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Helicity
Selected AbstractsControl of Morphology and Helicity of Chiral Mesoporous Silica,ADVANCED MATERIALS, Issue 5 2006H. Jin Chiral ordered mesoporous silica has been synthesized by using a chiral surfactant (N -myristoyl- L -alanine sodium salt) as a template, 3-aminopropyltriethoxysilane as a co-structure directing agent, and tetraethoxylsilane as an inorganic source. The helicity and the morphology of the mesoporous silica are determined by the stirring rate during the chiral surfactant self-assembly (see Figure), providing new insight into the chiral self-assembly of molecules. [source] Nanometer-Range Communication of Stereochemical Information by Reversible Switching of Molecular Helicity,ANGEWANDTE CHEMIE, Issue 38 2010Dr. Jordi Solà Ein Ferngespräch: Die Inversion der Konfiguration eines stereogenen Zentrums verursachte eine nachweisbare Änderung der Position einer 40,Bindungen (2.5,nm) entfernten stereochemischen 13C-Sonde. Die Information wurde wie illustriert über eine Inversion des Schraubensinns der dazwischenliegenden Helix übermittelt. 13C-NMR-Signale dienten als Ausgabe. [source] Control of the Helicity of Poly(phenylacetylene)s: From the Conformation of the Pendant to the Chirality of the Backbone,ANGEWANDTE CHEMIE, Issue 8 2010Iria Louzao Dr. Auswahl der Gangrichtung: Das Konformerengleichgewicht der Substituenten eines Poly(phenylacetylens), und mit diesem die Helizität des Polymers, lässt sich reversibel verändern. Durch Komplexierung mit Metallkationen wie Ba2+ oder einen Wechsel in der Lösungsmittelpolarität kann die gewünschte Gangrichtung ausgewählt werden. Die mechanistische Grundlage dieses Phänomens wird im Detail erklärt. [source] pH-Switchable Helicity of DNA-Templated Assemblies,ANGEWANDTE CHEMIE, Issue 43 2009Oligothymin wurde bei der Aggregation komplementärer nichtchiraler Naphthaline als Templat verwendet. Je nach Protonierungsgrad der Naphthaline entstehen links- oder rechtsgängige Helices (siehe Bild). Der Aggregationsprozess wurde mit CD-Messungen und UV/Vis-Spektroskopie studiert. [source] Helicity in electron microscopy images,a comment on Wang TF, Chen LT and Wang AH 2008 BioEssays 30:48,56.BIOESSAYS, Issue 8 2008Professor Edward H. Egelman No abstract is available for this article. [source] {4,10-Bis[2-(2-oxidobenzylideneamino-,2N,O)benzyl]-1,7-dioxa-4,10-diazacyclododecane-,4O1,N4,O3,N10}ytterbium(III) perchlorate acetonitrile solvateACTA CRYSTALLOGRAPHICA SECTION C, Issue 8 2006Marina González-Lorenzo In the crystal structure of the title compound, [Yb(C36H38N4O4)]ClO4·CH3CN, the ytterbium ion is eight-coordinated and deeply buried in the cavity of the dianionic Schiff base ligand. The coordination polyhedron may be described as a distorted square antiprism that shows a twist angle of 29.5,(1)° between the two square planes. The receptor adopts a syn arrangement, with both pendent arms on the same side of the crown group, and there are two helicities (one associated with this layout of the pendent arms and the other with the conformation of the crown ring), which give rise to enantiomeric pairs of diastereoisomers, viz. ,(,,,,) and ,(,,,,). [source] Theoretical Determination of the Vibrational Raman Optical Activity Signatures of Helical Polypropylene ChainsCHEMPHYSCHEM, Issue 11 2006Ewa Lamparska Abstract Raman and vibrational Raman optical activity (VROA) spectra of helical conformers of polypropylene chains are simulated using ab initio methods to unravel the relationships between the vibrational signatures and the primary and secondary structures of the chains. For a polypropylene chain containing three units, conformational effects are shown to lead to more acute signatures for VROA than for Raman spectra. In addition to regular polypropylene chains, which can display right and left helicities with the same probability, chirality and therefore helicity are enforced by substituting one chain end with a phenyl group. The simulations predict that the threefold helical structures, which correspond to (TG)N conformations of the backbone, have a specific VROA backward signature in the form of an intense couplet around 1100 cm,1. This couplet is associated with collective wagging and twisting motions, while most of its intensity comes from the anisotropic invariants combining normal coordinate derivatives of the electric dipole,electric dipole polarizability and of the electric dipole,magnetic dipole polarizability. A similar signature has already been found in model helical polyethylene chains, whereas it is very weak in forward VROA. [source] Lysine-based peptide nucleic acids (PNAs) with strong chiral constraint: Control of helix handedness and DNA binding by chiralityCHIRALITY, Issue S1 2005Tullia Tedeschi Abstract Two enantiomeric chiral PNAs bearing three adjacent d - or l -lysine-based residues in the middle of the strand ("chiral box" PNAs, sequence H-GTAGALysTLysCLysACT-NH2) have been used as models in order to comprehensively study the effects of the stereogenic centers on PNA conformation and on PNA binding properties to complementary PNA and DNA strands. The binding properties of the two enantiomeric PNAs and of their homologous achiral PNA have been extensively studied by UV and CD spectroscopy and by mass spectrometry, both in the antiparallel and in the parallel mode with complementary PNA and DNA strands. In the antiparallel PNA:PNA duplexes, l -Lys PNA were found to form left-handed, and d -Lys PNA right handed helices, while in parallel duplexes, the reversed helicities were observed. Correspondingly, the preferred mode of binding and the best mismatch recognition of the d -Lys containing PNA with (right handed) DNA was found to be in the antiparallel orientation, while that of l -Lys PNA was found to be in the parallel mode. A rationale which correlates the preferred handedness of the PNA-PNA duplexes to the directionality of the binding to complementary DNA duplexes has been devised according to structural data and considering the "retro,inverso" concept widely used for peptides. Chirality 17:S196,S204, 2005. © 2005 Wiley-Liss, Inc. [source] Syntheses, Spectroscopic Studies, and Crystal Structures of Chiral [Rh(aminocarboxylato)(,4 -cod)] and Chiral [Rh(amino alcohol)(,4 -cod)](acetate) Complexes with an Example of a Spontaneous Resolution of a Racemic Mixture into Homochiral Helix-EnantiomersEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 11 2006Mohammed Enamullah Abstract The dimeric complex acetato(,4 -cycloocta-1,5-diene)rhodium(I), [Rh(O2CMe)(,4 -cod)]2 (cod = cycloocta-1,5-diene), reacts with amino acids [HAA = L -alanine, (S)-2-amino-2-phenylacetic acid (L -phenylglycine), N -methylglycine, and N -phenylglycine] and with the amino alcohol (S)-2-amino-2-phenylethanol to afford the aminocarboxylato(,4 -cycloocta-1,5-diene)rhodium(I) complexes [Rh(AA)(,4 -cod)] (AA = deprotonated amino acid = aminocarboxylato ligand) and [(S)-2-amino-2-phenylethanol](,4 -cycloocta-1,5-diene)rhodium(I) acetate, [Rh{(S)-HOCH2,CH(Ph)-NH2}(,4 -cod)](O2CMe) (V). The complexes are characterized by IR, UV/Vis, 1H/13C NMR and mass spectroscopy. The achiral N -phenylglycine ligand gives a chiral N -phenylglycinato complex [Rh(O2C,CH2,NHPh)(,4 -cod)] (IV) with the amine nitrogen atom becoming the stereogenic center upon metal coordination. Complex IV crystallizes in the tetragonal, chiral space group P43 and the crystal structure reveals twofold spontaneous resolution of a racemic mixture into homochiral helix-enantiomers. The investigated crystal contained only one type of helix, namely (left-handed or M- ) 43 -helical chains. This is traced first to an intermolecular N,H···O hydrogen bonding from the stereogenic amino group to a neighboring unligated carboxyl oxygen atom that connects only molecules of the same (R)-configuration into (left-handed or M- ) 43 -helical chains. This intrachain homochirality is supplemented, secondly, by the interlocking of adjacent chains with their corrugated van der Waals surface to allow for an interchain transmission of the sense of helicity, building the single crystal from the same homochiral helix-enantiomer. The enantiomeric amino alcohol complex V crystallizes in the monoclinic, noncentrosymmetric (Sohncke) space group P21. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source] SMAP-29 has two LPS-binding sites and a central hingeFEBS JOURNAL, Issue 4 2002Brian F. Tack The CD spectra of SMAP-29, an antimicrobial peptide from sheep, showed disordered structure in aqueous buffers, and significant helicity in membrane-like environments, including SDS micelles, lipopolysaccharide (LPS) dispersions, and trifluoroethanol buffer systems. A structure determined by NMR in 40% perdeuterated trifluoroethanol indicated that residues 8,17 were helical, residues 18,19 formed a hinge, and residues 20,28 formed an ordered, hydrophobic segment. SMAP-29 was flexible in 40% trifluoroethanol, forming two sets of conformers that differed in the relative orientation of the N-terminal domain. We used a chromogenic Limulus assay to determine the EC50 of the peptide (the concentration that bound 50% of the added LPS). Studies with full-length and truncated SMAP-29 molecules revealed that each end of the holopeptide contained an LPS-binding domain. The higher affinity LPS-binding domain was situated in the flexible N-terminal portion. LPS binding to full-length SMAP-29 showed positive cooperativity, so the EC50 of the peptide (2.6 µm) was considerably lower than that of the individual LPS-binding domains. LPS-binding studies with a mixture of truncated peptides revealed that this cooperativity was primarily intramolecular (i.e. involving the N- and C-terminal LPS-binding sites of the same peptide molecule). CAP-18[106,142], an antimicrobial cathelicidin peptide of rabbits, resembled SMAP-29 in that it contained N- and C-terminal LPS-binding domains, had an EC50 of 2.5 µm, and bound LPS with positive cooperativity. We conclude that the presence of multiple binding sites that function cooperatively allow peptides such as SMAP-29 and CAP-18 to bind LPS with high affinity. [source] The assembly factor P17 from bacteriophage PRD1 interacts with positively charged lipid membranesFEBS JOURNAL, Issue 20 2000Juha M. Holopainen The interactions of the assembly factor P17 of bacteriophage PRD1 with liposomes were investigated by static light scattering, fluorescence spectroscopy, and differential scanning calorimetry. Our data show that P17 binds to positively charged large unilamellar vesicles composed of the zwitterionic 1-palmitoyl-2-oleoyl-phosphatidylcholine and sphingosine, whereas only a weak interaction is evident for 1-palmitoyl-2-oleoyl-phosphatidylcholine vesicles. P17 does not bind to negatively charged membranes composed of 1-palmitoyl-2-oleoyl-phosphatidylglycerol and 1-palmitoyl-2-oleoyl-phosphatidylcholine. Our differential scanning calorimetry results reveal that P17 slightly perturbs the phase behaviour of neutral phosphatidylcholine and negatively charged multilamellar vesicles. In contrast, the phase transition temperature of positively charged dimyristoylphosphatidylcholine/sphingosine multilamellar vesicles (molar ratio 9 : 1, respectively) is increased by approximately 2.4 °C and the half width of the enthalpy peak broadened from 1.9 to 5.6 °C in the presence of P17 (protein : lipid molar ratio 1 : 47). Moreover, the enthalpy peak is asymmetrical, suggesting that lipid phase separation is induced by P17. Based on the far-UV CD spectra, the ,-helicity of P17 increases upon binding to positively charged micelles composed of Triton X-100 and sphingosine. We propose that P17 can interact with positively charged lipid membranes and that this binding induces a structural change on P17 to a more tightly packed and ordered structure. [source] Single particle representation of parabose extension of conformal supersymmetryFORTSCHRITTE DER PHYSIK/PROGRESS OF PHYSICS, Issue 4-5 2008I. Salom Abstract We consider generalized conformal supersymmetry constructed as parabose N = 4 algebra. It is shown that Green's ansatz representations have, in this context, natural interpretation as multi particle spaces. The simplest nontrivial representation is shown to correspond to a massless particle of arbitrary helicity, and some peculiar properties of this space are pointed out. [source] Hydrophobic Functional Group Initiated Helical Mesostructured Silica for Controlled Drug Release,ADVANCED FUNCTIONAL MATERIALS, Issue 23 2008Lei Zhang Abstract In this paper a novel one-step synthetic pathway that controls both functionality and morphology of functionalized periodic helical mesostructured silicas by the co-condensation of tetraethoxysilane and hydrophobic organoalkoxysilane using achiral surfactants as templates is reported. In contrast to previous methods, the hydrophobic interaction between hydrophobic functional groups and the surfactant as well as the intercalation of hydrophobic groups into the micelles are proposed to lead to the formation of helical mesostructures. This study demonstrates that hydrophobic interaction and intercalation can promote the production of long cylindrical micelles, and that the formation of helical rod-like morphology is attributed to the spiral transformation from bundles of hexagonally-arrayed and straight rod-like composite micelles due to the reduction in surface free energy. It is also revealed that small amounts of mercaptopropyltrimethoxysilane, vinyltrimethoxysilane, and phenyltrimethoxysilane can cause the formation of helical mesostructures. Furthermore, the helical mesostructured silicas are employed as drug carriers for the release study of the model drug aspirin, and the results show that the drug release rate can be controlled by the morphology and helicity of the materials. [source] Characterization of conantokin Rl -A: molecular phylogeny as structure/function studyJOURNAL OF PEPTIDE SCIENCE, Issue 8 2010Konkallu H. Gowd Abstract A multidisciplinary strategy for discovery of new Conus venom peptides combines molecular genetics and phylogenetics with peptide chemistry and neuropharmacology. Here we describe application of this approach to the conantokin family of conopeptides targeting NMDA receptors. A new conantokin from Conus rolani, ConRl -A, was identified using molecular phylogeny and subsequently synthesized and functionally characterized. ConRl -A is a 24-residue peptide containing three ,-carboxyglutamic acid residues with a number of unique sequence features compared to conantokins previously characterized. The HPLC elution of ConRl -A suggested that this peptide exists as two distinct, slowly exchanging conformers. ConRl -A is predominantly helical (estimated helicity of 50%), both in the presence and absence of Ca++. The order of potency for blocking the four NMDA receptor subtypes by ConRl -A was NR2B > NR2D > NR2A > NR2C. This peptide has a greater discrimination between NR2B and NR2C than any other ligand reported so far. In summary, ConRl -A is a new member of the conantokin family that expands our understanding of structure/function of this group of peptidic ligands targeted to NMDA receptors. Thus, incorporating phylogeny in the discovery of novel ligands for the given family of ion channels or receptors is an efficient means of exploring the megadiverse group of peptides from the genus Conus. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd. [source] Structure,function relationship studies of PTH(1,11) analogues containing sterically hindered dipeptide mimeticsJOURNAL OF PEPTIDE SCIENCE, Issue 8 2007Nereo Fiori Abstract The N -terminal 1,34 fragment of parathyroid hormone (PTH) is fully active in vitro and in vivo and reproduces all biological responses characteristic of the native intact PTH. In order to develop safer and non-parenteral PTH-like bone anabolic agents, we have studied the effect of introducing conformationally constrained dipeptide mimetics into the N -terminal portion of PTH in an effort to generate miniaturized PTH-mimetics. To this end, we have synthesized and conformationally and biologically characterized PTH(1,11) analogues containing 3R -carboxy-6S -amino-7,5-bicyclic thiazolidinlactam (7,5-bTL), a rigidified dipeptide mimetic unit. The wild type sequence of PTH(1,11) is H-Ser-Val-Ser-Glu-Ile-Gln-Leu-Met-His-Asn-Leu-NH2. The following pseudo-undecapeptides were prepared: [Ala1, 7,5-bTL3, 4, Nle8, Arg11]hPTH(1,11)NH2 (I); [Ala1, 7,5-bTL6, 7, Nle8, Arg11]hPTH(1,11)NH2 (II); [Ala1, Nle8, 7,5-bTL9, 10, Arg11]hPTH(1,11)NH2 (III). In aqueous solution containing 20% TFE, only analogue I exhibited the typical CD pattern of the ,-helical conformation. NMR experiments and molecular dynamics calculations located the ,-helical stretch in the sequence Ile5 -His9. The dipeptide mimetic unit 7,5-bTL induces a type III ,-turn, occupying the positions i , 1 and i of the turn. Analogue II exhibited an equilibrium between a type I ,-turn and an ,-helix, and analogue III did not show any ordered structure. Biological tests revealed poor activity for all analogues (EC50 > 0.1 mM). Apparently, the relative side-chain orientation of Val2, Ile5 and Met8 can be critical for effective analogue-receptor interaction. Considering helicity as an essential property to obtain active PTH agonists, one must decorate the correctly positioned dipeptide mimetic azabicycloalkane scaffold with substitutions corresponding to the displaced amino acids. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd. [source] HP(2,9)-magainin 2(1,12), a synthetic hybrid peptide, exerts its antifungal effect on Candida albicans by damaging the plasma membraneJOURNAL OF PEPTIDE SCIENCE, Issue 4 2004Yoonkyung Park Abstract In our previous study, HP(2,9)-MA(1,12), HP-MA for short, a hybrid peptide incorporating residues 2,9 of Helicobacter pylori ribosomal protein L1 (HP) and residues 1,12 of magainin 2 (MA) was shown to have strong antibacterial activity. In this study the antifungal activity of HP-MA was evaluated using various fungi, and it was shown that the activity was increased when compared with the parent peptides. In order to investigate the fungicidal mechanism(s) of HP-MA its action against fungal cell membranes was examined by the potassium-release test, which showed that HP-MA caused an increase in the amount of K+ released from the cells. Furthermore, HP-MA induced significant morphological changes. These facts suggested that the fungicidal effect of HP-MA involves damaging the fungal cell membranes. CD investigators suggested that the ,-helical structure of these peptides plays an important role in their antibiotic effect, but that ,-helicity is less directly correlated with the enhanced antibiotic activity of the hybrid. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd. [source] Antibiotic activity of pentadecapeptides modelled from amino acid descriptorsJOURNAL OF PEPTIDE SCIENCE, Issue 2 2001Tore Lejon Abstract Pentadecapeptides based on modified murine lactoferricin (LFM) sequences show varying degrees of antibacterial activity against Escherichia coli and Staphylococcus aureus. By means of projections to latent structures (PLS), a good correlation is obtained if the biological activity is modelled as a function of variables describing peptide properties, e.g. ,-helicity, hydrophobicity/hydrophilicity and charge. Using variables derived from a principal component analysis (PCA) of all naturally occurring amino acids, it is possible to describe the amino acid content of the peptides using three variables per amino acid position. The resulting descriptor matrix is then used to develop quantitative structure,activity relationships (QSAR). It is shown that the theoretically derived descriptors model the activity of the peptides better than the earlier model, and that properties of the peptides other than antibacterial activity can be predicted. Copyright © 2001 European Peptide Society and John Wiley & Sons, Ltd. [source] Synthesis and chiroptical properties of L -valine-containing poly(phenylacetylene)s with (a)chiral pendant terminal groupsJOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 6 2006Lo Ming Lai Abstract Poly(phenylacetylene)s containing L -valine residues (P1) with (a)chiral pendant terminal groups R(*) [,(HCC{C6H4CONHCH[CH(CH3)2]COOR(*)})n,]; R(*) = 1-octyl (P1o), (1S,2R,5S)-(+)-menthyl [P1(+)], (1R,2S,5R)-(,)-menthyl [P1(,)] are designed and synthesized. The polymers are prepared by organorhodium catalysts in high yields (yield up to 88%) with high molecular weights (Mw up to ,6.4 × 105). Their structures and properties are characterized by NMR, IR, TGA, UV, and circular dichroism analyses. All the polymers are thermally fairly stable (Td , 320 °C). The chiral moieties induce the poly(phenylacetylene) chains to helically rotate in a preferred direction. The chirality of the pendant terminal groups affects little the helicity of the polymers but their bulkiness stabilizes the helical conformation against solvent perturbation. The backbone conjugation and chain helicity of the polymers can be modulated continuously and reversibly by acid. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 2117,2129, 2006 [source] Non-ideal evolution of non-axisymmetric, force-free magnetic fields in a magnetarMONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 4 2008A. Mastrano ABSTRACT Recent numerical magnetohydrodynamic calculations by Braithwaite and collaborators support the ,fossil field' hypothesis regarding the origin of magnetic fields in compact stars and suggest that the resistive evolution of the fossil field can explain the reorganization and decay of magnetar magnetic fields. Here, these findings are modelled analytically by allowing the stellar magnetic field to relax through a quasi-static sequence of non-axisymmetric, force-free states, by analogy with spheromak relaxation experiments, starting from a random field. Under the hypothesis that the force-free modes approach energy equipartition in the absence of resistivity, the output of the numerical calculations is semiquantitatively recovered: the field settles down to a linked poloidal,toroidal configuration, which inflates and becomes more toroidal as time passes. A qualitatively similar (but not identical) end state is reached if the magnetic field evolves by exchanging helicity between small and large scales according to an ,-dynamo-like, mean-field mechanism, arising from the fluctuating electromotive force produced by the initial random field. The impossibility of matching a force-free internal field to a potential exterior field is discussed in the magnetar context. [source] Impact of tangled magnetic fields on fossil radio bubblesMONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 2 2007M. Ruszkowski ABSTRACT There is growing consensus that feedback from active galactic nuclei (AGN) is the main mechanism responsible for stopping cooling flows in clusters of galaxies. AGN are known to inflate buoyant bubbles that supply mechanical power to the intracluster gas [intracluster medium (ICM)]. High Reynolds number hydrodynamical simulations show that such bubbles get entirely disrupted within 100 Myr, as they rise in cluster atmospheres, which is contrary to observations. This artificial mixing has consequences for models trying to quantify the amount of heating and star formation in cool core clusters of galaxies. It has been suggested that magnetic fields can stabilize bubbles against disruption. We perform magnetohydrodynamical simulations of fossil bubbles in the presence of tangled magnetic fields using the high-order pencil code. We focus on the physically motivated case where thermal pressure dominates over magnetic pressure and consider randomly oriented fields with and without maximum helicity and a case where large-scale external fields drape the bubble. We find that helicity has some stabilizing effect. However, unless the coherence length of magnetic fields exceeds the bubble size, the bubbles are quickly shredded. As observations of Hydra A suggest that length-scale of magnetic fields may be smaller than typical bubble size, this may suggest that other mechanisms, such as viscosity, may be responsible for stabilizing the bubbles. However, since Faraday rotation observations of radio lobes do not constrain large-scale ICM fields well if they are aligned with the bubble surface, the draping case may be a viable alternative solution to the problem. A generic feature found in our simulations is the formation of magnetic wakes where fields are ordered and amplified. We suggest that this effect could prevent evaporation by thermal conduction of cold H, filaments observed in the Perseus cluster. [source] Coronal activity from dynamos in astrophysical rotatorsMONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 3 2000Eric G. Blackman We show that a steady mean-field dynamo in astrophysical rotators leads to an outflow of relative magnetic helicity and thus magnetic energy available for particle and wind acceleration in a corona. The connection between energy and magnetic helicity arises because mean-field generation is linked to an inverse cascade of magnetic helicity. To maintain a steady state in large magnetic Reynolds number rotators, there must then be an escape of relative magnetic helicity associated with the mean field, accompanied by an equal and opposite contribution from the fluctuating field. From the helicity flow, a lower limit on the magnetic energy deposited in the corona can be estimated. Steady coronal activity including the dissipation of magnetic energy, and formation of multi-scale helical structures therefore necessarily accompanies an internal dynamo. This highlights the importance of boundary conditions which allow this to occur for non-linear astrophysical dynamo simulations. Our theoretical estimate of the power delivered by a mean-field dynamo is consistent with that inferred from observations to be delivered to the solar corona, the Galactic corona, and Seyfert 1 AGN coronae. [source] An enhanced-physics-based scheme for the NS-, turbulence modelNUMERICAL METHODS FOR PARTIAL DIFFERENTIAL EQUATIONS, Issue 6 2010William W. Miles Abstract We study a new enhanced-physics-based numerical scheme for the NS-alpha turbulence model that conserves both energy and helicity. Although most turbulence models (in the continuous case) conserve only energy, NS-alpha is one of only a very few that also conserve helicity. This is one reason why it is becoming accepted as the most physically accurate turbulence model. However, no numerical scheme for NS-alpha, until now, conserved both energy and helicity, and thus the advantage gained in physical accuracy by modeling with NS-alpha could be lost in a computation. This report presents a finite element numerical scheme, and gives a rigorous analysis of its conservation properties, stability, solution existence, and convergence. A key feature of the analysis is the identification of the discrete energy and energy dissipation norms, and proofs that these norms are equivalent (provided a careful choice of filtering radius) in the discrete space to the usual energy and energy dissipation norms. Numerical experiments are given to demonstrate the effectiveness of the scheme over usual (helicity-ignoring) schemes. A generalization of this scheme to a family of high-order NS-alpha-deconvolution models, which combine the attractive physical properties of NS-alpha with the high accuracy gained by combining ,-filtering with van Cittert approximate deconvolution. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 2010 [source] Photoluminescence microscopy of as-grown individual single-walled carbon nanotubes on Si/SiO2 substratesPHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 13 2006Oliver Kiowski Abstract We present far-field photoluminescence (PL) imaging at room temperature of tens of micrometer long individual single-walled carbon nanotubes (SWNTs) grown and measured directly on a Si/SiO2 surface. The SWNTs are grown by Chemical Vapour Deposition (CVD) with ethanol as carbon source and contact the surface with their full length. We detect the PL and its variations along SWNTs in a home-built laser microscope with a spatial resolution of ,400 nm. We are able to reliably assign (n, m)-structure of SWNTs by measuring PL spectra in the range of 800,1600 nm as function of the excitation wavelength varying between 710 and 860 nm. This allows us to check structural integrity (changes of helicity) along the tube. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Optical spin orientation of a single manganese atomPHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue 6 2010C. Le Gall Abstract An optical spin orientation is achieved for a Mn atom localized in a semiconductor quantum dot using quasiresonant excitation at zero magnetic field. Optically created spin polarized carriers generate an energy splitting of the Mn spin and enable magnetic moment orientation controlled by the photon helicity and energy. The dynamics and the magnetic field dependence of the optical pumping mechanism shows that the spin lifetime of an isolated Mn atom at zero magnetic field is controlled by a magnetic anisotropy induced by the built-in strain in the quantum dots. Relaxation times exceeding the micro-second range are measured (© 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Helical opposition in poly(2-methoxyaniline) by tuning the concentration of salts in reaction solutionPOLYMER INTERNATIONAL, Issue 9 2010Guo-Li Yuan Abstract The synthesis and application of helical polyaniline derivatives (PANIs) have attracted much interest. However, most of these syntheses have been carried out in organic solutions. In our previous reports, helical PANIs were successfully realized in aqueous solution. Because helical architecture in the backbones of PANIs is an induced rather than the natural arrangement, it is significant to study the change in helicity in aqueous solution, especially opposition or reversion. One excess-handed helicity was induced in poly(2-methoxyaniline) (PMOA) by electrochemical polymerization of 2-methoxyaniline at pH = 2.5 in the presence of protonated ,-cyclodextrin sulfate (CDS, H+). When 0.04 mol L,1 NaCl was added to the reaction solution, the PMOA backbone took on an opposite excess of one-handed helicity, which was confirmed by induced circular dichroism. Such a result originates from the dynamic switch between electrostatic and hydrogen-bonding interactions. The helix-inducing process in PMOA depends on the interaction between PMOA and chiral CDS. Due to the competition of Na+ Cl, with PMOA+ CDS,, the electrostatic interaction between PMOA and CDS is limited or weakened. Thus, the slightly preferred interaction between them switches from electrostatic to hydrogen bonding. Simultaneously, the interaction positions and distance are changed. The changed steric hindrance induces PMOA into adopting an opposite excess-handed helicity. Copyright © 2010 Society of Chemical Industry [source] Temperature-dependent structural changes in intrinsically disordered proteins: Formation of ,,helices or loss of polyproline II?PROTEIN SCIENCE, Issue 8 2010Magnus Kjaergaard Abstract Structural characterization of intrinsically disordered proteins (IDPs) is mandatory for deciphering their potential unique physical and biological properties. A large number of circular dichroism (CD) studies have demonstrated that a structural change takes place in IDPs with increasing temperature, which most likely reflects formation of transient ,,helices or loss of polyproline II (PPII) content. Using three IDPs, ACTR, NHE1, and Spd1, we show that the temperature-induced structural change is common among IDPs and is accompanied by a contraction of the conformational ensemble. This phenomenon was explored at residue resolution by multidimensional NMR spectroscopy. Intrinsic chemical shift referencing allowed us to identify regions of transiently formed helices and their temperature-dependent changes in helicity. All helical regions were found to lose rather than gain helical structures with increasing temperature, and accordingly these were not responsible for the change in the CD spectra. In contrast, the nonhelical regions exhibited a general temperature-dependent structural change that was independent of long-range interactions. The temperature-dependent CD spectroscopic signature of IDPs that has been amply documented can be rationalized to represent redistribution of the statistical coil involving a general loss of PPII conformations. [source] Dioxane contributes to the altered conformation and oligomerization state of a designed engrailed homeodomain variantPROTEIN SCIENCE, Issue 4 2005Geoffrey K. Hom Abstract Our goal was to compute a stable, full-sequence design of the Drosophila melanogaster engrailed homeodomain. Thermal and chemical denaturation data indicated the design was significantly more stable than was the wild-type protein. The data were also nearly identical to those for a similar, later full-sequence design, which was shown by NMR to adopt the homeodomain fold: a three-helix, globular monomer. However, a 1.65 Å crystal structure of the design described here turned out to be of a completely different fold: a four-helix, rodlike tetramer. The crystallization conditions included ,25% dioxane, and subsequent experiments by circular dichroism and sedimentation velocity analytical ultracentrifugation indicated that dioxane increases the helicity and oligomerization state of the designed protein. We attribute at least part of the discrepancy between the target fold and the crystal structure to the presence of a high concentration of dioxane. [source] Gas-phase behavior of noncovalent transmembrane segment complexesRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 24 2008Linda M. M. Weigang Specific helix oligomerization between transmembrane segments (TMSs) is often promoted by motifs like GxxxG. Disruption of this motif in the transmembrane segments of vesicular stomatitis virus G-protein and of glycophorin A results in a reduced dimerization level studied by in vivo systems like ToxR. This paper reports the influence of sequence motifs like GxxxG in solution and the gas phase. The transmembrane segments may behave differently in the gas and liquid phase, because of the absence of surrounding solvent molecules in the gas phase. Comparison of experiments depending on peptide properties performed in the gas and liquid phase discloses that the peptides retain ,some memory' of their liquid-phase structure in the gas phase. A direct correlation has been found between helicity in solution as determined by circular dichroism and dimerization in the gas phase monitored by electrospray mass spectrometry. These results show that a proper folding in solution is required for oligomerization. On the other hand, sequence-specific oligomerization depending on the GxxxG motif was not observed with the mass spectrometric detection. Further on, neither concentration-dependent complex studies nor studies regarding complex stability in the gas phase , via collision-induced dissociation (CID) , led to sequence-specific differences. Finally, the findings show that in mass spectrometric measurements noncovalent interactions of studied TMSs is rather more dependent on the secondary structure and proper folding than on their primary structure. Copyright © 2008 John Wiley & Sons, Ltd. [source] Control of helix sense in protein-mimicking backbone by the noncovalent chiral effectTHE CHEMICAL RECORD, Issue 3 2007Yoshihito Inai Abstract We have reviewed our previous work regarding induction or control of a peptide helix sense through chiral stimulus to the peptide chain terminus. An optically inactive 310 -helix designed mainly with unusual ,-amino acid residues was commonly employed. Such an N-terminal-free peptide generates a preferred helix sense by chiral acid molecule. A helix sense pre-directed in chiral sequence is also influenced or controlled by the chiral sign of such external molecule. Here free amide groups in the 310 -helical N-terminus participate in the formation of a multipoint coordinated complex. The terminal asymmetry produces the noncovalent chiral domino effect (NCDE) to influence the whole helix sense. The NCDE-mediated control of helicity provides the underlying chiral nature of protein-mimicking helical backbones: notably, chiral recognition at the terminus and modulation of helical propensity through chiral stimulus. The above items from our previous reports have been outlined and reviewed together with their significance in biopolymer science and chiral chemistry. © 2007 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 7: 191,202; 2007: Published online in Wiley Inter-Science (www.interscience.wiley.com) DOI 10.1002/tcr.20116 [source] The chiral helical structure of a copper(II) complex with a tridentate Schiff base ligandACTA CRYSTALLOGRAPHICA SECTION C, Issue 8 2009Wen-Juan Shi In the title salt, catena -poly[[[aquacopper(II)]-,-3-(2-pyridylmethyleneamino)propanoato-,4N,N,,O:O,] perchlorate], {[Cu(C9H9N2O2)(H2O)]ClO4}n, the monomeric unit contains a square-based pyramidal CuII centre. The four basal positions are occupied by a tridentate anionic Schiff base ligand which furnishes an NNO-donor set, with the fourth basal position being occupied by an O-donor atom from the carboxylate group of an adjacent Schiff base ligand. The coordination sphere is completed by a water molecule at the apical position. Interestingly, each carboxylate group in the ligand forms a syn,anti -configured bridge between two CuII centres, leading to left-handed chiral helicity. The framework also exhibits O,H...O hydrogen bonds involving the water molecules and an O atom of the perchlorate anion. [source] | ||||||||||||||||||||||||||||||||||