the Performance of Different Deformable Image Registration Algorithms in Helical, Axial and Cone-Beam CT Images of a Mobile Phantom

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jaskowiak, J; Ahmad, S; Ali, I

Purpose: To investigate quantitatively the performance of different deformable-image-registration algorithms (DIR) with helical (HCT), axial (ACT) and cone-beam CT (CBCT) by evaluating the variations in the CT-numbers and lengths of targets moving with controlled motion-patterns. Methods: Four DIR-algorithms including demons, fast-demons, Horn-Schunk and Locas-Kanade from the DIRART-software are used to register CT-images of a mobile-phantom. A mobile-phantom is scanned with different imaging techniques that include helical, axial and cone-beam CT. The phantom includes three targets with different lengths that are made from water-equivalent material and inserted in low-density-foam which is moved with adjustable motion-amplitudes and frequencies. Results: Most of themore » DIR-algorithms are able to produce the lengths of the stationary-targets, however, they do not produce the CT-number values in CBCT. The image-artifacts induced by motion are more regular in CBCT imaging where the mobile-target elongation increases linearly with motion-amplitude. In ACT and HCT, the motion-artifacts are irregular where some mobile -targets are elongated or shrunk depending on the motion-phase during imaging. The DIR-algorithms are successful in deforming the images of the mobile-targets to the images of the stationary-targets producing the CT-number values and length of the target for motion-amplitudes < 20 mm. Similarly in ACT, all DIR-algorithms produced the actual CT-number and length of the stationary-targets for motion-amplitudes < 15 mm. As stronger motion-artifacts are induced in HCT and ACT, DIR-algorithms fail to produce CT-values and shape of the stationary-targets and fast-demons-algorithm has worst performance. Conclusion: Most of DIR-algorithms produce the CT-number values and lengths of the stationary-targets in HCT and ACT images that has motion-artifacts induced by small motion-amplitudes. As motion-amplitudes increase, the DIR-algorithms fail to deform mobile-target images to the stationary-images in HCT and ACT. In CBCT, DIR-algorithms are successful in producing length and shape of the stationary-targets, however, they fail to produce the accurate CT-number level.« less

Harmonic Analysis of the Fluorescence Response of Bimane Adducts of Colicin E1 at Helices 6, 7, and 10*

PubMed Central

Ho, Derek; Lugo, Miguel R.; Merrill, A. Rod

2013-01-01

The pre-channel state of helices 6, 7, and 10 (Val447–Gly475 and Ile508–Ile522) of colicin E1 was investigated by a site-directed fluorescence labeling technique. A total of 44 cysteine variants were purified and covalently labeled with monobromobimane fluorescent probe. A variety of fluorescence properties of the bimane fluorophore were measured for both the soluble and membrane-bound states of the channel peptide, including the fluorescence emission maximum, fluorescence anisotropy, and membrane bilayer penetration depth. Using site-directed fluorescence labeling combined with our novel helical periodicity analysis method, the data revealed that helices 6, 7, and 10 are separate amphipathic α-helices with a calculated periodicity of T = 3.34 ± 0.08 for helix 6, T = 3.56 ± 0.03 for helix 7, and T = 2.99 ± 0.12 for helix 10 in the soluble state. In the membrane-bound state, the helical periodicity was determined to be T = 3.00 ± 0.15 for helix 6, T = 3.68 ± 0.03 for helix 7, and T = 3.47 ± 0.04 for helix 10. Dual fluorescence quencher analysis showed that both helices 6 and 7 adopt a tilted topology that correlates well with the analysis based on the fluorescence anisotropy profile. These data provide further support for the umbrella model of the colicin E1 channel domain. PMID:23264635

Shear-induced conformational ordering, relaxation, and crystallization of isotactic polypropylene.

PubMed

An, Haining; Li, Xiangyang; Geng, Yong; Wang, Yunlong; Wang, Xiao; Li, Liangbin; Li, Zhongming; Yang, Chuanlu

2008-10-02

The shear-induced coil-helix transition of isotactic polypropylene (iPP) has been studied with time-resolved Fourier transform infrared spectroscopy at various temperatures. The effects of temperature, shear rate, and strain on the coil-helix transition were studied systematically. The induced conformational order increases with the shear rate and strain. A threshold of shear strain is required to induce conformational ordering. High temperature reduces the effect of shear on the conformational order, though a simple correlation was not found. Following the shear-induced conformational ordering, relaxation of helices occurs, which follows the first-order exponential decay at temperatures well above the normal melting point of iPP. The relaxation time versus temperature is fitted with an Arrhenius law, which generates an activation energy of 135 kJ/mol for the helix-coil transition of iPP. At temperatures around the normal melting point, two exponential decays are needed to fit well on the relaxation kinetic of helices. This suggests that two different states of helices are induced by shear: (i) isolated single helices far away from each other without interactions, which have a fast relaxation kinetic; (ii) aggregations of helices or helical bundles with strong interactions among each other, which have a much slower relaxation process. The helical bundles are assumed to be the precursors of nuclei for crystallization. The different helix concentrations and distributions are the origin of the three different processes of crystallization after shear. The correlation between the shear-induced conformational order and crystallization is discussed.

THE EFFECTS OF SPATIAL SMOOTHING ON SOLAR MAGNETIC HELICITY PARAMETERS AND THE HEMISPHERIC HELICITY SIGN RULE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ocker, Stella Koch; Petrie, Gordon, E-mail: socker@oberlin.edu, E-mail: gpetrie@nso.edu

The hemispheric preference for negative/positive helicity to occur in the northern/southern solar hemisphere provides clues to the causes of twisted, flaring magnetic fields. Previous studies on the hemisphere rule may have been affected by seeing from atmospheric turbulence. Using Hinode /SOT-SP data spanning 2006–2013, we studied the effects of two spatial smoothing tests that imitate atmospheric seeing: noise reduction by ignoring pixel values weaker than the estimated noise threshold, and Gaussian spatial smoothing. We studied in detail the effects of atmospheric seeing on the helicity distributions across various field strengths for active regions (ARs) NOAA 11158 and NOAA 11243, in addition tomore » studying the average helicities of 179 ARs with and without smoothing. We found that, rather than changing trends in the helicity distributions, spatial smoothing modified existing trends by reducing random noise and by regressing outliers toward the mean, or removing them altogether. Furthermore, the average helicity parameter values of the 179 ARs did not conform to the hemisphere rule: independent of smoothing, the weak-vertical-field values tended to be negative in both hemispheres, and the strong-vertical-field values tended to be positive, especially in the south. We conclude that spatial smoothing does not significantly affect the overall statistics for space-based data, and thus seeing from atmospheric turbulence seems not to have significantly affected previous studies’ ground-based results on the hemisphere rule.« less

The Helicity Injected Torus (HIT) Program

NASA Astrophysics Data System (ADS)

Jarboe, T. R.; Gu, P.; Hamp, W.; Izzo, V.; Jewell, P.; Liptac, J.; McCollam, K. J.; Nelson, B. A.; Raman, R.; Redd, A. J.; Shumlak, U.; Sieck, P. E.; Smith, R. J.; Jain, K. K.; Nagata, M.; Uyama, T.

2000-10-01

The purpose of the Helicity Injected Torus (HIT) program is to develop current drive techniques for low-aspect-ratio toroidal plasmas. The present HIT-II spherical tokamak experiment is capable of both Coaxial Helicity Injection (CHI) and transformer action current drive. The HIT-II device itself is modestly sized (major radius R = 0.3 m, minor radius a = 0.2 m, with an on-axis magnetic field of up to Bo = 0.5 T), but has demonstrated toroidal plasma currents of up to 200 kA, using either CHI or transformer drive. An overview of ongoing research on HIT-II plasmas, including recent results, will be presented. An electron-locking model has been developed for helicity injection current drive; a description of this model will be presented, as well as comparisons to experimental results from the HIT and HIT-II devices. Empirical results from both the HIT program and past spheromak research, buttressed by theoretical developments, have led to the design of the upcoming HIT-SI (Helicity Injected Torus with Steady Inductive helicity injection) device (T.R. Jarboe, Fusion Technology 36, p. 85, 1999). HIT-SI will be able to form a high-beta spheromak, a low aspect ratio RFP or a spherical tokamak using constant inductive helicity injection. The HIT-SI design and construction progress will be presented.