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Sample records for 1d chain structures

  1. Magnetic properties driven by local structure in quasi-1D Ising chain system cobaltate system

    NASA Astrophysics Data System (ADS)

    Kim, Bongjae; Kim, Beom Hyun; Kim, Kyoo; Choi, Hong Chul; Park, Sang-Yeon; Jeong, Y.-H.; Min, B. I.

    2012-02-01

    Using ab-initio band structure method and the microscopic model calculation, the origins of the large orbital magnetic moment and unique magnetic anisotropy in the quasi-1D magnetic cobaltate, α-CoV2O6, is investigated. Unique crystal electric field effect in α-CoV2O6 is combined with the strong spin-orbit coupling, results in intriguing magnetic properties of the system. Based on the estimated strengths of the intra- and the inter-chain exchange interaction, experimentally found 1/3 magnetization plateau in the MH curve can be attributed to spin-flop mechanism. Origin of the reduced magnetic entropy behavior is found to be the strong uniaxial magnetic anisotropy in the quasi-1D Ising chain system.

  2. Crystal structures of bovine CD1d reveal altered αGalCer presentation and a restricted A' pocket unable to bind long-chain glycolipids.

    PubMed

    Wang, Jing; Guillaume, Joren; Pauwels, Nora; Van Calenbergh, Serge; Van Rhijn, Ildiko; Zajonc, Dirk M

    2012-01-01

    NKT cells play important roles in immune surveillance. They rapidly respond to pathogens by detecting microbial glycolipids when presented by the non-classical MHC I homolog CD1d. Previously, ruminants were considered to lack NKT cells due to the lack of a functional CD1D gene. However, recent data suggest that cattle express CD1d with unknown function. In an attempt to characterize the function of bovine CD1d, we assessed the lipid binding properties of recombinant Bos taurus CD1d (boCD1d) in vitro. BoCD1d is able to bind glycosphingolipids (GSLs) with fatty acid chain lengths of C₁₈, while GSLs with fatty acids of C₂₄ do not bind. Crystal structures of boCD1d bound to a short-chain C₁₂-di-sulfatide antigen, as well as short-chain C₁₆-αGalCer revealed that the Á pocket of boCD1d is restricted in size compared to that of both mouse and human CD1d, explaining the inability of long chain GSL's to bind to boCD1d. Moreover, while di-sulfatide is presented similarly compared to the presentation of sulfatide by mouse CD1d, αGalCer is presented differently at the cell surface, due to an amino acid Asp151Asn substitution that results in loss of intimate contacts between the αGalCer headgroup and CD1d. The altered αGalCer presentation by boCD1d also explains its lack of cross-activation of mouse iNKT cells and raises the interesting question of the nature and function of bovine lipid-reactive T cells.

  3. Crystal Structures of Bovine CD1d Reveal Altered αGalCer Presentation and a Restricted A’ Pocket Unable to Bind Long-Chain Glycolipids

    PubMed Central

    Wang, Jing; Guillaume, Joren; Pauwels, Nora; Van Calenbergh, Serge; Van Rhijn, Ildiko; Zajonc, Dirk M.

    2012-01-01

    NKT cells play important roles in immune surveillance. They rapidly respond to pathogens by detecting microbial glycolipids when presented by the non-classical MHC I homolog CD1d. Previously, ruminants were considered to lack NKT cells due to the lack of a functional CD1D gene. However, recent data suggest that cattle express CD1d with unknown function. In an attempt to characterize the function of bovine CD1d, we assessed the lipid binding properties of recombinant Bos taurus CD1d (boCD1d) in vitro. BoCD1d is able to bind glycosphingolipids (GSLs) with fatty acid chain lengths of C18, while GSLs with fatty acids of C24 do not bind. Crystal structures of boCD1d bound to a short-chain C12-di-sulfatide antigen, as well as short-chain C16-αGalCer revealed that the Á pocket of boCD1d is restricted in size compared to that of both mouse and human CD1d, explaining the inability of long chain GSL’s to bind to boCD1d. Moreover, while di-sulfatide is presented similarly compared to the presentation of sulfatide by mouse CD1d, αGalCer is presented differently at the cell surface, due to an amino acid Asp151Asn substitution that results in loss of intimate contacts between the αGalCer headgroup and CD1d. The altered αGalCer presentation by boCD1d also explains its lack of cross-activation of mouse iNKT cells and raises the interesting question of the nature and function of bovine lipid-reactive T cells. PMID:23110152

  4. Structural variation from heterometallic cluster-based 1D chain to heterometallic tetranuclear cluster: Syntheses, structures and magnetic properties

    SciTech Connect

    Zhang, Shu-Hua; Zhao, Ru-Xia; Li, He-Ping; Ge, Cheng-Min; Li, Gui; Huang, Qiu-Ping; Zou, Hua-Hong

    2014-08-15

    Using the solvothermal method, we present the comparative preparation of ([Co{sub 3}Na(dmaep){sub 3}(ehbd)(N{sub 3}){sub 3}]·DMF){sub n} (1) and [Co{sub 2}Na{sub 2}(hmbd){sub 4}(N{sub 3}){sub 2}(DMF){sub 2}] (2), where Hehbd is 3-ethoxy-2-hydroxy-benzaldehyde, Hhmbd is 3-methoxy-2-hydroxy-benzaldehyde, and Hdmaep is 2-dimethylaminomethyl-6-ethoxy-phenol, which was synthesized by an in-situ reaction. Complexes 1 and 2 were characterized by elemental analysis, IR spectroscopy, and X-ray single-crystal diffraction. Complex 1 is a novel heterometallic cluster-based 1-D chain and 2 is a heterometallic tetranuclear cluster. The (Co{sub 3}{sup II}Na) and (Co{sub 2}{sup II}Na{sub 2}) cores display dominant ferromagnetic interaction from the nature of the binding modes through μ{sub 1,1,1}-N{sub 3}{sup –} (end-on, EO). - Graphical abstract: Two novel cobalt complexes have been prepared. Compound 1 consists of tetranuclear (Co{sub 3}{sup II}Na) units, which further formed a 1-D chain. Compound 2 is heterometallic tetranuclear cluster. Two complexes display dominant ferromagnetic interaction. - Highlights: • Two new heterometallic complexes have been synthesized by solvothermal method. • The stereospecific blockade of the ligands in the synthesis system seems to be the most important synthetic parameter. • The magnetism studies show that 1 and 2 exhibit ferromagnetic interactions. • Complex 1 shows slowing down of magnetization and not blocking of magnetization.

  5. Heat Capacity of 1D Molecular Chains

    NASA Astrophysics Data System (ADS)

    Bagatskii, M. I.; Barabashko, M. S.; Sumarokov, V. V.; Jeżowski, A.; Stachowiak, P.

    2017-04-01

    The heat capacity of 1D chains of nitrogen and methane molecules (adsorbed in the outer grooves of bundles of closed-cap single-walled carbon nanotubes) has been studied in the temperature ranges 2-40 and 2-60 K, respectively. The temperature dependence of the heat capacity of 1D chains of nitrogen molecules below 3 K is close to a linear. It was found that the rotational heat capacity of methane molecules is a significant part of the total heat capacity of the chains throughout the whole investigated temperature range, whereas in the case of nitrogen, the librations are significant only above 15 K. The dependence of the heat capacity for methane below 10 K indicates the presence of a Schottky anomaly caused by the tunneling between the lowest energy levels of the CH4 molecule rotational spectra. Characteristic features observed in the temperature dependence of the heat capacity of 1D methane crystals are also discussed.

  6. Structural Modulation from 1D Chain to 3D Framework: Improved Thermostability, Insensitivity, and Energies of Two Nitrogen-Rich Energetic Coordination Polymers.

    PubMed

    Guo, Zhaoqi; Wu, Yunlong; Deng, Chongqing; Yang, Guoping; Zhang, Jiangong; Sun, Zhihua; Ma, Haixia; Gao, Chao; An, Zhongwei

    2016-11-07

    Two new energetic coordination polymers (CPs) [Pb(BT)(H2O)3]n (1) and [Pb3(DOBT)3(H2O)2]n·(4H2O)n (2) with 1D and 3D structures were synthesized by employing two rational designed ligands, 1H,1'H-5,5'-bitetrazole (H2BT) and 1H,1'H-[5,5'-bitetrazole]-1,1'-diol ligands (DHBT), respectively. Thermal analyses and sensitivity tests show that the 3D architecture reinforces the network of 2 which has higher thermal stability and lower sensitivity than that of 1. Through oxygen-bomb combustion calorimetry the molar enthalpy of formation of 2 is derived to be much higher than that of 1 as well as the reported CPs. Herein, more importantly, the heats of detonation (ΔHdet) were calculated according to the decomposition products of TG-DSC-MS-FTIR simultaneous analyses for the first time. The calculated results show that ΔHdet of 2 is 23% higher than that of 1. This research demonstrates that 3D energetic CP with outstanding energetic properties can be obtained through efficient and reasonable design.

  7. Self-assembled 1D magnetic Ising chains: epitaxial islands of Co/Ru(0001)

    NASA Astrophysics Data System (ADS)

    Li, Dongqi; Yu, Chengtao; Pearson, John; Bader, Samuel

    2002-03-01

    We have self-assembled magnetic Co dot chains via epitaxial island decoration of grooved Ru(0001) to create a model 1D system. Co wedge-like structures of 0-60 nm thick were deposited onto flat and grooved Ru(0001) substrates via molecular beam epitaxy at 350¢ªC and characterized ex-situ with atomic force and the magnetic force microscopy (MFM), and magneto-optic Kerr effect. The grooved substrate has a saw-tooth profile with spacing of order of 1 um, due to residual polishing scratches / step bunching. Co forms strain-induced, quasi-hexagonal dots of 70-500 nm in diameter and 1-20 nm high, depending on nominal dosage. On grooved substrate, the dots self align into chains along the groove near the top and bottom of the saw-tooth structure.[1] The dots are ferromagnetically coupled along the chain and exhibit magnetic single-domains with in-plane uniaxial anisotropy along the grooves. The inter-dot magnetic pair correlation was deduced from the MFM images of the dot-chains, and can be understood in terms of the classic 1D Ising model. * Work supported by DOE BES-MS under #W-31-109-ENG-38. 1. Chengtao Yu, Dongqi Li, J. Pearson, and S.D. Bader, Appl. Phys. Lett. 78, 1228 (2001); ibid. 79, 3848 (2001).

  8. Nanojet-induced modes in 1D chains of microspheres

    NASA Astrophysics Data System (ADS)

    Kapitonov, A. M.; Astratov, V. N.

    2007-02-01

    We report on the light transport phenomena in linear chains composed of several tens of touching spherical microcavities. A new optical mode type, namely nanojet-induced modes (NIMs) is observed. These modes result from the optical coupling of microspheres acting as a series of micro-lenses, which periodically focus propagating wave into photonic nanojets. Theoretically, formation of periodic nanojets has been predicted in Z. Chen et al., Opt. Lett. 31, 389 (2006). The chains were produced by means of the self-assembly directed by micro-flows of water suspension of polystyrene microspheres. The mean size of spheres was varied in the 2-10 micron range. To couple light to NIMs we used built-in emission sources formed by several locally excited dye-doped microcavities from the same chain. Conversion of modes emitted by the light source into the NIMs results in losses of several dB per sphere in the vicinity (first few tens of spheres) of such sources. At longer distances we found an attenuation rate as small as 0.5 dB per sphere that reveals low intrinsic propagation loss for NIMs. The NIMs have potential applications for coupling and guiding of light in compact arrays of spherical cavities with extremely high quality (Q) whispering gallery modes.

  9. A novel cryogenic magnetic refrigerant metal-organic framework based on 1D gadolinium(III) chain

    NASA Astrophysics Data System (ADS)

    Tang, Qun; Li, Peng-Fei; Zou, Zhi-Ming; Liu, Zheng; Liu, Shu-Xia

    2017-02-01

    A metal-organic framework (MOF) based on gadolinium ion (Gd3+) and tricarboxylate ligand, [Gd(BTPCA)(H2O)]·2DMF·3H2O (Gd-BTPCA) (H3BTPCA =1,1‧,1‧-(benzene-1,3,5-triyl)tripiperidine-4-carboxylic acid; DMF=dimethylformamide), was synthesized and structurally characterized. The adjacent Gd3+ ions are intraconnected by the carboxylate groups of the BTPCA3- ligands to form a 1D Gd3+ ion chain. The 1D Gd3+ ion chains are interconnected by the BTPCA3- ligands, giving rise to a 3D framework with 1D open channel. The magnetic studies indicate that Gd-BTPCA exhibits weak ferromagnetic interactions, and acts as a cryogenic magnetic refrigerant having the magnetic entropy change (-ΔSm) of 20.40 J kg-1 K-1 for ΔH =7 T at 3 K.

  10. From 1D chain to 3D network: a new family of inorganic-organic hybrid semiconductors MO3(L)(x) (M = Mo, W; L = organic linker) built on perovskite-like structure modules.

    PubMed

    Zhang, Xiao; Hejazi, Mehdi; Thiagarajan, Suraj J; Woerner, William R; Banerjee, Debasis; Emge, Thomas J; Xu, Wenqian; Teat, Simon J; Gong, Qihan; Safari, Ahmad; Yang, Ronggui; Parise, John B; Li, Jing

    2013-11-20

    MO3 (M = Mo, W) or VI-VI binary compounds are important semiconducting oxides that show great promise for a variety of applications. In an effort to tune and enhance their properties in a systematic manner we have applied a designing strategy to deliberately introduce organic linker molecules in these perovskite-like crystal lattices. This approach has led to a wealth of new hybrid structures built on one-dimensional (1D) and two-dimensional (2D) VI-VI modules. The hybrid semiconductors exhibit a number of greatly improved properties and new functionality, including broad band gap tunability, negative thermal expansion, largely reduced thermal conductivity, and significantly enhanced dielectric constant compared to their MO3 parent phases.

  11. A novel coordination polymer containing both interdigitated 1D chains and interpenetrated 2D grids.

    PubMed

    Ayyappan, Ponnaiyan; Evans, Owen R; Lin, Wenbin

    2002-07-01

    A hydro(solvo)thermal reaction between zinc perchlorate and ethyl ester of a new pyridinecarboxylate bridging ligand of approximately 17.6 A in length yields a unique coordination polymer which contains both interdigitated infinite 1D chains and interpenetrated 2D rhombohedral grids [Zn(2.5)(L)(4)(mu(3)-OH)] x (H(2)O)(5), 1, where L is 3-[[4-(4-pyridylethenyl)phenyl]ethenyl]benzoate. The 1D chains contain mu(3)-bridged hydroxy groups and have a [Zn(4)(mu(3)-OH)(2)(L)(6)] stoichiometry, while the 2D grids have a Zn(L)(2) formula and diagonal distances of 31.7 and 25.2 A. Crystal data for 1: monoclinic space group P2/c, a = 15.686(2) A, b = 12.6103(16) A, c = 38.999(5) A, beta = 98.397(2) degrees, and Z = 4.

  12. Analysis of the rotational structure in the high-resolution infrared spectra of trans-hexatriene-1,1-d2 and -cis-1-d1

    NASA Astrophysics Data System (ADS)

    Craig, Norman C.; Fuson, Hannah A.; Tian, Hengfeng; Blake, Thomas A.

    2012-09-01

    Mixtures of trans-hexatriene-1,1-d2, -cis-1-d1, and -trans-1-d1 have been synthesized. Anharmonic frequencies and harmonic intensities were predicted with the B3LYP/cc-pVTZ model for the out-of-plane (a″) modes of the three isotopologues. Assignments are proposed for most of the a″ vibrational modes above 500 cm-1. Ground state (GS) rotational constants have been determined for the 1,1-d2 and cis-1-d1 species from the analysis of rotational structure of C-type bands in the high-resolution (0.0015 cm-1) infrared spectra in a mixture of the three isotopologues. The GS constants for the 1,1-d2 species are A0 = 0.8018850(6), B0 = 0.0418540(6), and C0 = 0.0397997(4) cm-1. The GS constants for the cis-1-d1 species are A0 = 0.809388(1), B0 = 0.043532(2), and C0 = 0.041320(1) cm-1. Small inertial defects confirm planarity for both species. These ground state rotational constants are intended for use in determining a semiexperimental equilibrium structure and evaluating the influence of chain length on π-electron delocalization in polyenes.

  13. Constitutive modeling and control of 1D smart composite structures

    NASA Astrophysics Data System (ADS)

    Briggs, Jonathan P.; Ostrowski, James P.; Ponte-Castaneda, Pedro

    1998-07-01

    Homogenization techniques for determining effective properties of composite materials may provide advantages for control of stiffness and strain in systems using hysteretic smart actuators embedded in a soft matrix. In this paper, a homogenized model of a 1D composite structure comprised of shape memory alloys and a rubber-like matrix is presented. With proportional and proportional/integral feedback, using current as the input state and global strain as an error state, implementation scenarios include the use of tractions on the boundaries and a nonlinear constitutive law for the matrix. The result is a simple model which captures the nonlinear behavior of the smart composite material system and is amenable to experiments with various control paradigms. The success of this approach in the context of the 1D model suggests that the homogenization method may prove useful in investigating control of more general smart structures. Applications of such materials could include active rehabilitation aids, e.g. wrist braces, as well as swimming/undulating robots, or adaptive molds for manufacturing processes.

  14. Analysis of Rotational Structure in the High-Resolution Infrared Spectra of the TRANS-HEXATRIENE-1,1-D2 and -CIS-1-D1 Species

    NASA Astrophysics Data System (ADS)

    Craig, Norman C.; Fuson, Hannah A.; Tian, Hengfeng; Blake, Thomas A.

    2011-06-01

    Hexatriene-1,1-D2 with some admixture of the cis-1-D1 and trans-1-D1 species was synthesized by reaction of 2,4-pentadienal and (methyl-D3)-triphenylphosphonium iodide (Wittig reagent). The trans isomer was isolated by preparative gas chromatography, and the high-resolution (0.0015 Cm-1) infrared spectrum was recorded on a Bruker IFS 125HR instrument. The rotational structure in two C-type bands for the 1,1-D2 species was analyzed. For this species the bands at 902.043 and 721.864 Cm-1 yielded composite ground state rotational constants of A0 = 0.801882(1), B0 = 0.041850(2), and C0 = 0.039804(1) Cm-1. For the cis-1-D1 species the C-type band at 803.018 Cm-1 gave A0 = 0.809384(2), B0 = 0.043530(3), and C0 = 0.041321(2) Cm-1. By iodine-catalyzed isomerization, we have obtained some of the much less favored cis isomer and hope to obtain microwave spectra for its three deuterium-substituted species. The rotational constants reported here contribute to data needed for determining a semi-experimental structure for trans-hexatriene, which should show that the structural consequences of pi-electron delocalization increase with the chain length of polyenes.

  15. Formation of Gd coordination polymer with 1D chains mediated by Bronsted acidic ionic liquids

    NASA Astrophysics Data System (ADS)

    Luo, Qianqian; Han, Ying; Lin, Hechun; Zhang, Yuanyuan; Duan, Chungang; Peng, Hui

    2017-03-01

    One dimensional coordination polymer Gd[(SO4)(NO3)(C2H6SO)2] (1) is prepared through the mediation of Bronsted acid ionic liquid, which crystallized in the monoclinic space of C2/c. In this polymer, adjacent Gd atoms are linked by two SO42- ions to generate a 1-D chain, and all oxygen atoms in SO42- groups are connected to three nearest Gd atoms in μ3:η1:η1:η2 fashion. Gd, S and N from SO42- and NO3- are precisely coplanar. The planar is coordinated by a pair of DMSO molecules, which is parallel and linked by hydrogen bonding to form a three-dimensional supramolecular network. Magnetic susceptibility measurement of 1 reveals weak antiferromagnetic interactions between the Gd (III) ions. It exhibits relatively large magneto-caloric effect with -ΔSm=28.8 J Kg-1 K-1 for ΔH=7 T.

  16. New Mononuclear Cu(II) Complexes and 1D Chains with 4-Amino-4H-1,2,4-triazole

    PubMed Central

    Dîrtu, Marinela M.; Boland, Yves; Gillard, Damien; Tinant, Bernard; Robeyns, Koen; Safin, Damir A.; Devlin, Eamonn; Sanakis, Yiannis; Garcia, Yann

    2013-01-01

    The crystal structures of two mononuclear Cu(II) NH2trz complexes [Cu(NH2trz)4(H2O)](AsF6)2 (I) and [Cu(NH2trz)4(H2O)](PF6)2 (II) as well as two coordination polymers [Cu(μ2-NH2trz)2Cl]Cl·H2O (III) and [Cu(μ2-NH2trz)2Cl] (SiF6)0.5·1.5H2O (IV) are presented. Cationic 1D chains with bridging bis-monodentate μ2-coordinated NH2trz and bridging μ2-coordinated chloride ligands are present in III and IV. In these coordination polymers, the Cu(II) ions are strongly antiferromagnetically coupled with J = −128.4 cm−1 for III and J = −143 cm−1 for IV (H = −J∑SiSi+1), due to the nature of the bridges between spin centers. Inter-chain interactions present in the crystal structures were taken into consideration, as well as g factors, which were determined experimentally, for the quantitative modeling of their magnetic properties. PMID:24300095

  17. The role of solitons in charge and energy transfer in 1D molecular chains

    NASA Astrophysics Data System (ADS)

    Ivić , Zoran

    1998-03-01

    The idea that polarons and solitons could play the crucial role in the transport processes in biological structures, has been critically reexamined on the basis of the general theory of self-trapping phenomena. The criteria which enable one to determine conditions for the existence and stability of polarons and solitons and to determine their character, in dependence of the values of the basic physical parameters of the system, were formulated. Validity of the so-called Davydov's soliton model was discussed on the basis of these criteria. It was found that the original Davydov's proposal, based upon the idea of the soliton creation due to the single excitation (particle, vibron, etc.) self-trapping, cannot explain the intramolecular energy transfer in α-helix and acetanilide. However, Davydov theory is flexible enough to describe the single electron transfer in some systems (α-helix and acetanilide for example). In the many-particle systems, dressing effect, due to the quantum nature of phonons, may cause the creation of the bound states of the several excitons in the molecular chain. The possibility of creation of the soliton states of this type is discussed for the simple Fröhlich's one-dimensional model. The regions of the system parameter space where different mechanisms dominate the behaviour of such entities are characterized.

  18. Topological defect formation in 1D and 2D spin chains realized by network of optical parametric oscillators

    NASA Astrophysics Data System (ADS)

    Hamerly, Ryan; Inaba, Kensuke; Inagaki, Takahiro; Takesue, Hiroki; Yamamoto, Yoshihisa; Mabuchi, Hideo

    2016-09-01

    A network of optical parametric oscillators (OPOs) is used to simulate classical Ising and XY spin chains. The collective nonlinear dynamics of this network, driven by quantum noise rather than thermal fluctuations, seeks out the Ising/XY ground state as the system transitions from below to above the lasing threshold. We study the behavior of this “Ising machine” for three canonical problems: a 1D ferromagnetic spin chain, a 2D square lattice and problems where next-nearest-neighbor couplings give rise to frustration. If the pump turn-on time is finite, topological defects form (domain walls for the Ising model, winding number and vortices for XY) and their density can be predicted from a numerical model involving a linear “growth stage” and a nonlinear “saturation stage”. These predictions are compared against recent data for a 10,000-spin 1D Ising machine.

  19. Tunable Design of Structural Colors Produced by Pseudo-1D Photonic Crystals of Graphene Oxide.

    PubMed

    Tong, Liping; Qi, Wei; Wang, Mengfan; Huang, Renliang; Su, Rongxin; He, Zhimin

    2016-07-01

    It is broadly observed that graphene oxide (GO) films appear transparent with a thickness of about several nanometers, whereas they appear dark brown or almost black with thickness of more than 1 μm. The basic color mechanism of GO film on a sub-micrometer scale, however, is not well understood. This study reports on GO pseudo-1D photonic crystals (p1D-PhCs) exhibiting tunable structural colors in the visible wavelength range owing to its 1D Bragg nanostructures. Striking structural colors of GO p1D-PhCs could be tuned by simply changing either the volume or concentration of the aqueous GO dispersion during vacuum filtration. Moreover, the quantitative relationship between thickness and reflection wavelength of GO p1D-PhCs has been revealed, thereby providing a theoretical basis to rationally design structural colors of GO p1D-PhCs. The spectral response of GO p1D-PhCs to humidity is also obtained clearly showing the wavelength shift of GO p1D-PhCs at differently relative humidity values and thus encouraging the integration of structural color printing and the humidity-responsive property of GO p1D-PhCs to develop a visible and fast-responsive anti-counterfeiting label. The results pave the way for a variety of potential applications of GO in optics, structural color printing, sensing, and anti-counterfeiting.

  20. Tandem repeats modify the structure of the canine CD1D gene.

    PubMed

    Looringh van Beeck, F A; Leegwater, P A J; Herrmann, T; Broere, F; Rutten, V P M G; Willemse, T; Van Rhijn, I

    2013-06-01

    Among the CD1 proteins that present lipid antigens to T cells, CD1d is the only one that stimulates a population of T cells with an invariant T-cell receptor known as NKT cells. Sequencing of a 722 nucleotide gap in the dog (Canis lupus familiaris) genome revealed that the canine CD1D gene lacks a sequence homologous to exon 2 of human CD1D, coding for the start codon and signal peptide. Also, the canine CD1D gene contains three different short tandem repeats that disrupt the expected gene structure. Because canine CD1D cDNA lacks sequences homologous to human exon 2 and 3, the functionality of canine CD1d protein may be affected, and this could have consequences for the development and activation of canine NKT cells.

  1. Multiple mobility edges in a 1D Aubry chain with Hubbard interaction in presence of electric field: Controlled electron transport

    NASA Astrophysics Data System (ADS)

    Saha, Srilekha; Maiti, Santanu K.; Karmakar, S. N.

    2016-09-01

    Electronic behavior of a 1D Aubry chain with Hubbard interaction is critically analyzed in presence of electric field. Multiple energy bands are generated as a result of Hubbard correlation and Aubry potential, and, within these bands localized states are developed under the application of electric field. Within a tight-binding framework we compute electronic transmission probability and average density of states using Green's function approach where the interaction parameter is treated under Hartree-Fock mean field scheme. From our analysis we find that selective transmission can be obtained by tuning injecting electron energy, and thus, the present model can be utilized as a controlled switching device.

  2. Characterizing gapped phases of a 1D spin chain with on-site and spatial symmetries

    NASA Astrophysics Data System (ADS)

    West, Colin; Prakash, Abhishodh; Wei, Tzu-Chieh

    We investigate the phase diagram of a spin-1 chain whose Hamiltonian is invariant under translation, lattice inversion and a global A4 symmetry in the spin degrees of freedom. The classification scheme by Chen, Gu, and Wen allows us to enumerate all possible phases under the given symmetry. Then, we determine which of these phases actually occur in the two-parameter Hamiltonian. Using numerical methods proposed by Pollmann and Turner (2012) we determine the characteristic projective parameters for the Symmetry Protected Topological (SPT) phases. In addition, we present a method for determining the projective commutation parameter in these phases. The resulting phase diagram is rich and contains at least nine different SPT phases. This work was supported in part by the National Science Foundation.

  3. Two unprecedented 1D coordination polymer chains based on tetranuclear copper(II) building blocks

    SciTech Connect

    Li Gaijuan; Xing Yan Song Shuyan; Xu Ning; Liu Xianchun; Su Zhongmin

    2008-09-15

    The reaction of copper(II) sulfate with pyridine in DMF or methanol yield two unprecedented Cu(II) coordination polymers {l_brace}[Cu{sub 4}({mu}{sub 4}-O)(py){sub 4}(SO{sub 4}){sub 4}][{mu}-Cu(py)(DMF){sub 2}]{r_brace}{sub n}(1) and {l_brace}[Cu{sub 4}({mu}{sub 4}-O)(py){sub 4}(SO{sub 4}){sub 4}][{mu}-Cu(py){sub 4}]{r_brace}{sub n}(2), respectively. Single-crystal X-ray diffraction indicated that compound 1 crystallizes in the monoclinic system, space group p2(1)/n, a=14.542(5) A, b=16.359(5) A, c=18.951(5) A, {beta}=92.047(5){sup o}, V=4505(2) A{sup 3}, Z=4 while 2 is monoclinic C2/c, a=23.078(5) A, b=10.214(5) A, c=23.142(5) A, {beta}=115.471(5){sup o}, V=4925(3) A{sup 3}, Z=4. Both of the two compounds consist of tetrahedral tetranuclear [Cu{sub 4}({mu}{sub 4}-O)(py){sub 4}(SO{sub 4}){sub 4}] clusters that are bridged by pentacoordinated Cu atom for 1 or hexacoordinated Cu atoms for 2 through the sulfate oxygen to form the infinite one-dimensional polymer chains. - Graphical abstract: Two unprecedented Cu(II) coordination polymers have been prepared by using solvothermal method; they consist of tetrahedral tetranuclear clusters that are bridged by unique Cu(II) atom through the sulfate oxygen to form the infinite one-dimensional polymer chains (a) for complex 1 and (b) for complex 2.

  4. Structure and Catalytic Mechanism of Human Steroid 5-Reductase (AKR1D1)

    SciTech Connect

    Costanzo, L.; Drury, J; Christianson, D; Penning, T

    2009-01-01

    Human steroid 5{beta}-reductase (aldo-keto reductase (AKR) 1D1) catalyzes reduction of {Delta}{sup 4}-ene double bonds in steroid hormones and bile acid precursors. We have reported the structures of an AKR1D1-NADP{sup +} binary complex, and AKR1D1-NADP{sup +}-cortisone, AKR1D1-NADP{sup +}-progesterone and AKR1D1-NADP{sup +}-testosterone ternary complexes at high resolutions. Recently, structures of AKR1D1-NADP{sup +}-5{beta}-dihydroprogesterone complexes showed that the product is bound unproductively. Two quite different mechanisms of steroid double bond reduction have since been proposed. However, site-directed mutagenesis supports only one mechanism. In this mechanism, the 4-pro-R hydride is transferred from the re-face of the nicotinamide ring to C5 of the steroid substrate. E120, a unique substitution in the AKR catalytic tetrad, permits a deeper penetration of the steroid substrate into the active site to promote optimal reactant positioning. It participates with Y58 to create a 'superacidic' oxyanion hole for polarization of the C3 ketone. A role for K87 in the proton relay proposed using the AKR1D1-NADP{sup +}-5{beta}-dihydroprogesterone structure is not supported.

  5. Synthesis, crystal structure, and properties of a 1-D terbium-substituted monolacunary Keggin-type polyoxotungstate.

    PubMed

    Ma, Pengtao; Si, Yanan; Wan, Rong; Zhang, Shaowei; Wang, Jingping; Niu, Jingyang

    2015-03-05

    A new 1-D linear chainlike terbium-substituted polyoxometalate [Tb(H2O)2(α-PW11O39)](4-) (1) has been synthesized in aqueous solution and characterized by elemental analysis, inductively coupled plasma atomic emission spectrometry (ICP-AES), X-ray powder diffraction (XRPD), IR spectrum, thermal analysis, electrospray ionization mass spectrometry (ESI-MS), and X-ray single-crystal diffraction. X-ray structural analysis reveals that 1 displays a 1-D linear chain containing [Tb(H2O)2(α-PW11O39)](4-) moieties. The Tb(III) cation incorporated into the monolacunary Keggin-type [α-PW11O39](7-) unit resides in a distorted monocapped triangular prismatic geometry and acts as a linker to join two adjacent [α-PW11O39](7-) units to form a 1-D chain structure. Solid-state photoluminescent property of 1 has been investigated at room temperature and the photoluminescent emission mainly results from the synergistic effect of the Tb(III) cation and the Na7[α-PW11O39] precursor. The ESI-MS spectrum of 1 confirms that the polyanion [Tb(H2O)(HPW11O39)](3-) is stable in aqueous solution.

  6. Two-step spin transition in a 1D Fe(II) 1,2,4-triazole chain compound.

    PubMed

    Dîrtu, Marinela M; Schmit, France; Naik, Anil D; Rusu, Ionela; Rotaru, Aurelian; Rackwitz, Sergej; Wolny, Juliusz A; Schünemann, Volker; Spinu, Leonard; Garcia, Yann

    2015-04-07

    A thermochromic 1D spin crossover coordination (SCO) polymer [Fe(βAlatrz)3](BF4)2⋅2 H2O (1⋅2 H2O), whose precursor βAlatrz, (1,2,4-triazol-4-yl-propionate) has been tailored from a β-amino acid ester is investigated in detail by a set of superconducting quantum interference device (SQUID), (57)Fe Mössbauer, differential scanning calorimetry, infrared, and Raman measurements. An hysteretic abrupt two-step spin crossover (T1/2(↓) = 230 K and T1/2(↑) = 235 K, and T1/2(↓) = 172 K and T1/2(↑) = 188 K, respectively) is registered for the first time for a 1,2,4-triazole-based Fe(II) 1D coordination polymer. The two-step SCO configuration is observed in a 1:2 ratio of low-spin/high-spin in the intermediate phase for a 1D chain. The origin of the stepwise transition was attributed to a distribution of chains of different lengths in 1⋅2 H2O after First Order Reversal Curves (FORC) analyses. A detailed DFT analysis allowed us to propose the normal mode assignment of the Raman peaks in the low-spin and high-spin states of 1⋅2 H2O. Vibrational spectra of 1⋅2 H2O reveal that the BF4(-) anions and water molecules play no significant role on the vibrational properties of the [Fe(βAlatrz)3](2+) polymeric chains, although non-coordinated water molecules have a dramatic influence on the emergence of a step in the spin transition curve. The dehydrated material [Fe(βAlatrz)3](BF4)2 (1) reveals indeed a significantly different magnetic behavior with a one-step SCO which was also investigated.

  7. Functional CD1d and/or NKT cell invariant chain transcript in horse, pig, African elephant and guinea pig, but not in ruminants

    PubMed Central

    Looringh van Beeck, Frank A.; Reinink, Peter; Hermsen, Roel; Zajonc, Dirk M.; Laven, Marielle J.; Fun, Axel; Troskie, Milana; Schoemaker, Nico J.; Morar, Darshana; Lenstra, Johannes A.; Vervelde, Lonneke; Rutten, Victor P.M.G.; van Eden, Willem; Van Rhijn, Ildiko

    2009-01-01

    CD1d-restricted invariant natural killer T cells (NKT cells) have been well characterized in humans and mice, but it is unknown whether they are present in other species. Here we describe the invariant TCR α chain and the full length CD1d transcript of pig and horse. Molecular modeling predicts that porcine (po) invariant TCR α chain/poCD1d/α-GalCer and equine (eq) invariant TCR α chain/eqCD1d/α-GalCer form complexes that are highly homologous to the human complex. Since a prerequisite for the presence of NKT cells is the expression of CD1d protein, we performed searches for CD1D genes and CD1d transcripts in multiple species. Previously, cattle and guinea pig have been suggested to lack CD1D genes. The CD1D genes of European taurine cattle (Bos taurus) are known to be pseudogenes because of disrupting mutations in the start codon and in the donor splice site of the first intron. Here we show that the same mutations are found in six other ruminants: African buffalo, sheep, bushbuck, bongo, N’Dama cattle, and roe deer. In contrast, intact CD1d transcripts were found in guinea pig, African elephant, horse, rabbit, and pig. Despite the discovery of a highly homologous NKT/CD1d system in pig and horse, our data suggest that functional CD1D and CD1d-restricted NKT cells are not universally present in mammals. PMID:19185921

  8. The structure of nanocomposite 1D cationic conductor crystal@SWNT.

    PubMed

    Kiselev, N A; Kumskov, A S; Zakalyukin, R M; Vasiliev, A L; Chernisheva, M V; Eliseev, A A; Krestinin, A V; Freitag, B; Hutchison, J L

    2012-06-01

    Nanocomposites consisting of one-dimensional (1D) crystals of the cationic conductors CuI, CuBr and AgBr inside single-walled carbon nanotubes, mainly (n, 0), were obtained using the capillary technique. 1D crystal structure models were proposed based on the high resolution transmission electron microscopy performed on a FEI Titan 80-300 at 80 kV with aberration correction. According to the models and image simulations there are two modifications of 1D crystal: hexagonal close-packed bromine (iodine) anion sublattice (growth direction <001>) and 1D crystal cubic structure (growth direction <112>) compressed transversely to the nanotube (D(m) ∼1.33 nm) axis. Tentatively this kind of 1D crystal can be considered as monoclinic. One modification of the anion sublattice reversibly transforms into the other inside the nanotube, probably initiated by electron beam heating. As demonstrated by micrographs, copper or silver cations can occupy octahedral positions or are statistically distributed across two tetrahedral positions. A 1DAgBr@SWNT (18, 0; 19, 0) pseudoperiodic 'lattice distortion' is revealed resulting from convolution of the nanotube wall function image with 1D cubic crystal function image.

  9. Structural resistance of chemically modified 1-D nanostructured titanates in inorganic acid environment

    SciTech Connect

    Marinkovic, Bojan A.; Fredholm, Yann C.; Morgado, Edisson

    2010-10-15

    Sodium containing one-dimensional nanostructured layered titanates (1-D NSLT) were produced both from commercial anatase powder and Brazilian natural rutile mineral sands by alkali hydrothermal process. The 1-D NSLT were chemically modified with proton, cobalt or iron via ionic exchange and all products were additionally submitted to intensive inorganic acid aging (pH = 0.5) for 28 days. The morphology and crystal structure transformations of chemically modified 1-D NSLT were followed by transmission electron microscopy, powder X-ray diffraction, selected area electron diffraction and energy dispersive spectroscopy. It was found that the original sodium rich 1-D NSLT and cobalt substituted 1-D NSLT were completely converted to rutile nanoparticles, while the protonated form was transformed in a 70%-30% (by weight) anatase-rutile nanoparticles mixture, very similar to that of the well-known TiO{sub 2}-photocatalyst P25 (Degussa). The iron substituted 1-D NSLT presented better acid resistance as 13% of the original structure and morphology remained, the rest being converted in rutile. A significant amount of remaining 1-D NSLT was also observed after the acid treatment of the product obtained from rutile sand. The results showed that phase transformation of NSLT into titanium dioxide polymorph in inorganic acid conditions were controllable by varying the exchanged cations. Finally, the possibility to transform, through acid aging, 1-D NSLT obtained from Brazilian natural rutile sand into TiO{sub 2}-polymorphs was demonstrated for the first time to the best of authors' knowledge, opening path for producing TiO{sub 2}-nanoproducts with different morphologies through a simple process and from a low cost precursor.

  10. Toward Structural Correctness: Aquatolide and the Importance of 1D Proton NMR FID Archiving.

    PubMed

    Pauli, Guido F; Niemitz, Matthias; Bisson, Jonathan; Lodewyk, Michael W; Soldi, Cristian; Shaw, Jared T; Tantillo, Dean J; Saya, Jordy M; Vos, Klaas; Kleinnijenhuis, Roel A; Hiemstra, Henk; Chen, Shao-Nong; McAlpine, James B; Lankin, David C; Friesen, J Brent

    2016-02-05

    The revision of the structure of the sesquiterpene aquatolide from a bicyclo[2.2.0]hexane to a bicyclo[2.1.1]hexane structure using compelling NMR data, X-ray crystallography, and the recent confirmation via full synthesis exemplify that the achievement of "structural correctness" depends on the completeness of the experimental evidence. Archived FIDs and newly acquired aquatolide spectra demonstrate that archiving and rigorous interpretation of 1D (1)H NMR data may enhance the reproducibility of (bio)chemical research and curb the growing trend of structural misassignments. Despite being the most accessible NMR experiment, 1D (1)H spectra encode a wealth of information about bonds and molecular geometry that may be fully mined by (1)H iterative full spin analysis (HiFSA). Fully characterized 1D (1)H spectra are unideterminant for a given structure. The corresponding FIDs may be readily submitted with publications and collected in databases. Proton NMR spectra are indispensable for structural characterization even in conjunction with 2D data. Quantum interaction and linkage tables (QuILTs) are introduced for a more intuitive visualization of 1D J-coupling relationships, NOESY correlations, and heteronuclear experiments. Overall, this study represents a significant contribution to best practices in NMR-based structural analysis and dereplication.

  11. Toward Structural Correctness: Aquatolide and the Importance of 1D Proton NMR FID Archiving

    PubMed Central

    2016-01-01

    The revision of the structure of the sesquiterpene aquatolide from a bicyclo[2.2.0]hexane to a bicyclo[2.1.1]hexane structure using compelling NMR data, X-ray crystallography, and the recent confirmation via full synthesis exemplify that the achievement of “structural correctness” depends on the completeness of the experimental evidence. Archived FIDs and newly acquired aquatolide spectra demonstrate that archiving and rigorous interpretation of 1D 1H NMR data may enhance the reproducibility of (bio)chemical research and curb the growing trend of structural misassignments. Despite being the most accessible NMR experiment, 1D 1H spectra encode a wealth of information about bonds and molecular geometry that may be fully mined by 1H iterative full spin analysis (HiFSA). Fully characterized 1D 1H spectra are unideterminant for a given structure. The corresponding FIDs may be readily submitted with publications and collected in databases. Proton NMR spectra are indispensable for structural characterization even in conjunction with 2D data. Quantum interaction and linkage tables (QuILTs) are introduced for a more intuitive visualization of 1D J-coupling relationships, NOESY correlations, and heteronuclear experiments. Overall, this study represents a significant contribution to best practices in NMR-based structural analysis and dereplication. PMID:26812443

  12. Formation of 1D adsorbed water structures on CaO(001)

    NASA Astrophysics Data System (ADS)

    Zhao, Xunhua; Bhattacharya, Saswata; Ghiringhelli, Luca M.; Levchenko, Sergey V.; Scheffler, Matthias

    2015-03-01

    Understanding the interaction of water with oxide surfaces is of fundamental importance for basic and engineering sciences. Recently, a spontaneous formation of one-dimensional (1D) adsorbed water structures have been observed on CaO(001). Interestingly, at other alkaline earth metal oxides, in particular MgO(001) and SrO(001), such structures have not been found experimentally. We calculate the relative stability of adsorbed water structures on the three oxides using density-functional theory combined with the ab initio atomistic thermodynamics. Low-energy structures at different coverages are obtained with a first-principles genetic algorithm. Finite-temperature vibrational spectra are calculated using ab initio molecular dynamics. We find a range of (T, p) conditions where 1D structures are thermodynamically stable on CaO(001). The orientation and vibrational spectra of the 1D structures are in agreement with the experiments. The formation of the 1D structures is found to be actuated by a symmetry breaking in the adsorbed water tetramer, as well as by a balance between water-water and water-substrate interactions, determined by the lattice constant of the oxide.

  13. A novel 1D chain of azido bridged copper(II) with a salen-type di-Schiff base ligand

    NASA Astrophysics Data System (ADS)

    Biswas, Saptarshi; Ghosh, Ashutosh

    2012-07-01

    One new complex of Cu(II), [(CuL)2Cu3(N3)6]n (1) has been synthesized by reacting the "ligand complex", [CuL] with copper acetate and sodium azide (NaN3) in methanol-water where the di-Schiff base ligand H2L = N,N‧-bis(α-methylsalicylidene)-1,3-propanediamine. The X-ray single crystal structural analysis shows that complex 1 consists of an incomplete face-sharing double cube of four Cu(II) ions with the formula of [(CuL)2Cu2(N3)2]2+ which are connected by [Cu(N3)4]2- unit to form a novel 1D chain.

  14. Investigation of 1-D crustal velocity structure beneath Izmir Gulf and surroundings by using local earthquakes

    NASA Astrophysics Data System (ADS)

    Polat, Orhan; Özer, Ćaglar

    2016-04-01

    In this study; we examined one dimensional crustal velocity structure of Izmir gulf and surroundings. We used nearly one thousand high quality (A and B class) earthquake data which recorded by Disaster and Emergency Management Presidency (AFAD) [1], Bogazici University (BU-KOERI) [2] and National Observatory of Athens (NOA) [3,4]. We tried several synthetic tests to understand power of new velocity structure, and examined phase residuals, RMS values and shifting tests. After evaluating these tests; we decided one dimensional velocity structure and minimum 1-D P wave velocities, hypocentral parameter and earthquake locations from VELEST algorithm. Distribution of earthquakes was visibly improved by using new minimum velocity structure.

  15. Synthesis, characterization and comparison of polyaniline 1D-structure controlled by poly(L-lactide) and poly(D-lactide)

    NASA Astrophysics Data System (ADS)

    Gu, Zhou-Jie; Shen, Qing

    2016-01-01

    1D-structural polyaniline (PANI) was controllably synthesized by utilizing the poly(L-lactide) (PLLA) and poly(D-lactide) (PDLA) as controllers. FESEM images showed that the morphology of 1D-structural PANI controlled by PDLA likes a joint obviously unlike PLLA controlled vertebra structure reported previously. To set the ratio of ANI/PLLA (ml/g) at 0.45/0.135, 0.45/0.270 and 0.45/0.540, the formed PANI 1D structure was changed in the cross-section as four round leaves, four non-round leaves and four sharp leaves, respectively. FTIR and XRD analysis indicated that the PLLA and PDLA both were doped in PANI chains while the PLLA was strongly in the electrons delocalization than that of the PDLA due probably to the L-type stronger in crystal polymorphism than that of the D-type.

  16. Structural and mechanistic insights into regulation of the retromer coat by TBC1d5

    PubMed Central

    Jia, Da; Zhang, Jin-San; Li, Fang; Wang, Jing; Deng, Zhihui; White, Mark A.; Osborne, Douglas G.; Phillips-Krawczak, Christine; Gomez, Timothy S.; Li, Haiying; Singla, Amika; Burstein, Ezra; Billadeau, Daniel D.; Rosen, Michael K.

    2016-01-01

    Retromer is a membrane coat complex that is recruited to endosomes by the small GTPase Rab7 and sorting nexin 3. The timing of this interaction and consequent endosomal dynamics are thought to be regulated by the guanine nucleotide cycle of Rab7. Here we demonstrate that TBC1d5, a GTPase-activating protein (GAP) for Rab7, is a high-affinity ligand of the retromer cargo selective complex VPS26/VPS29/VPS35. The crystal structure of the TBC1d5 GAP domain bound to VPS29 and complementary biochemical and cellular data show that a loop from TBC1d5 binds to a conserved hydrophobic pocket on VPS29 opposite the VPS29–VPS35 interface. Additional data suggest that a distinct loop of the GAP domain may contact VPS35. Loss of TBC1d5 causes defective retromer-dependent trafficking of receptors. Our findings illustrate how retromer recruits a GAP, which is likely to be involved in the timing of Rab7 inactivation leading to membrane uncoating, with important consequences for receptor trafficking. PMID:27827364

  17. Uranium(VI) coordination polymers with pyromellitate ligand: Unique 1D channel structures and diverse fluorescence

    SciTech Connect

    Zhang, Yingjie; Bhadbhade, Mohan; Karatchevtseva, Inna; Price, Jason R.; Liu, Hao; Zhang, Zhaoming; Kong, Linggen; Čejka, Jiří; Lu, Kim; Lumpkin, Gregory R.

    2015-03-15

    Three new coordination polymers of uranium(VI) with pyromellitic acid (H{sub 4}btca) have been synthesized and structurally characterized. (ED)[(UO{sub 2})(btca)]·(DMSO)·3H{sub 2}O (1) (ED=ethylenediammonium; DMSO=dimethylsulfoxide) has a lamellar structure with intercalation of ED and DMSO. (NH{sub 4}){sub 2}[(UO{sub 2}){sub 6}O{sub 2}(OH){sub 6}(btca)]·~6H{sub 2}O (2) has a 3D framework built from 7-fold coordinated uranyl trinuclear units and btca ligands with 1D diamond-shaped channels (~8.5 Å×~8.6 Å). [(UO{sub 2}){sub 2}(H{sub 2}O)(btca)]·4H{sub 2}O (3) has a 3D network constructed by two types of 7-fold coordinated uranium polyhedron. The unique μ{sub 5}-coordination mode of btca in 3 enables the formation of 1D olive-shaped large channels (~4.5 Å×~19 Å). Vibrational modes, thermal stabilities and fluorescence properties have been investigated. - Graphical abstract: Table of content: three new uranium(VI) coordination polymers with pyromellitic acid (H{sub 4}btca) have been synthesized via room temperature and hydrothermal synthesis methods, and structurally characterized. Two to three dimensional (3D) frameworks are revealed. All 3D frameworks have unique 1D large channels. Their vibrational modes, thermal stabilities and photoluminescence properties have been investigated. - Highlights: • Three new coordination polymers of U(VI) with pyromellitic acid (H{sub 4}btca). • Structures from a 2D layer to 3D frameworks with unique 1D channels. • Unusual µ{sub 5}-(η{sub 1}:η{sub 2}:η{sub 1}:η{sub 2:}η{sub 1}) coordination mode of btca ligand. • Vibrational modes, thermal stabilities and luminescent properties reported.

  18. Synthesis and characterization of a 1D chain-like Cu{sub 6} substituted sandwich-type phosphotungstate with pendant dinuclear Cu–azido complexes

    SciTech Connect

    Li, Yan-Ying; Zhao, Jun-Wei; Wei, Qi; Yang, Bai-Feng; Yang, Guo-Yu

    2014-02-15

    A novel Cu–azido complex modified hexa-Cu{sup II} substituted sandwich-type phosphotungstate [Cu(en){sub 2}]([Cu{sub 2}(en){sub 2}(μ-1,1-N{sub 3}){sub 2}(H{sub 2}O)]{sub 2}[Cu{sub 6}(en){sub 2}(H{sub 2}O){sub 2}(B-α-PW{sub 9}O{sub 34}){sub 2}])·6H{sub 2}O (1) (en=ethylene-diamine) has been prepared under hydrothermal conditions and structurally characterized by elemental analyses, IR spectra, powder X-ray diffraction (PXRD) and single-crystal X-ray diffraction. 1 displays a beautiful 1-D chain architecture constructed from sandwich-type [Cu{sub 2}(en){sub 2}(μ-1,1-N{sub 3}){sub 2}(H{sub 2}O)]{sub 2}[Cu{sub 6}(en){sub 2}(H{sub 2}O){sub 2}(B-α-PW{sub 9}O{sub 34}){sub 2}]{sup 2−} units and [Cu(en){sub 2}]{sup 2+} linkers. To our knowledge, 1 represents the first hexa-Cu{sup II} sandwiched phosphotungstate with supporting Cu–azido complexes. - Graphical abstract: The first hexa-Cu{sup II} sandwiched phosphotungstate with supporting Cu–azido complexes has been prepared and characterized. Display Omitted - Highlights: • Hexa-copper-substituted phosphotungstate. • Cu–azido complexes modified hexa-Cu{sup II} substituted sandwich-type polyoxometalate. • 1-D chain architecture built by hexa-copper-substituted polyoxotungstate units.

  19. Low band gap frequencies and multiplexing properties in 1D and 2D mass spring structures

    NASA Astrophysics Data System (ADS)

    Aly, Arafa H.; Mehaney, Ahmed

    2016-11-01

    This study reports on the propagation of elastic waves in 1D and 2D mass spring structures. An analytical and computation model is presented for the 1D and 2D mass spring systems with different examples. An enhancement in the band gap values was obtained by modeling the structures to obtain low frequency band gaps at small dimensions. Additionally, the evolution of the band gap as a function of mass value is discussed. Special attention is devoted to the local resonance property in frequency ranges within the gaps in the band structure for the corresponding infinite periodic lattice in the 1D and 2D mass spring system. A linear defect formed of a row of specific masses produces an elastic waveguide that transmits at the narrow pass band frequency. The frequency of the waveguides can be selected by adjusting the mass and stiffness coefficients of the materials constituting the waveguide. Moreover, we pay more attention to analyze the wave multiplexer and DE-multiplexer in the 2D mass spring system. We show that two of these tunable waveguides with alternating materials can be employed to filter and separate specific frequencies from a broad band input signal. The presented simulation data is validated through comparison with the published research, and can be extended in the development of resonators and MEMS verification.

  20. Quantum soliton in 1D Heisenberg spin chains with Dzyaloshinsky-Moriya and next-nearest-neighbor interactions

    NASA Astrophysics Data System (ADS)

    Djoufack, Z. I.; Tala-Tebue, E.; Nguenang, J. P.; Kenfack-Jiotsa, A.

    2016-10-01

    We report in this work, an analytical study of quantum soliton in 1D Heisenberg spin chains with Dzyaloshinsky-Moriya Interaction (DMI) and Next-Nearest-Neighbor Interactions (NNNI). By means of the time-dependent Hartree approximation and the semi-discrete multiple-scale method, the equation of motion for the single-boson wave function is reduced to the nonlinear Schrödinger equation. It comes from this present study that the spectrum of the frequencies increases, its periodicity changes, in the presence of NNNI. The antisymmetric feature of the DMI was probed from the dispersion curve while changing the sign of the parameter controlling it. Five regions were identified in the dispersion spectrum, when the NNNI are taken into account instead of three as in the opposite case. In each of these regions, the quantum model can exhibit quantum stationary localized and stable bright or dark soliton solutions. In each region, we could set up quantum localized n-boson Hartree states as well as the analytical expression of their energy level, respectively. The accuracy of the analytical studies is confirmed by the excellent agreement with the numerical calculations, and it certifies the stability of the stationary quantum localized solitons solutions exhibited in each region. In addition, we found that the intensity of the localization of quantum localized n-boson Hartree states increases when the NNNI are considered. We also realized that the intensity of Hartree n-boson states corresponding to quantum discrete soliton states depend on the wave vector.

  1. Quantum soliton in 1D Heisenberg spin chains with Dzyaloshinsky-Moriya and next-nearest-neighbor interactions.

    PubMed

    Djoufack, Z I; Tala-Tebue, E; Nguenang, J P; Kenfack-Jiotsa, A

    2016-10-01

    We report in this work, an analytical study of quantum soliton in 1D Heisenberg spin chains with Dzyaloshinsky-Moriya Interaction (DMI) and Next-Nearest-Neighbor Interactions (NNNI). By means of the time-dependent Hartree approximation and the semi-discrete multiple-scale method, the equation of motion for the single-boson wave function is reduced to the nonlinear Schrödinger equation. It comes from this present study that the spectrum of the frequencies increases, its periodicity changes, in the presence of NNNI. The antisymmetric feature of the DMI was probed from the dispersion curve while changing the sign of the parameter controlling it. Five regions were identified in the dispersion spectrum, when the NNNI are taken into account instead of three as in the opposite case. In each of these regions, the quantum model can exhibit quantum stationary localized and stable bright or dark soliton solutions. In each region, we could set up quantum localized n-boson Hartree states as well as the analytical expression of their energy level, respectively. The accuracy of the analytical studies is confirmed by the excellent agreement with the numerical calculations, and it certifies the stability of the stationary quantum localized solitons solutions exhibited in each region. In addition, we found that the intensity of the localization of quantum localized n-boson Hartree states increases when the NNNI are considered. We also realized that the intensity of Hartree n-boson states corresponding to quantum discrete soliton states depend on the wave vector.

  2. Supramolecular open-framework based on 1-D iron phosphate-diphosphate chains assembled through hydrogen bonding

    SciTech Connect

    Salvado, Miguel A.; Pertierra, Pilar; Trobajo, Camino; Garcia, Jose R.

    2008-05-15

    Fe(H{sub 2}PO{sub 4})(H{sub 2}P{sub 2}O{sub 7}).C{sub 5}H{sub 5}N, a new iron(III) phosphate with an open-framework has been synthesized hydrothermally using pyridine as organic template. The crystal structure was solved ab initio using conventional powder X-ray diffraction data. The unit cell is orthorhombic, a=9.5075(2), b=10.1079(1), c=13.3195(2) A, space group P2{sub 1}2{sub 1}2{sub 1}, Z=4. The structure consists of FeO{sub 6} octahedra joined by H{sub 2}PO{sub 4} and H{sub 2}P{sub 2}O{sub 7} groups forming linear chains interconnected by hydrogen bonding to give rise to a supramolecular framework enclosing tunnels in which the pyridine molecules reside. - Graphical abstract: The low temperature hydrothermal synthesis offers many possibilities in the preparation of new materials with mixed octahedral-tetrahedral open-frameworks. Fe(H{sub 2}PO{sub 4})(H{sub 2}P{sub 2}O{sub 7}).C{sub 5}H{sub 5}N is constituted by linear chains of FeO{sub 6} octahedra joined through of both dihydrogenphosphate and dihydrogendiphosphate bridges, interconnected by hydrogen bonds, originating channels where the pyridine molecules are located.

  3. 1d, 2d, and 3d periodic structures: Electromagnetic characterization, design, and measurement

    NASA Astrophysics Data System (ADS)

    Brockett, Timothy John

    Periodic structures have many useful applications in electromagnetics including phased arrays, frequency selective surfaces, and absorbing interfaces. Their unique properties can be used to provide increased performance in antenna gain, electromagnetic propagation, and electromagnetic absorption. In antenna arrays, repeating elements create a larger eective aperture, increasing the gain of the antenna and the ability to scan the direction of the main beam. Three-dimensional periodic structures, such as an array of shaped pillars such as columns, cones, or prisms have the potential of improving electromagnetic absorption, improving performance in applications such as solar cell eciency and absorbing interfaces. Furthermore, research into periodic structures is a continuing endeavor where novel approaches and analysis in appropriate applications can be sought. This dissertation will address the analysis, diagnostics, and enhancement of 1D, 2D, and 3D periodic structures for antenna array applications and solar cell technology. In particular, a unique approach to array design will be introduced to prevent the appearance of undesirable grating lobes in large antenna arrays that employ subarrays. This approach, named the distortion diagnostic procedure, can apply directly to 1D and 2D periodic structures in the form of planar antenna arrays. Interesting corollaries included here are developments in millimeter-wave antenna measurements including spiral planar scanning, phaseless measurements, and addressing antennas that feature an internal source. Finally, analysis and enhancement of 3D periodic structures in nanostructure photovoltaic arrays and absorbing interfaces will be examined for their behavior and basic operation in regards to improved absorption of electromagnetic waves.

  4. Thermodynamic nature of vitrification in a 1D model of a structural glass former

    SciTech Connect

    Semenov, A. N.

    2015-07-28

    We propose a new spin-glass model with no positional quenched disorder which is regarded as a coarse-grained model of a structural glass-former. The model is analyzed in the 1D case when the number N of states of a primary cell is large. For N → ∞, the model exhibits a sharp freezing transition of the thermodynamic origin. It is shown both analytically and numerically that the glass transition is accompanied by a significant growth of a static length scale ξ pointing to the structural (equilibrium) nature of dynamical slowdown effects in supercooled liquids.

  5. Thermodynamic nature of vitrification in a 1D model of a structural glass former

    NASA Astrophysics Data System (ADS)

    Semenov, A. N.

    2015-07-01

    We propose a new spin-glass model with no positional quenched disorder which is regarded as a coarse-grained model of a structural glass-former. The model is analyzed in the 1D case when the number N of states of a primary cell is large. For N → ∞, the model exhibits a sharp freezing transition of the thermodynamic origin. It is shown both analytically and numerically that the glass transition is accompanied by a significant growth of a static length scale ξ pointing to the structural (equilibrium) nature of dynamical slowdown effects in supercooled liquids.

  6. Thermodynamic nature of vitrification in a 1D model of a structural glass former.

    PubMed

    Semenov, A N

    2015-07-28

    We propose a new spin-glass model with no positional quenched disorder which is regarded as a coarse-grained model of a structural glass-former. The model is analyzed in the 1D case when the number N of states of a primary cell is large. For N → ∞, the model exhibits a sharp freezing transition of the thermodynamic origin. It is shown both analytically and numerically that the glass transition is accompanied by a significant growth of a static length scale ξ pointing to the structural (equilibrium) nature of dynamical slowdown effects in supercooled liquids.

  7. Controlled Self-Assembly of Cyclophane Amphiphiles: From 1D Nanofibers to Ultrathin 2D Topological Structures

    SciTech Connect

    Cai, Zhengxu; Li, Lianwei; Lo, Wai-Yip; Zhao, Donglin; Wu, Qinghe; Zhang, Na; Su, Yu-An; Chen, Wei; Yu, Luping

    2016-07-05

    A novel series of amphiphilic TC-PEG molecules were designed and synthesized based on the orthogonal cyclophane unit. These molecules were able to self-assemble from 1D nanofibers and nanobelts to 2D ultrathin nanosheets (3 nm thick) in a controlled way by tuning the length of PEG side chains. The special structure of the cyclophane moiety allowed control in construction of nanostructures through programmed noncovalent interactions (hydrophobic hydrophilic interaction and pi-pi interaction). The self-assembled nanostructures were characterized by combining real space imaging (TEM, SEM, and AFM) and reciprocal space scattering (GIWAXS) techniques. This unique supramolecular system may provide a new strategy for the design of materials with tunable nanomorphology and functionality.

  8. Study of phase transformation and crystal structure for 1D carbon-modified titania ribbons

    SciTech Connect

    Zhou, Lihui Zhang, Fang; Li, Jinxia

    2014-02-15

    One-dimensional hydrogen titanate ribbons were successfully prepared with hydrothermal reaction in a highly basic solution. A series of one-dimensional carbon-modified TiO{sub 2} ribbons were prepared via calcination of the mixture of hydrogen titanate ribbons and sucrose solution under N{sub 2} flow at different temperatures. The phase transformation process of hydrogen titanate ribbons was investigated by in-situ X-ray diffraction at various temperatures. Besides, one-dimensional carbon-modified TiO{sub 2} ribbons calcined at different temperatures were characterized by X-ray diffraction, scanning electron microscopy, transmission electron microscopy, nitrogen adsorption isotherms, diffuse reflectance ultraviolet–visible spectroscopy, and so on. Carbon-modified TiO{sub 2} ribbons showed one-dimensional ribbon crystal structure and various crystal phases of TiO{sub 2}. After being modified with carbon, a layer of uniform carbon film was coated on the surface of TiO{sub 2} ribbons, which improved their adsorption capacity for methyl orange as a model organic pollutant. One-dimensional carbon-modified TiO{sub 2} ribbons also exhibited enhanced visible-light absorbance with the increase of calcination temperatures. - Highlights: • The synthesis of 1D carbon-modified TiO{sub 2} ribbons. • The phase transformation of 1D carbon-modified TiO{sub 2} ribbons. • 1D carbon-modified TiO{sub 2} exhibites enhanced visible-light absorbance.

  9. Computational Study and Analysis of Structural Imperfections in 1D and 2D Photonic Crystals

    SciTech Connect

    Maskaly, Karlene Rosera

    2005-06-01

    increasing RMS roughness. Again, the homogenization approximation is able to predict these results. The problem of surface scratches on 1D photonic crystals is also addressed. Although the reflectivity decreases are lower in this study, up to a 15% change in reflectivity is observed in certain scratched photonic crystal structures. However, this reflectivity change can be significantly decreased by adding a low index protective coating to the surface of the photonic crystal. Again, application of homogenization theory to these structures confirms its predictive power for this type of imperfection as well. Additionally, the problem of a circular pores in 2D photonic crystals is investigated, showing that almost a 50% change in reflectivity can occur for some structures. Furthermore, this study reveals trends that are consistent with the 1D simulations: parameter changes that increase the absolute reflectivity of the photonic crystal will also increase its tolerance to structural imperfections. Finally, experimental reflectance spectra from roughened 1D photonic crystals are compared to the results predicted computationally in this thesis. Both the computed and experimental spectra correlate favorably, validating the findings presented herein.

  10. Tight-Binding Approximations in 1D and 2D Coupled-Cavity Photonic Crystal Structures

    NASA Astrophysics Data System (ADS)

    Day, Nicole C. L.

    Light confinement and controlling an optical field has numerous applications in the field of telecommunications for optical signals processing. When the wavelength of the electromagnetic field is on the order of the period of a photonic microstructure, the field undergoes reflection, refraction, and coherent scattering. This produces photonic bandgaps, forbidden frequency regions or spectral stop bands where light cannot exist. Dielectric perturbations that break the perfect periodicity of these structures produce what is analogous to an impurity state in the bandgap of a semiconductor. The defect modes that exist at discrete frequencies within the photonic bandgap are spatially localized about the cavity-defects in the photonic crystal. In this thesis the properties of two tight-binding approximations (TBAs) are investigated in one-dimensional and two-dimensional coupled-cavity photonic crystal structures. We require an efficient and simple approach that ensures the continuity of the electromagnetic field across dielectric interfaces in complex structures. In this thesis we develop E- and D-TBAs to calculate the modes in finite 1D and 2D two-defect coupled-cavity photonic crystal structures. In the E- and D-TBAs we expand the coupled-cavity [vector electron]-modes in terms of the individual [vector electron]- and [vector D meson]-modes, respectively. We investigate the dependence of the defect modes, their frequencies and quality factors on the relative placement of the defects in the photonic crystal structures. We then elucidate the differences between the two TBA formulations, and describe the conditions under which these formulations may be more robust when encountering a dielectric perturbation. Our 1D analysis showed that the 1D modes were sensitive to the structure geometry. The antisymmetric D mode amplitudes show that the D. TBA did not capture the correct (tangential [vector electron]-field) boundary conditions. However, the D-TBA did not yield

  11. Computation of 1-D shock structure using nonlinear coupled constitutive relations and generalized hydrodynamic equations

    NASA Astrophysics Data System (ADS)

    Zhao, Wenwen; Jiang, Zhongzheng; Chen, Weifang

    2016-11-01

    The moment methods in rarefied gas dynamics could be divided into generalized hydrodynamic equations (GHE) and extended hydrodynamic equations (EHE), e.g., Burnett equations, Grad equations and R-13 equations, theoretically. Eu firstly developed the GHE based on a non-equilibrium canonical distribution function and demonstrated the thermodynamically consistent of this model. Subsequently, nonlinear coupled constitutive relations (NCCR) was proposed by Myong by omitting the product of heat flux and velocity gradient in GHE to reduce the computational complexity. According to the successful application in 1-D shock wave structure and 2-D flat plate flow, the capability of NCCR has already been demonstrated successfully. The motivation of this study was to investigate the different behavior of NCCR and GHE for monatomic and diatomic gases in one-dimensional shock structure problems. Therefore, argon and nitrogen shock structure was calculated using both GHE and NCCR model up to Ma=50. The 3rd order MUSCL scheme for inviscid term and the 2nd order central difference scheme for viscid scheme were employed to carry out the computations. Finally, the present results including shock wave profile and its qualitative properties by NCCR and GHE are compared with that of DSMC and NS equations. The results showed that the GHE yield 1-D shock wave in much closer agreement with DSMC results than do the NCCR model without considering the computational complexity and efficiency in present cases.

  12. Self-assembly of silver(I) coordination polymers from aminopyrimidyl derivatives and malonate acid: From 1D chain to 2D layer

    NASA Astrophysics Data System (ADS)

    Sun, Di; Zhang, Na; Xu, Qin-Juan; Luo, Geng-Geng; Huang, Rong-Bin; Zheng, Lan-Sun

    2010-04-01

    Two new silver(I) coordination polymers (CPs) of the formula [Ag 2(dmapym) 4(mal)·H 2O] n ( 1) and [Ag 3(apym) 3(mal)NO 3] n ( 2) (dmapym = 2-amino-4,6-dimethylprimidine, apym = 2-aminopyrimidine, H 2mal = malonate) have been synthesized by reactions of AgNO 3 and 2-aminopyrimidyl ligands with malonate under the ammoniacal condition. Both complexes have been characterized by element analysis, IR and single-crystal X-ray diffraction. The monodentate dmapym and tridentate mal ligands link Ag(I) ions to give complex 1 a one-dimensional (1D) H-shaped chain structure. The complex 2 is a two-dimensional (2D) double sheet structure constructed by (4, 4) single sheet. Additionally, the hydrogen-bonding and C-H⋯π interactions also direct the self-assembly of supramolecular architectures. The photoluminescence properties of the 1 and 2 were investigated in the solid state at room temperature.

  13. Observation of ferromagnetic and antiferromagnetic coupling in 1-D and 2-D extended structures of copper(II) terephthalates

    SciTech Connect

    Deakin, L.; Arif, A.M.; Miller, J.S.

    1999-11-01

    The reaction between CuCl{sub 2}{center{underscore}dot}2H{sub 2}O and disodium terephthalate, Na{sub 2}tp, in aqueous solution simultaneously produces chain, bis(aqua)[{mu}-(terephthalato-{kappa}O:{kappa}O{prime})]copper(II), monohydrate, Cutp(OH{sub 2}){sub 2}{center{underscore}dot}H{sub 2}O (1), and layered, bis(aqua)[{mu}-(terephthalato-{kappa}O)]copper(II), Cutp(OH{sub 2}){sub 2} (2), structured materials. 1 (C{sub 8}H{sub 10}CuO{sub 7}) belongs to the orthorhombic P2{sub 1}2{sub 1}2 space group [a = 6.3015(4) {angstrom}, b = 6.8743(4) {angstrom}, c = 22.9972(14) {angstrom}, and Z = 4] and incorporates tp in a bridging bis-monodentate binding mode and Cu(II) in a tetragonally elongated octahedron. 2 (C{sub 8}H{sub 10}CuO{sub 6}) which belongs to the orthorhombic Pmc2{sub 1} space group [a = 10.7421(8) {angstrom}, b = 7.2339(10) {angstrom}, c = 5.7143(13) {angstrom}, and Z = 2] incorporates tp in a mono-bidentate binding mode and Cu(II) in a distorted square pyramid. 1 and 2 exhibit axial X-band powder EPR spectra with G{sub {perpendicular}} = 2.08, g{sub {parallel}} = 2.29 (1) and g{sub {perpendicular}} = 2.07, g{sub {parallel}} = 2.29 (2) at 300 K. 1 obeys the Curie-Weiss law at high temperatures ({theta} = {minus}7.2 K) and at low temperatures behaves as 1-D magnetic chains with an exchange-coupling constant of J/k{sub B} = {minus}9.15 K (H = {minus}2JS{sub 1}{center{underscore}dot}S{sub 2}). This material displays a spontaneous moment below 2 K under small applied magnetic fields, consistent with the presence of spin canting. 2 exhibits ferromagnetic interactions with {theta} = +0.8 K. Along the 1-D chain where coordinated water forms the bridge between metal centers, the coupling between Cu(II) is J/k{sub B} = +0.6 K. The fit of the magnetic susceptibility for 2 using a molecular field correction, which takes into consideration antiferromagnetic interactions between chains via the tp ligand, yields J{prime}/k{sub B} = {minus}0.13 K.

  14. Uranium(VI) coordination polymers with pyromellitate ligand: Unique 1D channel structures and diverse fluorescence

    NASA Astrophysics Data System (ADS)

    Zhang, Yingjie; Bhadbhade, Mohan; Karatchevtseva, Inna; Price, Jason R.; Liu, Hao; Zhang, Zhaoming; Kong, Linggen; Čejka, Jiří; Lu, Kim; Lumpkin, Gregory R.

    2015-03-01

    Three new coordination polymers of uranium(VI) with pyromellitic acid (H4btca) have been synthesized and structurally characterized. (ED)[(UO2)(btca)]·(DMSO)·3H2O (1) (ED=ethylenediammonium; DMSO=dimethylsulfoxide) has a lamellar structure with intercalation of ED and DMSO. (NH4)2[(UO2)6O2(OH)6(btca)]·~6H2O (2) has a 3D framework built from 7-fold coordinated uranyl trinuclear units and btca ligands with 1D diamond-shaped channels (~8.5 Å×~8.6 Å). [(UO2)2(H2O)(btca)]·4H2O (3) has a 3D network constructed by two types of 7-fold coordinated uranium polyhedron. The unique μ5-coordination mode of btca in 3 enables the formation of 1D olive-shaped large channels (~4.5 Å×~19 Å). Vibrational modes, thermal stabilities and fluorescence properties have been investigated.

  15. Crystal structure of TBC1D15 GTPase-activating protein (GAP) domain and its activity on Rab GTPases.

    PubMed

    Chen, Yan-Na; Gu, Xin; Zhou, X Edward; Wang, Weidong; Cheng, Dandan; Ge, Yinghua; Ye, Fei; Xu, H Eric; Lv, Zhengbing

    2017-04-01

    TBC1D15 belongs to the TBC (Tre-2/Bub2/Cdc16) domain family and functions as a GTPase-activating protein (GAP) for Rab GTPases. So far, the structure of TBC1D15 or the TBC1D15·Rab complex has not been determined, thus, its catalytic mechanism on Rab GTPases is still unclear. In this study, we solved the crystal structures of the Shark and Sus TBC1D15 GAP domains, to 2.8 Å and 2.5 Å resolution, respectively. Shark-TBC1D15 and Sus-TBC1D15 belong to the same subfamily of TBC domain-containing proteins, and their GAP-domain structures are highly similar. This demonstrates the evolutionary conservation of the TBC1D15 protein family. Meanwhile, the newly determined crystal structures display new variations compared to the structures of yeast Gyp1p Rab GAP domain and TBC1D1. GAP assays show that Shark and Sus GAPs both have higher catalytic activity on Rab11a·GTP than Rab7a·GTP, which differs from the previous study. We also demonstrated the importance of arginine and glutamine on the catalytic sites of Shark GAP and Sus GAP. When arginine and glutamine are changed to alanine or lysine, the activities of Shark GAP and Sus GAP are lost.

  16. Structural transformation in monolayer materials: a 2D to 1D transformation.

    PubMed

    Momeni, Kasra; Attariani, Hamed; LeSar, Richard A

    2016-07-20

    Reducing the dimensions of materials to atomic scales results in a large portion of atoms being at or near the surface, with lower bond order and thus higher energy. At such scales, reduction of the surface energy and surface stresses can be the driving force for the formation of new low-dimensional nanostructures, and may be exhibited through surface relaxation and/or surface reconstruction, which can be utilized for tailoring the properties and phase transformation of nanomaterials without applying any external load. Here we used atomistic simulations and revealed an intrinsic structural transformation in monolayer materials that lowers their dimension from 2D nanosheets to 1D nanostructures to reduce their surface and elastic energies. Experimental evidence of such transformation has also been revealed for one of the predicted nanostructures. Such transformation plays an important role in bi-/multi-layer 2D materials.

  17. Method of single expression: an exact solution for wavelength scale 1D photonic structure computer modeling

    NASA Astrophysics Data System (ADS)

    Baghdasaryan, Hovik V.; Knyazyan, Tamara M.

    2003-12-01

    The principles of the method of single expression (MSE) for boundary problems solution in classical electrodynamics are presented. In the MSE the solution of the Helmholtz's equation is presented in the special form of a single expression describing resultant amplitude and phase distributions in the medium. This form of solution presenation permits to pass over the restrictions of the superposition principle and to solve both linear and nonlinear problems with ths same ease. In the MSE the Helmholtz's equation is reformulated to the set of first order differential equations and the boundary problem is solved numerically. No approximations are implied either in Helmholtz's equation or in boundary conditions. Using the MSE steady-state boundary problems are modeled for wavelength scale multilayer and modulated 1D photonic structures including amplification and nonuniformity evoked by intense electromagnetic field.

  18. Four 1-D metal-organic polymers self-assembled from semi-flexible benzimidazole-based ligand: Syntheses, structures and fluorescent properties

    NASA Astrophysics Data System (ADS)

    Zhou, Chun-lin; Wang, Shi-min; Liu, Sai-nan; Yu, Tian-tian; Li, Rui-ying; Xu, Hong; Liu, Zhong-yi; Sun, Huan; Cheng, Jia-jia; Li, Jin-peng; Hou, Hong-wei; Chang, Jun-biao

    2016-08-01

    Four one-dimensional (1-D) metal-organic polymers based on methylene-bis(1,1‧-benzimidazole)(mbbz), namely, {[Hg(mbbz)(SCN)2]·1/3H2O}n (1), [Co(mbbz)(Cl)2]n (2), {[Co(mbbz)(SO4)]·CH3OH}n (3) and {[Zn(mbbz)(SO4)]·CH3OH}n (4) have been successfully synthesized and structurally characterized. Single-crystal X-ray diffraction reveals that polymers 1 and 2 exhibit interesting 1-D double helical chain structures, while polymers 3 and 4 are 1-D double chain structures due to the bridging effect of mbbz ligands and sulfate anions. These polymers containing the mbbz-based ligand have a high degree of dependence on the corresponding counter anions. Furthermore, the fluorescence properties of the four polymers were also investigated in the solid state, showing the fluorescence signal changes in comparing with that of free ligand mbbz.

  19. Synthesis, crystal structures, magnetic and luminescent properties of unique 1D p-ferrocenylbenzoate-bridged lanthanide complexes

    SciTech Connect

    Yan, P.F.; Zhang, F.M.; Li, G.M.; Zhang, J.W.; Sun, W.B.; Suda, M.; Einaga, Y.

    2009-07-15

    Treatments of p-ferrocenylbenzoate [p-NaOOCH{sub 4}C{sub 6}Fc, Fc=(eta{sup 5}-C{sub 5}H{sub 5})Fe(eta{sup 5}-C{sub 5}H{sub 4})] with Ln(NO{sub 3}){sub 3}.nH{sub 2}O afford seven p-ferrocenylbenzoate lanthanide complexes {l_brace}[Ln(OOCH{sub 4}C{sub 6}Fc){sub 2}(mu{sub 2}-OOCH{sub 4}C{sub 6}Fc){sub 2}(H{sub 2}O){sub 2}](H{sub 3}O){r_brace}{sub n} [Ln=Ce (1), Pr (2), Sm (3), Eu (4), Gd (5), Tb (6) and Dy (7)]. X-ray crystallographic analysis reveals that the isomorphous complexes {l_brace}[Ce(OOCH{sub 4}C{sub 6}Fc){sub 2}(mu{sub 2}-OOCH{sub 4}C{sub 6}Fc){sub 2}(H{sub 2}O){sub 2}](H{sub 3}O){r_brace}{sub n} (1) and {l_brace}[Pr(OOCH{sub 4}C{sub 6}Fc){sub 2}(mu{sub 2}-OOCH{sub 4}C{sub 6}Fc){sub 2}(H{sub 2}O){sub 2}](H{sub 3}O){r_brace}{sub n} (2) form a unique 1D double-bridged infinite chain structure bridged by mu{sub 2}-OOCH{sub 4}C{sub 6}Fc groups. Each Ln(III) ion adopts a dodecahedron coordination environment with eight coordinated oxygen atoms from two terminal monodentate coordinated FcC{sub 6}H{sub 4}COO{sup -} units, two terminal monodentate coordinated H{sub 2}O molecules and four mu{sub 2}-{sup -}OOCH{sub 4}C{sub 6}Fc units. The luminescent spectra reveal that only 4 and 6 exhibit characteristic emissions of lanthanide ions, Eu(III) and Tb(III) ions, respectively. The variable-temperature magnetic properties of 5 and 7 suggest that a ferromagnetic coupling between spin carriers may exist in 5. - Graphical abstract: Seven p-ferrocenylbenzoate lanthanide coordination polymers were synthesized. Given is the perspective view of a unique 1D double-bridged infinite chain structure of 1, excitation and emission spectra of 6 and plots of chi{sub m}T vs. T and chi{sub m}{sup -1} vs. T of 5.

  20. Structural repertoire of immunoglobulin λ light chains.

    PubMed

    Chailyan, Anna; Marcatili, Paolo; Cirillo, Davide; Tramontano, Anna

    2011-05-01

    The immunoglobulin λ isotype is present in nearly all vertebrates and plays an important role in the human immune system. Despite its importance, few systematic studies have been performed to analyze the structural conformation of its variable regions, contrary to what is the case for κ and heavy chains. We show here that an analysis of the structures of λ chains allows the definition of a discrete set of recurring conformations (canonical structures) of their hypervariable loops and, most importantly, the identification of sequence constraints that can be used to predict their structure. We also show that the structural repertoire of λ chains is different and more varied than that of the κ chains, consistently with the current view of the involvement of the two major light-chain families in complementary strategies of the immune system to ensure a fine tuning between diversity and stability in antigen recognition.

  1. Switching waves and dissipative structures in a chain of spasers

    SciTech Connect

    Andrianov, E S; Pukhov, A A; Dorofeenko, Aleksandr V; Vinogradov, Aleksei P; Lisyansky, Aleksandr A

    2012-09-30

    We have considered the physical mechanism of optical bistability in a spaser in the field of an external optical wave. We have studied the effect of this phenomenon on the dynamics of a 1D chain of coupled spasers. It is shown that such a chain demonstrates the behaviour typical of open nonlinear systems. In particular, for high Joule losses in a spaser, a nonlinear switching autowave propagates in the chain, thereby evolving the spasers' state from a low population inversion state into a high population inversion state or vice versa. The control parameter that determines the type of switching is the amplitude of the external optical wave. For low Joule losses there emerge quasi-periodic dissipative structures whose formation dynamics is of 'self-assembly' nature. (optical fibres, lasers and amplifiers. properties and applications)

  2. Syntheses, crystal structures and properties of two 1-D cadmium(II) coordination polymers based on 1,1'-(1,3-propanediyl)bis-1H-benzimidazole

    SciTech Connect

    Yang Huaixia; Meng Xiangru; Liu Yun; Hou Hongwei Fan Yaoting; Shen Xiaoqing

    2008-09-15

    The combination of framework-builders 1,1'-(1,3-propanediyl)bis-1H-benzimidazole (pbbm), Cd(II) ion and framework-regulator ClO{sub 4}{sup -} or SO{sub 4}{sup 2-} provides two new coordination polymers [Cd(pbbm){sub 2}(ClO{sub 4}){sub 2}]{sub n}(1) and {l_brace}[Cd(pbbm)SO{sub 4}(H{sub 2}O){sub 2}].CH{sub 3}OH{r_brace}{sub n}(2). Both of them display 1-D chain framework, but their detailed structures are clearly different from each other. 1 displays a 1-D ribbon of rings framework, 2 features an interesting infinite 1-D looped chain structure composed of two kinds of rings, the smaller 8-membered ring and the larger 20-membered ring. The antimicrobial activities of the two polymers were tested by the agar diffusion method and the results indicated that they exhibited antimicrobial activities against bacterial strands. The measurement of the non-isothermal kinetics of the thermal decomposition of 2 reveals that there are at least three steps that occur in its decomposition process. - Graphical abstract: Two new Cd(II)-containing complexes have been synthesized and characterized by single-crystal X-ray diffraction. The antimicrobial activity and the non-isothermal kinetics of the thermal decomposition of the polymers were also investigated. Display Omitted.

  3. The Role of the Impedivity in the Magnetotelluric Response of 1D and 2D Structures

    NASA Astrophysics Data System (ADS)

    Esposito, Roberta; Giulia Di Giuseppe, Maria; Troiano, Antonio; Patella, Domenico; Mariano Castelo Branco, Raimundo

    2014-05-01

    The influence of the resistivity dispersion on the magnetotelluric (MT) response is analyzed. MT uses the natural electromagnetic (EM) field to determine the electrical resistivity of the subsoil and retrieve the geometry of lithospheric structures, revealing the presence of bodies as metallic deposits, hydrocarbons reservoirs, geothermal fluids. The frequency range of the EM field used varies from 10-4 to 104 Hz. If the soil is polarizable, the dispersion of the resistivity, whose characteristic frequency interval is between 10-2 and 102 Hz, may affect MT responses. Resistivity dispersion is a known phenomenology, which constitutes the basis of the Induced Polarization (IP) prospecting method. In the frequency domain (FD), the dispersion consists in a variation of the resistivity parameter as the frequency of the exciting current is changed. The dispersive resistivity, called impedivity, is a complex function of the frequency. At vanishing frequency, however, the impedivity is real and coincides with the classical resistivity parameter used in DC geoelectrical methods. A real asymptote is also approached as the frequency tends to infinity. The complex physical and chemical fluid-metal-rock interactions may produce induced polarization effects, which are related to the dispersion in rocks. This is manifested on the MT response, creating a distortion on the experimental curves. Disregarding the distortion effect may lead to misleading interpretation of the surveyed structures. We show the results from simulation of the MT responses, when dispersion is assumed to characterize the electrical properties of a region of the explored half-space. Initially, a 1D-layered earth is considered, with intermediate layer assumed to be dispersive. The influence of the dispersion amplitude on the shape of the MT responses is evaluated. The dispersion alters the shape of the curves in a way that, without any external constraints, may make the interpretation of the curves quite

  4. Structure of Human Ferritin L Chain

    SciTech Connect

    Wang,Z.; Li, C.; Ellenburg, M.; Soistman, E.; Ruble, J.; Wright, B.; Ho, J.; Carter, D.

    2006-01-01

    Ferritin is the major iron-storage protein present in all cells. It generally contains 24 subunits, with different ratios of heavy chain (H) to light chain (L), in the shape of a hollow sphere hosting up to 4500 ferric Fe atoms inside. H-rich ferritins catalyze the oxidation of iron(II), while L-rich ferritins promote the nucleation and storage of iron(III). Several X-ray structures have been determined, including those of L-chain ferritins from horse spleen (HoSF), recombinant L-chain ferritins from horse (HoLF), mouse (MoLF) and bullfrog (BfLF) as well as recombinant human H-chain ferritin (HuHF). Here, structures have been determined of two crystal forms of recombinant human L-chain ferritin (HuLF) obtained from native and perdeuterated proteins. The structures show a cluster of acidic residues at the ferrihydrite nucleation site and at the iron channel along the threefold axis. An ordered Cd{sup 2+} structure is observed within the iron channel, offering further insight into the route and mechanism of iron transport into the capsid. The loop between helices D and E, which is disordered in many other L-chain structures, is clearly visible in these two structures. The crystals generated from perdeuterated HuLF will be used for neutron diffraction studies.

  5. Electronic and structural properties of 3D, 2D and 1D materials

    NASA Astrophysics Data System (ADS)

    Ribeiro, Filipe Joao

    In this work several applications of the ab initio pseudopotential density functional theory method are presented. With this method it is possible to calculate the electronic ground state properties of many systems like bulk solids, surfaces, nanotubes, and nanowires, and draw conclusions about the systems structural and electronic properties. With modifications of this approach excited states can also be treated. The first chapter of this thesis gives a brief description of the computational techniques employed. The second chapter describes results of calculations on the structural and electronic properties of carbon and germanium. We try to shed some light on a still poorly understood structural phase transition of graphite under pressure at low temperatures, which is different from the high temperature regime. Next, we study the phase transition path of germanium under pressure and predict the existence of a new phase. The following chapter explores the possibility of superconductivity in the graphite-like compound BC3 since there are many similarities between the electronic structure of this material and the 39 K superconductor MgB2. Subsequently, results of calculations on the adsorption of indium atoms on carbon nanotubes and graphite-like surfaces are presented. These studies explain some very interesting experimental results of In migration on nanotubes in an electrical potential. In the following chapters the electronic properties of very thin metallic MoSe nanowires are studied, and the different regimes of stability of metallic monatomic chains of Au, Al, Ag, Pd, Rh, and Ru are investigated and compared. Chapter 7 addresses the possible polymerization of C60 molecules inside carbon and boron nitride nanotubes. Finally, the propagation of a light signal in a medium with gains and losses is investigated, and the possibility of a discontinuity in the index of refraction is discussed.

  6. Entangling strings of neutral atoms in 1D atomic pipeline structures.

    PubMed

    Dorner, U; Fedichev, P; Jaksch, D; Lewenstein, M; Zoller, P

    2003-08-15

    We study a string of neutral atoms with nearest neighbor interaction in a 1D beam splitter configuration, where the longitudinal motion is controlled by a moving optical lattice potential. The dynamics of the atoms crossing the beam splitter maps to a 1D spin model with controllable time dependent parameters, which allows the creation of maximally entangled states of atoms by crossing a quantum phase transition. Furthermore, we show that this system realizes protected quantum memory, and we discuss the implementation of one- and two-qubit gates in this setup.

  7. Synthesis, structure and magnetic properties of 5-(4-Sulfophenylazo) salicylate-bridged 1D coordination polymers containing linear trinuclear metal clusters

    NASA Astrophysics Data System (ADS)

    Liu, Hong; Song, Li-jun; Ju, Zhan-feng; Li, Wei; Zhang, Jie

    2008-03-01

    Three new trinuclear metal complexes with an azobenzene-containing ligand [M 3(Sasa) 2(Py) 2(H 2O) 8] (Na 2HSasa = 5-(4-Sulfophenylazo) salicylic acid disodium salt; Py = pyridine; M = Cu, Co, Zn), are synthesized through the interface diffusion and structurally characterized by single crystal X-ray diffraction, XRPD analysis and spectral methods. The metal ions in distorted octahedral coordination environments are connected by Sasa ligands to form 1D coordination polymer chain containing the linear trinuclear units with single syn-anti carboxylate bridges. The extensive hydrogen bonding interactions hold these chains together into 3D supramolecular network. Weak antiferromagnetic interactions between adjacent metal ions with J = -1.85 cm -1 and J = -2.81 cm -1 dominate the magnetic properties of Cu(II) and Co(II) complexes, separately.

  8. Synthesis, crystal structures, magnetic and luminescent properties of unique 1D p-ferrocenylbenzoate-bridged lanthanide complexes

    NASA Astrophysics Data System (ADS)

    Yan, P. F.; Zhang, F. M.; Li, G. M.; Zhang, J. W.; Sun, W. B.; Suda, M.; Einaga, Y.

    2009-07-01

    Treatments of p-ferrocenylbenzoate [ p-NaOOCH 4C 6Fc, Fc=( η5-C 5H 5)Fe( η5-C 5H 4)] with Ln(NO 3) 3· nH 2O afford seven p-ferrocenylbenzoate lanthanide complexes {[ Ln(OOCH 4C 6Fc) 2( μ2-OOCH 4C 6Fc) 2(H 2O) 2](H 3O)} n [ Ln=Ce ( 1), Pr ( 2), Sm ( 3), Eu ( 4), Gd ( 5), Tb ( 6) and Dy ( 7)]. X-ray crystallographic analysis reveals that the isomorphous complexes {[Ce(OOCH 4C 6Fc) 2( μ2-OOCH 4C 6Fc) 2(H 2O) 2](H 3O)} n ( 1) and {[Pr(OOCH 4C 6Fc) 2( μ2-OOCH 4C 6Fc) 2(H 2O) 2](H 3O)} n ( 2) form a unique 1D double-bridged infinite chain structure bridged by μ2-OOCH 4C 6Fc groups. Each Ln(III) ion adopts a dodecahedron coordination environment with eight coordinated oxygen atoms from two terminal monodentate coordinated FcC 6H 4COO - units, two terminal monodentate coordinated H 2O molecules and four μ2- -OOCH 4C 6Fc units. The luminescent spectra reveal that only 4 and 6 exhibit characteristic emissions of lanthanide ions, Eu(III) and Tb(III) ions, respectively. The variable-temperature magnetic properties of 5 and 7 suggest that a ferromagnetic coupling between spin carriers may exist in 5.

  9. Structural Origins of Martian Pit Chains

    NASA Astrophysics Data System (ADS)

    Wyrick, D.; Ferrill, D. A.; Morris, A. P.; Colton, S. L.; Sims, D. W.

    2003-12-01

    Pit craters are circular to elliptical depressions found in alignments (chains), which in many cases coalesce into linear troughs, and are common on the surface of Mars. Pit craters lack an elevated rim, ejecta deposits, or lava flows that are associated with impact craters or calderas. It is generally agreed that these features are formed by collapse into a subsurface cavity. Hypotheses regarding the formation of pit crater chains require development of a substantial subsurface void to accommodate collapse of the overlying sediments. Suggested mechanisms of formation include: collapsed lava tubes, dike swarms, collapsed magma chamber, karst dissolution, fissuring beneath loose material, and dilational faulting. The research described here is intended to constrain current interpretations of pit crater chain formation by analyzing their distribution and morphology. The western hemisphere of Mars was systematically mapped using Mars Orbiter Camera (MOC) images to generate ArcView Geographic Information System (GIS) coverages. All visible pit crater chains were mapped, including their orientations and associations with other structures. We found that pit chains commonly occur in areas that show regional extension or local fissuring. There is a strong correlation between pit chains and fault-bounded grabens. Frequently, there are transitions along strike from (i) visible faulting to (ii) faults and pits to (iii) pits alone. We performed a detailed quantitative analysis of pit crater morphology using MOC narrow angle images, Thermal Emission Imaging System (THEMIS) visual images and Mars Orbiter Laser Altimeter (MOLA) data. This allowed us to interpret a pattern of pit chain evolution and calculate pit depth, slope, and volume. The information collected in the study was then compared with non-Martian examples of pit chains and physical analog models. We evaluated the various mechanisms for pit chain development based on the data collected and conclude that dilational

  10. Structure of confined films of chain alcohols

    SciTech Connect

    Mugele, Friedrich; Baldelli, Steven; Somorjai, Gabor A.; Salmeron, Miquel

    1999-09-30

    The structure of thin films of simple chain alcohols (1-octanol and 1-undecanol) confined between two atomically smooth mica surfaces has been investigated using a surface forces apparatus (SFA). In both systems, the substrate-molecule interaction leads to a strongly bound first layer on each surface. Additional liquid organizes into highly compressible bilayers, which could be expelled by applying sufficiently high pressure.

  11. Detonation Structure Under Chain Branching Kinetics

    NASA Astrophysics Data System (ADS)

    Liang, Z.; Bauwens, L.

    2006-07-01

    Hydrogen-oxygen chemistry is characterized by a chain branching mechanism that yields three explosion limits. While a detailed kinetic scheme appropriate for hydrogen-oxygen should produce correct results, in many circumstances, a simpler yet reasonably realistic model will be warranted. In particular, it is easier to develop a clear understanding of the reaction zone structure using a simpler model, that includes only the key mechanisms. To that effect, we consider a four-step chain branching scheme that exhibits an explosion behavior with three limits, which behaves at least qualitatively like hydrogen chemistry. We focus in particular on the structure of the initiation and chain branching zones, using a combination between numerical simulation and analysis. Numerical simulations using this chemical model show distinctive keystone figures in the flow field, close to observations in hydrogen-oxygen detonation experiments. The structure of the chain branching zone is resolved using a perturbation analysis, which clarifies the differences between explosion and no-explosion regions and allows for an evaluation of the induction length in the steady wave. The analysis assumes both high activation energy and a slow initiation. Three cases are identified, respectively, with pressure and temperature located within the explosion region, close to the explosion limit and within the no-explosion region. The induction length is shorter and the reaction rate is faster by several orders of magnitude in the explosion region.

  12. Magnetic structure and exchange interactions in quasi-1D MnCl2(urea)2

    PubMed Central

    Manson, Jamie L.; Huang, Qing-zhen; Brown, Craig M.; Lynn, Jeffrey W.; Stone, Matthew B.; Singleton, John; Xiao, Fan

    2016-01-01

    MnCl2(urea)2 is a new linear chain coordination polymer that exhibits slightly counter-rotated MnCl4 rhomboids along the chain-axis. The material crystallizes in the non-centrosymmetric orthorhombic space group Iba2, with each Mn(II) ion equatorially surrounded by four Cl− that lead to bi-bridged ribbons. Urea ligands coordinate via O-atoms in the axial positions. Hydrogen bonds of the Cl⋯H-N and O⋯H-N type link the chains into a quasi-3D network. Magnetic susceptibility data reveal a broad maximum at 9 K that is consistent with short-range magnetic order. Pulsed-field magnetization measurements conducted at 0.6 K show that a fully polarized magnetic state is achieved at Bsat = 19.6 T with a field-induced phase transition occurring at 2.8 T. Neutron diffraction studies made on a powdered sample of MnCl2(urea)2 reveal that long-range magnetic order occurs below TN = 3.2(1) K. Additional Bragg peaks due to antiferromagnetic (AFM) ordering can be indexed according to the Ib’a2’ magnetic space group and propagation vector τ = [0, 0, 0]. Rietveld profile analysis of these data reveal a Néel-type collinear ordering of Mn(II) ions with an ordered magnetic moment of 4.06(6) μB (5 μB is expected for isotropic S = 5/2) oriented along the b-axis, i.e., perpendicular to the chain-axis that runs along the c-direction. Owing to potential for spatial exchange anisotropy and the pitfalls in modeling bulk magnetic data, we analyzed inelastic neutron scattering data to retrieve the exchange constants; Jc = 2.22 K (intrachain), Ja = −0.10 K (interchain) and D = −0.14 K with J > 0 assigned to AFM coupling. This J configuration is most unusual and contrasts the more commonly observed case of AFM-coupled FM-chains. PMID:26645988

  13. 3D and 2D structural characterization of 1D Al/Al2 O3 biphasic nanostructures.

    PubMed

    Miró, M Martinez; Veith, M; Lee, J; Soldera, F; Mücklich, F; Bennewitz, R; Aktas, C

    2015-05-01

    1D Al/Al2 O3 nanostructures have been synthesized by chemical vapour deposition (CVD) of the molecular precursor [(t) BuOAlH2 ]2 . The deposited nanostructures grow chaotically on the substrate forming a layer with a high porosity (80%). Depending on the deposition time, diverse nanostructured surfaces with different distribution densities were achieved. A three-dimensional (3D) reconstruction has been evaluated for every nanostructure density using the Focus Ion Beam (FIB) tomography technique and reconstruction software tools. Several structural parameters such as porosity, Euler number, geometrical tortuosity and aspect ratio have been quantified through the analysis with specified software of the reconstructions. Additionally roughness of the prepared surfaces has been characterized at micro- and nanoscale using profilometry and AFM techniques, respectively. While high aspects ratio around 20-30 indicates a strong anisotropy in the structure, high porosity values (around 80%) is observed as a consequence of highly tangled geometry of such 1D nanostructures.

  14. Assembling carbon fiber–graphene–carbon fiber hetero-structures into 1D–2D–1D junction fillers and patterned structures for improved microwave absorption

    NASA Astrophysics Data System (ADS)

    Li, Huimin; Liu, Lin; Li, Hai-Bing; Song, Wei-Li; Bian, Xing-Ming; Zhao, Quan-Liang; Chen, Mingji; Yuan, Xujin; Chen, Haosen; Fang, Daining

    2017-04-01

    Since carbon-based structures of various dimensions, including one-dimensional (1D) carbon nanotubes, two-dimensional (2D) graphene and three-dimensional (3D) carbon foams, have attracted significant attention as microwave absorption fillers, we present an exceptional hetero-junction filler with a 1D–2D–1D feature, achieved by manipulating 2D graphene into 1D carbon fibers in the fiber-extruding process under the electric field. The as-fabricated 1D–2D–1D structural fillers exhibited much-improved dielectric properties and promoted microwave absorption performance in their composites, which is linked to the establishment of enhanced polarization capability, the generation of increased electric loss pathway and the creation of more favorable electromagnetic energy consumption conditions. The results suggest that employing 2D graphene in the 1D–2D–1D nanostructures played the critical role in tuning the electromagnetic response ability, because of its intrinsic electric advantages and dimensional features. To broaden the effective absorption bandwidth, periodic pattern-absorbing structures were designed, which showed combined absorption advantages for various thicknesses. Our strategy for fabricating 1D–2D–1D structural fillers illuminates a universal approach for manipulating dimensions and structures in the nanotechnology.

  15. Syntheses, crystal structures, and characterization of three 1D, 2D and 3D complexes based on mixed multidentate N- and O-donor ligands

    SciTech Connect

    Yang, Huai-Xia; Liang, Zhen; Hao, Bao-Lian; Meng, Xiang-Ru

    2014-10-15

    Three new 1D to 3D complexes, namely, ([Ni(btec)(Himb){sub 2}(H{sub 2}O){sub 2}]·6H{sub 2}O){sub n} (1), ([Cd(btec){sub 0.5}(imb)(H{sub 2}O)]·1.5H{sub 2}O){sub n} (2), and ([Zn(btec){sub 0.5}(imb)]·H{sub 2}O){sub n} (3) (H{sub 4}btec=1,2,4,5-benzenetetracarboxylic acid, imb=2-(1H-imidazol-1-methyl)-1H-benzimidazole) have been synthesized by adjusting the central metal ions. Single-crystal X-ray diffraction analyses reveal that complex 1 possesses a 1D chain structure which is further extended into the 3D supramolecular architecture via hydrogen bonds. Complex 2 features a 2D network with Schla¨fli symbol (5{sup 3}·6{sup 2}·7)(5{sup 2}·6{sup 4}). Complex 3 presents a 3D framework with a point symbol of (4·6{sup 4}·8)(4{sup 2}·6{sup 2}·8{sup 2}). Moreover, their IR spectra, PXRD patterns, thermogravimetric curves, and luminescent emissions were studied at room temperature. - Graphical abstract: Three new 1D to 3D complexes with different structural and topological motifs have been obtained by modifying the central metal ions. Additionally, their IR, TG analyses and fluorescent properties are also investigated. - Highlights: • Three complexes based on mixed multidentate N- and O-donor ligands. • The complexes are characterized by IR, luminescence and TGA techniques. • Benzenetetracarboxylates display different coordination modes in complexes 1–3. • Changing the metal ions can result in complexes with completely different structures.

  16. New coordination polymers from 1D chain, 2D layer to 3D framework constructed from 1,2-phenylenediacetic acid and 1,3-bis(4-pyridyl)propane flexible ligands

    SciTech Connect

    Xin Lingyun; Liu Guangzhen; Wang Liya

    2011-06-15

    The hydrothermal reactions of Cd, Zn, or Cu(II) acetate salts with H{sub 2}PHDA and BPP flexible ligands afford three new coordination polymers, including [Cd(PHDA)(BPP)(H{sub 2}O)]{sub n}(1), [Zn(PHDA)(BPP)]{sub n}(2), and [Cu{sub 2}(PHDA){sub 2}(BPP)]{sub n}(3) (H{sub 2}PHDA=1,2-phenylenediacetic acid, BPP=1,3-bis(4-pyridyl)propane). The single-crystal X-ray diffractions reveal that all three complexes feature various metal carboxylate subunits extended further by the BPP ligands to form a diverse range of structures, displaying a remarked structural sensitivity to metal(II) cation. Complex 1 containing PHDA-bridged binuclear cadmium generates 1D double-stranded chain, complex 2 results in 2D{yields}2D interpenetrated (4,4) grids, and complex 3 displays a 3D self-penetrated framework with 4{sup 8}6{sup 6}8 rob topology. In addition, fluorescent analyses show that both 1 and 2 exhibit intense blue-violet photoluminescence in the solid state. - Graphical Abstract: We show diverse supramolecular frameworks based on the same ligands (PHDA and BPP) and different metal acetate salts including 1D double-stranded chain, 2D {yields} 2D twofold interpenetrated layer, and 3D self-penetration networks. Highlights: > Three metal(II = 2 /* ROMAN ) coordination polymers were synthesized using H{sub 2}PHDA and BPP. > The diversity of structures show a remarked sensitivity to metal(II) center. > Complexes show the enhancement of fluorescence compared to that of free ligand.

  17. Temperature tuning of band-structure of 1D periodic elastic composites

    NASA Astrophysics Data System (ADS)

    Sadeghi, H.; Srivastava, A.; Griswold, R.; Nemat-Nasser, S.

    2012-04-01

    In this paper we show that the bandstructure of a periodic elastic composite, in addition to being dependent upon the micro-constituents and their microarchitecture, may also be controlled by changing the temperature. The essential idea is to fabricate a periodic composite with constituent materials which have temperature dependent elastic properties. As temperature is changed, such a composite is expected to exhibit a bandstructure which changes with the temperature dependent properties of its micro-constituents. For our purpose, we use polyurea and steel to make a 1-D periodic composite. Ultrasonic measurements are done on the sample from 0.5 kHz to 1.5 MHz under changing temperature and the change in the second passband is studied. It is observed that the change in the bandstructure is significant when the temperature is changed from -50°C to 50°C. Experimental results are compared with the theoretical calculations and it is shown that good agreement exists for the observed bandstructure.

  18. Transmission properties analysis of 1D PT-symmetric photonic structures

    NASA Astrophysics Data System (ADS)

    Mossakowska-Wyszyńska, Agnieszka; Witoński, Piotr; Szczepański, Paweł

    2016-12-01

    The transmission properties of one dimensional PT-symmetric photonic crystal (PC) structure with gain and loss regions are presented. Obtained characteristics illustrate the influence of the structures parameters such as the ratio of the PC period to the operating wavelength, the number of the primitive cells creating PC, the loss and gain level (imaginary part of the refractive indices) on reflection and transmission coefficients. It demonstrates strong nonreciprocal response of the structure.

  19. Structure of confined films of chain alcohols

    SciTech Connect

    Mugele, F.; Baldelli, S.; Somorjai, G.A.; Salmeron, M.

    2000-04-13

    The structure of thin films of simple chain alcohols (1-octanol and 1-undecanol) confined between two atomically smooth mica surfaces has been investigated using a surface forces apparatus. Contact angle measurements and optical sum frequency generation were used for additional characterization. In both systems, the substrate-molecule interaction leads to a strongly bound first layer on each surface. Additional liquid organizes into highly compressible bilayers, which could be expelled by applying sufficiently high pressure.

  20. Modeling structures of 1D PhC for telecommunication applications

    NASA Astrophysics Data System (ADS)

    Zawistowski, Zygmunt J.; Jaskorzyńska, BoŻena

    2016-09-01

    Effective method of modeling 1-dimensional photonic crystals structures is presented. As an illustration of the method a concept of widely tunable narrow band drop filter is described. As an active electro-optic material a liquid crystal is used. Very good parameters are obtained so the presented structure is suitable for fast packet switched wavelength division multiplexing networks (WDM).

  1. Exploring group 14 structures: 1D to 2D to 3D.

    PubMed

    Wen, Xiao-Dong; Cahill, Thomas J; Hoffmann, Roald

    2010-06-11

    Various one-, two- and three-dimensional Group 14 (C, Si, Ge, Sn, and Pb) element structures at P = 1 atm are studied in this work. As expected, coordination number (CN)--not an unambiguous concept for extended structures--plays an important part in the stability of structures. Carbon not only favors four-coordination, but also is quite happy with pi-bonding, allowing three- and even two-coordination to compete. Highly coordinated (CN > 4) discrete carbon molecules are rare; that "saturation of valence" is reflected in the instability of C extended structures with CN > 4. Si and Ge are quite similar to each other in their preferences. They are less biased in their coordination than C, allowing (as their molecular structures do) CN = 5 and 6, but tending towards four-coordination. Sn and Pb 3D structures are very flexible in their bonding, so that in these elements four- to twelve-coordinate structures are close in energy. This lack of discrimination among ordered structures also points to an approach to the liquid state, consistent with the low melting point of Sn and Pb. The Group 14 liquid structures we simulate in molecular dynamics calculations show the expected, effective, first coordination number increase from 5.1 for Si to 10.4 for Pb. A special point of interest emerging from our study is the instability of potential multilayer graphene structures down Group 14. Only for C will these be stable; for all the other Group 14 elements pristine, unprotected, bi- and multilayer graphenes should collapse, forming "vertical" bonds as short as the in-plane ones.

  2. o-, m-, and p-Pyridyl isomer effects on construction of 1D loop-and-chains: Silver(I) coordination polymers with Y-type tridentate ligands

    NASA Astrophysics Data System (ADS)

    Kim, Jeong Gyun; Cho, Yoonjung; Lee, Haeri; Lee, Young-A.; Jung, Ok-Sang

    2016-10-01

    Self-assembly of silver(I) hexafluorophosphate with unique Y-type tridentate ligands (2,6-bis[(2-picolinoyloxy-5-methylphenyl)methyl]-p-tolylpicolinate (o-L), 2-nicotinoyloxy- (m-L), and 2-isonicotinoyloxy- (p-L)) produces single crystals consisting of 1D loop-and-chain coordination polymers of [Ag(o-L)](PF6)·Me2CO·CHCl3, [Ag(m-L)](PF6)·Me2CO, and [Ag3(p-L)2](PF6)3·2H2O·2C2H5OH·4CH2Cl2 with quite different trigonal prismatic, trigonal, and linear silver(I) coordination geometry, respectively. Coordinating ability of the three ligands for AgPF6 is in the order of p-L > o-L > m-L. The solvate molecules of [Ag(o-L)](PF6)·Me2CO·CHCl3 can be removed, and be replaced reversibly in the order of acetone ≫ chloroform ≈ dichloromethane ≫ benzene, without destruction of its skeleton.

  3. Optical reflectance and omnidirectional bandgaps in Fibonacci quasicrystals type 1-D multilayer structures containing exponentially graded material

    NASA Astrophysics Data System (ADS)

    Singh, Bipin K.; Thapa, Khem B.; Pandey, Praveen C.

    2013-06-01

    A theoretical study of optical reflectance and reflection bands of 1-D photonic quasi-crystals (Fibonacci type arrangement) composed of exponentially graded material is presented. The proposed structures consist of two different layers, one of them is of constant refractive index (L) and the other one is of exponentially graded refractive index (S) dielectric materials. Four different generations (2nd, 3rd, 4th and 5th) of the Fibonacci sequence for 10 periods in one dimension (1-D) are considered and compared in view of their optical reflectance and bandgaps for both TE and TM polarisations. Also, we proposed some heterostructures made by the combination of different Fibonacci generations and their periods to obtain suitable omnidirectional reflection band. We used the transfer matrix method (TMM) to obtain the reflectance, bandgaps and omnidirectional reflectional bandgaps (ODR) of such structures in near infrared spectrum (800-2200 nm) at different angles of incidence. We show that ODR exists in these types of structures. The number of ODRs and total bandgap depend on the Fibonacci generations. Extraordinary ODR bandgaps are obtained in the case of heterostructures formed by the combination of different generations of the Fibonacci sequence. The ODR for these structures is similar to the ODR of photonic crystals containing left-handed materials. This work would be useful to study the Fibonacci type photonic crystals having graded index materials and also it will open new window to design several photonic crystal devices like sensors, reflectors, etc. in the infrared region.

  4. Electrophysiological and Structural Remodeling in Heart Failure Modulate Arrhythmogenesis. 1D Simulation Study

    PubMed Central

    Gomez, Juan F.; Cardona, Karen; Romero, Lucia; Ferrero, Jose M.; Trenor, Beatriz

    2014-01-01

    Background Heart failure is a final common pathway or descriptor for various cardiac pathologies. It is associated with sudden cardiac death, which is frequently caused by ventricular arrhythmias. Electrophysiological remodeling, intercellular uncoupling, fibrosis and autonomic imbalance have been identified as major arrhythmogenic factors in heart failure etiology and progression. Objective In this study we investigate in silico the role of electrophysiological and structural heart failure remodeling on the modulation of key elements of the arrhythmogenic substrate, i.e., electrophysiological gradients and abnormal impulse propagation. Methods Two different mathematical models of the human ventricular action potential were used to formulate models of the failing ventricular myocyte. This provided the basis for simulations of the electrical activity within a transmural ventricular strand. Our main goal was to elucidate the roles of electrophysiological and structural remodeling in setting the stage for malignant life-threatening arrhythmias. Results Simulation results illustrate how the presence of M cells and heterogeneous electrophysiological remodeling in the human failing ventricle modulate the dispersion of action potential duration and repolarization time. Specifically, selective heterogeneous remodeling of expression levels for the Na+/Ca2+ exchanger and SERCA pump decrease these heterogeneities. In contrast, fibroblast proliferation and cellular uncoupling both strongly increase repolarization heterogeneities. Conduction velocity and the safety factor for conduction are also reduced by the progressive structural remodeling during heart failure. Conclusion An extensive literature now establishes that in human ventricle, as heart failure progresses, gradients for repolarization are changed significantly by protein specific electrophysiological remodeling (either homogeneous or heterogeneous). Our simulations illustrate and provide new insights into this

  5. Local duality in spin structure functions g1(p) and g1(d)

    SciTech Connect

    Yelena Prok

    2006-02-01

    Inclusive double spin asymmetries obtained by scattering polarized electrons off polarized protons and deuterons have been analyzed to address the issue of quark hadron duality in the polarized spin structure functions gp 1 and gd 1. A polarized electron beam, solid polarized NH3 and ND3 targets and the CEBAF Large Acceptance Spectrometer (CLAS) in Hall B were used to collect the data. The resulting gp 1 and gd 1 were averaged over the nucleon resonance energy region (M

  6. Effects of magnetic site disorder of the 1-D Ising spin chain compounds Ca3(Co,Mn)2O6 with dilute doping

    NASA Astrophysics Data System (ADS)

    Casas, Brian; Lampen, Paula; Phan, Manh-Huong; Srikanth, Hariharan; Kovak, Jozef; Skorvanek, Ivan

    2015-03-01

    The spin chain compound Ca3Co2O6 has been extensively studied due to a number of unusual properties originating from geometrically frustrated Ising-like spin chains arranged in a triangular lattice. These quasi one dimensional structures provide an ideal environment to study dilute magnetic disorder in spin-glass like systems. Disorder controlled via chemical doping has been observed to weaken the spin glass behavior and disrupt a number of metamagnetic transitions found in pristine Ca3Co2O6. We report a systematic study of the effects of dilute Mn doping (x = 0.05 - 0.50) in Ca3Co2-xMnxO6 synthesized via a sol-gel method. Detailed AC and DC magnetization measurements performed on a SQUID magnetometer reveal the suppression of the step-like metamagnetic transitions by a doping of x = 0.25. The relaxation time is found to decrease with increasing Mn content, showing the destruction of the spin-glass like behavior. Our observations yield new insight into the role of site disorder on the glassy behavior in spin chain systems. Research was supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under Award No. DE-FG02-07ER46438.

  7. Non-native side chain IR probe in peptides: ab initio computation and 1D and 2D IR spectral simulation.

    PubMed

    Zheng, Michael L; Zheng, David C; Wang, Jianping

    2010-02-18

    Infrared frequency region of 2000-2600 cm(-1) (i.e., ca. 4-5 microm in wavelength) is a well-known open spectral window for peptides and proteins. In this work, six unnatural amino acids (unAAs) were designed to have characteristic absorption bands located in this region. Key chemical groups that served as side chains in these unAAs are C[triple bond]C, Phe-C[triple bond]C, N=C=O, N=C=S, P-H, and Si-H, respectively. Cysteine (a natural AA having S-H in side chain) was also studied for comparison. The anharmonic vibrational properties, including frequencies, anharmonicities, and intermode couplings, were examined using the density functional theory. Broadband linear infrared (IR) and two-dimensional (2D) IR spectra were simulated for each molecule. It is found that all of the side chain modes have significant overtone diagonal anharmonicities. All have moderate transition dipole strengths except the C[triple bond]C and S-H stretching modes, in comparison with the C=O stretching mode. In each case, a collection of 2D IR cross peaks were predicted to appear due to the presence of the side chain groups, whose strengths are closely related to the intramolecular anharmonic interactions, and to the transition dipole strengths of the coupled vibrators. Further, potential energy distribution analysis and high-order anharmonic constant computation showed that these IR probes possess a varying degree of mode localization. The results suggest that these IR probes are potentially useful in complementing the well-studied amide-I mode, to investigate structures and dynamics of peptides and proteins.

  8. Structure elucidation of organic compounds from natural sources using 1D and 2D NMR techniques

    NASA Astrophysics Data System (ADS)

    Topcu, Gulacti; Ulubelen, Ayhan

    2007-05-01

    In our continuing studies on Lamiaceae family plants including Salvia, Teucrium, Ajuga, Sideritis, Nepeta and Lavandula growing in Anatolia, many terpenoids, consisting of over 50 distinct triterpenoids and steroids, and over 200 diterpenoids, several sesterterpenoids and sesquiterpenoids along with many flavonoids and other phenolic compounds have been isolated. For Salvia species abietanes, for Teucrium and Ajuga species neo-clerodanes for Sideritis species ent-kaurane diterpenes are characteristic while nepetalactones are specific for Nepeta species. In this review article, only some interesting and different type of skeleton having constituents, namely rearranged, nor- or rare diterpenes, isolated from these species will be presented. For structure elucidation of these natural diterpenoids intensive one- and two-dimensional NMR techniques ( 1H, 13C, APT, DEPT, NOE/NOESY, 1H- 1H COSY, HETCOR, COLOC, HMQC/HSQC, HMBC, SINEPT) were used besides mass and some other spectroscopic methods.

  9. Flow Structure Determined Enhancing and Inhibiting Convective Heat Transfers in Quasi 1D Magnetic Fluid

    NASA Astrophysics Data System (ADS)

    Luo, Weili; Huang, Jun; Liu, Tianshu

    2016-11-01

    We have found previously that the convective flow in magnetic fluid responds to applied magnetic fields differently, depending on the relative direction of the gradient of temperature to that of the field. In this work we report the velocity profiles from these flows obtained from optical flow method. The peculiar magnetic driving force as well as the special configurations give rise to unique flow patterns, distinctly depends on the specific relative orientation of the temperature to that of field. The streamline plots indicate formation of local or global flow structures that explain the different effects of field on the heat transfer in the sample. For one configuration, the magneto-thermo convection causing the "heat" to be localized, stopping the equilibration process in the system. We will discuss the different responses to the applied magnetic fields for two different sample configurations in terms of relative orientation of the temperature and field gradients.

  10. Quark-Hadron Duality in Spin Structure Functions $g_1^p$ and $g_1^d$

    SciTech Connect

    P.E. Bosted; K.V. Dharmawardane; G.E. Dodge; T.A. Forest; S.E. Kuhn; Y. Prok

    2006-07-25

    New measurements of the spin structure functions of the proton and deuteron g{sub 1}{sup p}(x, Q{sup 2}) and g{sub 1}{sup d}(x, Q{sup 2}) in the nucleon resonance region are compared with extrapolations of target-mass-corrected next-to-leading-order (NLO) QCD fits to higher energy data. Averaged over the entire resonance region (W < 2 GeV), the data and QCD fits are in good agreement in both magnitude and Q{sup 2} dependence for Q{sup 2} > 1.7 GeV{sup 2}/c{sup 2}. This ''global'' duality appears to result from cancellations among the prominent ''local'' resonance regions: in particular strong {sigma}{sub 3/2} contributions in the {Delta}(1232) region appear to be compensated by strong {sigma}{sub 1/2} contributions in the resonance region centered on 1.5 GeV. These results are encouraging for the extension of NLO QCD fits to lower W and Q{sup 2} than have been used previously.

  11. Exponents of the spectral functions and dynamical structure factor of the 1D Lieb-Liniger Bose gas

    NASA Astrophysics Data System (ADS)

    Carmelo, J. M. P.; Sacramento, P. D.

    2016-06-01

    We study the (k , ω) -plane finite-energy line shape of the zero-temperature one-boson removal spectral function (ω < 0) , one-boson addition spectral function (ω > 0) , and charge dynamical structure factor (ω > 0) of the 1D Lieb-Liniger Bose gas with repulsive boson interaction c > 0. Our analysis of the problem focuses on the line shape at finite excitation energies in the vicinity of these functions spectrum upper (ω < 0) or lower (ω > 0) threshold. Specifically, we derive the exact momentum, interaction, and density dependences of the exponents controlling such a line shape in each of the N = 1 , 2 , 3 , … momentum subdomains k ∈ [(N - 1) 2 πn , N 2 πn ] . Here n = N / L is the boson density, N the boson number, and L the system length. In the thermodynamic limit considered in our study nearly all spectral weight of the dynamical correlation functions is for large values of n / c contained in the N = 1 momentum subdomain k ∈ [ 0 , 2 πn ] . As n / c decreases a small fraction of that weight is transferred to the remaining set of N = 2 , 3 , 4 , … momentum subdomains, particularly to the N = 2 subdomain. In the case of the momentum subdomain k ∈ [ 0 , 2 πn ] , our exact results agree with those of previous studies. For that subdomain the above exponents are plotted as a function of the momentum for several n / c values. Our derivation of the line shapes of the three dynamical correlation functions relies on the use of a simplified form of the pseudofermion dynamical theory of the fermionic 1D Hubbard model suitably modified in this paper for the 1D Bose gas.

  12. Hydrothermal synthesis, crystal structure and properties of a novel chain coordination polymer constructed by tetrafunctional phosphonate anions and cobalt ions

    SciTech Connect

    Guan, Lei; Wang, Ying

    2015-08-15

    A novel cobalt phosphonate, [Co(HL)(H{sub 2}O){sub 3}]{sub n} (1) (L=N(CH{sub 2}PO{sub 3}H){sub 3}{sup 3−}) has been synthesized by hydrothermal reaction at 150 °C and structurally characterized by X-ray diffraction, infrared spectroscopy, elemental and thermogravimetric analysis. Complex 1 features a 1D chain structure with double-channel built from CoO{sub 6} octahedra bridged together by the phosphonate groups. Each cobalt ion is octahedrally coordinated by three phosphonate oxygen atoms and three water molecules. The coordinated water molecules can form the hydrogen bonds with the phosphonate oxygen atoms to link the 1D chains, building a 2D layered structure, further resulting in a 3D network. The luminescence spectrum indicates an emission maximum at 435 nm. The magnetic susceptibility curve exhibits a dominant antiferromagnetic behavior with a weakly ferromagnetic component at low temperatures. - Graphical abstract: The connectivity between cobalt ions and the ligands results in a chain structure with a 1D double-channel structure, which is constructed by A-type subrings and B-type subrings. - Highlights: • The tetrafunctional phosphonate ligand was used as the ligand. • A novel chain structure can be formed by A-type rings and B-type rings. • Two types of rings can form a 1D double-channel structure, along the c-axis.

  13. Structural Basis of the Interaction between Tuberous Sclerosis Complex 1 (TSC1) and Tre2-Bub2-Cdc16 Domain Family Member 7 (TBC1D7).

    PubMed

    Qin, Jiayue; Wang, Zhizhi; Hoogeveen-Westerveld, Marianne; Shen, Guobo; Gong, Weimin; Nellist, Mark; Xu, Wenqing

    2016-04-15

    Mutations in TSC1 or TSC2 cause tuberous sclerosis complex (TSC), an autosomal dominant disorder characterized by the occurrence of benign tumors in various vital organs and tissues. TSC1 and TSC2, the TSC1 and TSC2 gene products, form the TSC protein complex that senses specific cellular growth conditions to control mTORC1 signaling. TBC1D7 is the third subunit of the TSC complex, and helps to stabilize the TSC1-TSC2 complex through its direct interaction with TSC1. Homozygous inactivation of TBC1D7 causes intellectual disability and megaencephaly. Here we report the crystal structure of a TSC1-TBC1D7 complex and biochemical characterization of the TSC1-TBC1D7 interaction. TBC1D7 interacts with the C-terminal region of the predicted coiled-coil domain of TSC1. The TSC1-TBC1D7 interface is largely hydrophobic, involving the α4 helix of TBC1D7. Each TBC1D7 molecule interacts simultaneously with two parallel TSC1 helices from two TSC1 molecules, suggesting that TBC1D7 may stabilize the TSC complex by tethering the C-terminal ends of two TSC1 coiled-coils.

  14. Photonic Crystals: Tunable Design of Structural Colors Produced by Pseudo-1D Photonic Crystals of Graphene Oxide (Small 25/2016).

    PubMed

    Tong, Liping; Qi, Wei; Wang, Mengfan; Huang, Renliang; Su, Rongxin; He, Zhimin

    2016-07-01

    The production of structural colors based on graphene oxide (GO) pseudo-one-dimensional photonic crystals (p1D-PhCs) in the visible spectrum is reported on page 3433 by W. Qi and co-workers. The structural colors could be tuned by simply changing either the volume or concentration of the aqueous GO dispersion. Moreover, GO p1D-PhCs exhibit visible and rapid responsiveness to humidity.

  15. Designed Quasi-1D Potential Structures Realized in Compositionally Graded InAs1-xPx Nanowires.

    PubMed

    Nylund, Gustav; Storm, Kristian; Lehmann, Sebastian; Capasso, Federico; Samuelson, Lars

    2016-02-10

    III-V semiconductor heterostructures are important components of many solid-state optoelectronic devices, but the ability to control and tune the electrical and optical properties of these structures in conventional device geometries is fundamentally limited by the bulk dimensionality and the inability to accommodate lattice-mismatched material combinations. Here we demonstrate how semiconductor nanowires may enable the creation of arbitrarily shaped one-dimensional potential structures for new types of designed device functionality. We describe the controlled growth of stepwise compositionally graded InAs1-xPx heterostructures defined along the axes of InAs nanowires, and we show that nanowires with sawtooth-shaped composition profiles behave as near-ideal unipolar diodes with ratchet-like rectification of the electron transport through the nanowires, in excellent agreement with simulations. This new type of designed quasi-1D potential structure represents a significant advance in band gap engineering and may enable fundamental studies of low-dimensional hot-carrier dynamics, in addition to constituting a platform for implementing novel electronic and optoelectronic device concepts.

  16. HOTCFGM-1D: A Coupled Higher-Order Theory for Cylindrical Structural Components with Through-Thickness Functionally Graded Microstructures

    NASA Technical Reports Server (NTRS)

    Pindera, Marek-Jerzy; Aboudi, Jacob

    1998-01-01

    The objective of this three-year project was to develop and deliver to NASA Lewis one-dimensional and two-dimensional higher-order theories, and related computer codes, for the analysis, optimization and design of cylindrical functionally graded materials/structural components for use in advanced aircraft engines (e.g., combustor linings, rotor disks, heat shields, blisk blades). To satisfy this objective, a quasi one-dimensional version of the higher-order theory, HOTCFGM-1D, and four computer codes based on this theory, for the analysis, design and optimization of cylindrical structural components functionally graded in the radial direction were developed. The theory is applicable to thin multi-phased composite shell/cylinders subjected to macroscopically axisymmetric thermomechanical and inertial loading applied uniformly along the axial direction such that the overall deformation is characterized by a constant average axial strain. The reinforcement phases are uniformly distributed in the axial and circumferential directions, and arbitrarily distributed in the radial direction, thereby allowing functional grading of the internal reinforcement in this direction.

  17. Ionothermal synthesis and crystal structures of metal phosphate chains

    SciTech Connect

    Wragg, David S.; Le Ouay, Benjamin; Beale, Andrew M.; O'Brien, Matthew G.; Slawin, Alexandra M.Z.; Warren, John E.; Prior, Timothy J.; Morris, Russell E.

    2010-07-15

    We have prepared isostructural aluminium and gallium phosphate chains by ionothermal reactions in 1-ethyl-3-methylimidazolium bromide and 1-ethylpyridinium bromide under a variety of conditions. The chains can be prepared as pure phases or along with three dimensional framework phases. The chains are favoured at shorter heating times and the crystallinity can be improved by addition of transition metal acetates and amines which are not included in the final structure. The chain can be prepared with or without the presence of hydrofluoric acid. - Graphical abstract: Chain structures prepared from ionic liquid solvents under a wide variety of synthesis conditions.

  18. Syntheses, structures, and photoluminescence of d 10 coordination architectures: From 1D to 3D complexes based on mixed ligands

    NASA Astrophysics Data System (ADS)

    Yuan, Gang; Shao, Kui-Zhan; Du, Dong-Ying; Wang, Xin-Long; Su, Zhong-Min

    2011-05-01

    Six new compounds, namely, {[Cd 3(Himpy) 3(tda) 2]·3H 2O} n ( 1), {[Zn 3(bipy) 2(tda) 2(H 2O) 2]·4H 2O} n ( 2), {[Cd 3(bipy) 3(tda) 2]·4H 2O} n ( 3), {[Cd 3(tda) 2(H 2O) 3Cl]·H 2O} n ( 4), {[Zn 2(tz)(tda)(H 2O) 2]·H 2O} n ( 5) and {[Cd 7(pz)(tda) 4(OAc)(H 2O) 7]·3H 2O} n ( 6) [H 3tda = 1H-1,2,3-triazole-4,5-dicarboxylic acid, Himpy = 2-(1H-imidazol-2-yl)pyridine, bipy = 2,2'-bipyridine, Htz = 1H-1,2,4-triazole, H 2pz = piperazine] have been prepared under hydrothermal condition and characterized by elemental analyses, infrared spectroscopy, powder X-ray diffraction and single-crystal X-ray diffraction analyses. Compound 1 is a 1D column-like structure and displays a 3D supramolecular network via the π···π stacking interaction. The compounds 2 and 3 exhibit similar 2D layer-like structure, which further extend to 3D supermolecular structure by the π···π stacking interaction. All of compounds 4- 6 display 3D framework with diverse topology constructed from the tda 3- ligands in different coordination modes and secondary ligands (or bridging atom) connecting metal ions. Furthermore, the thermal stabilities and photoluminescent properties of compounds 1- 6 were studied.

  19. Molecular cable-like 1-D iodic spiral chains covered with triple helices stabilized in guest-included chiral porous framework.

    PubMed

    Tadokoro, Makoto; Tanaka, Yasuko; Noguchi, Khoichiro; Sugaya, Tomoaki; Isoda, Kyosuke

    2012-07-21

    The supramolecular crystal {[Pr(DMFA)](3)[Ni(II)(Hbim)(3)](2)I}(n) with intricate chiral networks of [Ni(II)(Hbim)(3)](-) molecules is reported. It includes a cationic architecture as a guest, constructed from chiral nanotubes that penetrate I(-) chains with spiral channels wrapped by triple helices. The I(-) chains have AC conductivity in crystals like a molecular cable.

  20. Quantifying side-chain conformational variations in protein structure

    NASA Astrophysics Data System (ADS)

    Miao, Zhichao; Cao, Yang

    2016-11-01

    Protein side-chain conformation is closely related to their biological functions. The side-chain prediction is a key step in protein design, protein docking and structure optimization. However, side-chain polymorphism comprehensively exists in protein as various types and has been long overlooked by side-chain prediction. But such conformational variations have not been quantitatively studied and the correlations between these variations and residue features are vague. Here, we performed statistical analyses on large scale data sets and found that the side-chain conformational flexibility is closely related to the exposure to solvent, degree of freedom and hydrophilicity. These analyses allowed us to quantify different types of side-chain variabilities in PDB. The results underscore that protein side-chain conformation prediction is not a single-answer problem, leading us to reconsider the assessment approaches of side-chain prediction programs.

  1. Quantifying side-chain conformational variations in protein structure.

    PubMed

    Miao, Zhichao; Cao, Yang

    2016-11-15

    Protein side-chain conformation is closely related to their biological functions. The side-chain prediction is a key step in protein design, protein docking and structure optimization. However, side-chain polymorphism comprehensively exists in protein as various types and has been long overlooked by side-chain prediction. But such conformational variations have not been quantitatively studied and the correlations between these variations and residue features are vague. Here, we performed statistical analyses on large scale data sets and found that the side-chain conformational flexibility is closely related to the exposure to solvent, degree of freedom and hydrophilicity. These analyses allowed us to quantify different types of side-chain variabilities in PDB. The results underscore that protein side-chain conformation prediction is not a single-answer problem, leading us to reconsider the assessment approaches of side-chain prediction programs.

  2. Controlled structures of a 1D chiral metallosalen polymer by photo- and solvent-induced partial depolymerization.

    PubMed

    Xi, Xiaobing; Dong, Taiwei; Li, Gao; Cui, Yong

    2011-04-07

    A 1D chiral metallosalen polymer with free pyridine groups is self-assembled and its molecular weight, conformation, architecture and optical property are controlled by depolymerization through sunlight irradiation or alcohol inclusions.

  3. Molecular tectonics: self-complementary supramolecular Se...N synthons directing assembly of 1D silver chains into 3D porous molecular architectures.

    PubMed

    Zhou, Ai-Ju; Zheng, Shao-Liang; Fang, Yue; Tong, Ming-Liang

    2005-06-27

    Reaction of 2,1,3-benzoselenadiazole (bsd) with AgNO3 results in the formation of a novel model example of a Se...N synthon directed molecular network of different polymorphs at different temperatures. Alpha-[Ag(bsd)2(NO3)] x 0.5bsd formed at ambient temperature, has a 3D porous molecular network constructed with monomeric [Ag(bsd)2(NO3)] motif, and has 1D channels that are encapsulated with 1D arrays of two-fold-disordered dimeric (bsd)2 guests aggregated by the self-complementary nonbonded Se...N interactions. This is the first molecular net directed by supramolecular Se...N synthons. The second polymorph, beta-[Ag(bsd)2(NO3)] x 0.5bsd, formed from an analogous reaction at 50 degrees C, contains a similar 3D molecular network constructed with tetrameric [Ag4(bsd)8(NO3)4] motif and 1D arrays of well-ordered dimeric (bsd)2 guests are encapsulated in the channels. Such ordered (bsd)2 dimers provide an excellent simplified dimeric model for MO calculations of intermolecular nonbonded Se...N interactions.

  4. Satellite-derived light extinction coefficient and its impact on thermal structure simulations in a 1-D lake model

    NASA Astrophysics Data System (ADS)

    Zolfaghari, Kiana; Duguay, Claude R.; Kheyrollah Pour, Homa

    2017-01-01

    A global constant value of the extinction coefficient (Kd) is usually specified in lake models to parameterize water clarity. This study aimed to improve the performance of the 1-D freshwater lake (FLake) model using satellite-derived Kd for Lake Erie. The CoastColour algorithm was applied to MERIS satellite imagery to estimate Kd. The constant (0.2 m-1) and satellite-derived Kd values as well as radiation fluxes and meteorological station observations were then used to run FLake for a meteorological station on Lake Erie. Results improved compared to using the constant Kd value (0.2 m-1). No significant improvement was found in FLake-simulated lake surface water temperature (LSWT) when Kd variations in time were considered using a monthly average. Therefore, results suggest that a time-independent, lake-specific, and constant satellite-derived Kd value can reproduce LSWT with sufficient accuracy for the Lake Erie station. A sensitivity analysis was also performed to assess the impact of various Kd values on the simulation outputs. Results show that FLake is sensitive to variations in Kd to estimate the thermal structure of Lake Erie. Dark waters result in warmer spring and colder fall temperatures compared to clear waters. Dark waters always produce colder mean water column temperature (MWCT) and lake bottom water temperature (LBWT), shallower mixed layer depth (MLD), longer ice cover duration, and thicker ice. The sensitivity of FLake to Kd variations was more pronounced in the simulation of MWCT, LBWT, and MLD. The model was particularly sensitive to Kd values below 0.5 m-1. This is the first study to assess the value of integrating Kd from the satellite-based CoastColour algorithm into the FLake model. Satellite-derived Kd is found to be a useful input parameter for simulations with FLake and possibly other lake models, and it has potential for applicability to other lakes where Kd is not commonly measured.

  5. Relationships between Th1 or Th2 iNKT Cell Activity and Structures of CD1d-Antigen Complexes: Meta-analysis of CD1d-Glycolipids Dynamics Simulations

    PubMed Central

    Laurent, Xavier; Renault, Nicolas; Farce, Amaury; Chavatte, Philippe; Hénon, Eric

    2014-01-01

    A number of potentially bioactive molecules can be found in nature. In particular, marine organisms are a valuable source of bioactive compounds. The activity of an α-galactosylceramide was first discovered in 1993 via screening of a Japanese marine sponge (Agelas mauritanius). Very rapidly, a synthetic glycololipid analogue of this natural molecule was discovered, called KRN7000. Associated with the CD1d protein, this α-galactosylceramide 1 (KRN7000) interacts with the T-cell antigen receptor to form a ternary complex that yields T helper (Th) 1 and Th2 responses with opposing effects. In our work, we carried out molecular dynamics simulations (11.5 µs in total) involving eight different ligands (conducted in triplicate) in an effort to find out correlation at the molecular level, if any, between chemical modulation of 1 and the orientation of the known biological response, Th1 or Th2. Comparative investigations of human versus mouse and Th1 versus Th2 data have been carried out. A large set of analysis tools was employed including free energy landscapes. One major result is the identification of a specific conformational state of the sugar polar head, which could be correlated, in the present study, to the biological Th2 biased response. These theoretical tools provide a structural basis for predicting the very different dynamical behaviors of α-glycosphingolipids in CD1d and might aid in the future design of new analogues of 1. PMID:25376021

  6. Local structure in hard-sphere chain-molecule fluids

    NASA Astrophysics Data System (ADS)

    Wasti, Sambid; Taylor, Mark

    2012-04-01

    The conformation of a polymer chain in solvent is coupled to the local structure of the solvent environment. For hard-sphere systems, a monomeric solvent acts to compress a flexible hard-sphere-solute chain and, for a dense system, the local solvent structure is imprinted onto the chain. Here we use Monte Carlo simulation, including bond-rebridging moves, to study the size and conformation of a hard sphere chain in a hard-sphere solvent as a function of both solvent density and solvent diameter. We also study the structure of a hard-sphere-chain solute in a hard-sphere-chain solvent. In the case of a 5-mer chain in 5-mer solvent we show that the effects of solvent can be mapped to a set of two-body solvation potentials. Following our previous work on hard-sphere chains in monomeric solvent [1], we explore the application of these short chain potentials to the study of longer chain-molecule fluids. [4pt] [1] M.P. Taylor and S. Ichida, J. Polym. Sci. B: Polym. Phys. 45, 3319 (2007).

  7. Local structure in hard-sphere chain-molecule fluids

    NASA Astrophysics Data System (ADS)

    Wasti, Sambid; Taylor, Mark

    2011-10-01

    The conformation of a polymer chain in solvent is coupled to the local structure of the solvent environment. For hard-sphere systems, a monomeric solvent acts to compress a flexible hard-sphere-solute chain and, for a dense system, the local solvent structure is imprinted onto the chain. Here we use Monte Carlo simulation, including bond-rebridging moves, to study the size and conformation of a hard sphere chain in a hard-sphere solvent as a function of both solvent density and solvent diameter. We also study the structure of a hard-sphere-chain solute in a hard-sphere-chain solvent. In the case of a 5-mer chain in 5-mer solvent we show that the effects of solvent can be mapped to a set of two-body solvation potentials. Following our previous work on hard-sphere chains in monomeric solvent [1], we explore the application of these short chain potentials to the study of longer chain-molecule fluids. [4pt] [1] M.P. Taylor and S. Ichida, J. Polym. Sci. B: Polym. Phys. 45, 3319 (2007).

  8. Surface-micromachined chain for use in microelectromechanical structures

    SciTech Connect

    Vernon, Sr., George E.

    2001-01-01

    A surface-micromachined chain and a microelectromechanical (MEM) structure incorporating such a chain are disclosed. The surface-micromachined chain can be fabricated in place on a substrate (e.g. a silicon substrate) by depositing and patterning a plurality of alternating layers of a chain-forming material (e.g. polycrystalline silicon) and a sacrificial material (e.g. silicon dioxide or a silicate glass). The sacrificial material is then removed by etching to release the chain for movement. The chain has applications for forming various types of MEM devices which include a microengine (e.g. an electrostatic motor) connected to rotate a drive sprocket, with the surface-micromachined chain being connected between the drive sprocket and one or more driven sprockets.

  9. Finite Markov Chains and Random Discrete Structures

    DTIC Science & Technology

    1994-07-26

    arrays with fixed margins 4. Persi Diaconis and Susan Holmes, Three Examples of Monte- Carlo Markov Chains: at the Interface between Statistical Computing...solutions for a math- ematical model of thermomechanical phase transitions in shape memory materials with Landau- Ginzburg free energy 1168 Angelo Favini

  10. Gold-induced nanowires on the Ge(100) surface yield a 2D and not a 1D electronic structure

    NASA Astrophysics Data System (ADS)

    de Jong, N.; Heimbuch, R.; Eliëns, S.; Smit, S.; Frantzeskakis, E.; Caux, J.-S.; Zandvliet, H. J. W.; Golden, M. S.

    2016-06-01

    Atomic nanowires on semiconductor surfaces induced by the adsorption of metallic atoms have attracted a lot of attention as possible hosts of the elusive, one-dimensional Tomonaga-Luttinger liquid. The Au/Ge(100) system in particular is the subject of controversy as to whether the Au-induced nanowires do indeed host exotic, 1D (one-dimensional) metallic states. In light of this debate, we report here a thorough study of the electronic properties of high quality nanowires formed at the Au/Ge(100) surface. The high-resolution ARPES data show the low-lying Au-induced electronic states to possess a dispersion relation that depends on two orthogonal directions in k space. Comparison of the E (kx,ky) surface measured using high-resolution ARPES to tight-binding calculations yields hopping parameters in the two different directions that differ by approximately factor of two. Additionally, by pinpointing the Au-induced surface states in the first, second, and third surface Brillouin zones and analyzing their periodicity in k||, the nanowire propagation direction seen clearly in STM can be imported into the ARPES data. We find that the larger of the two hopping parameters corresponds, in fact, to the direction perpendicular to the nanowires (tperp). This proves that the Au-induced electron pockets possess a two-dimensional, closed Fermi surface, and this firmly places the Au/Ge(100) nanowire system outside potential hosts of a Tomonaga-Luttinger liquid. We combine these ARPES data with scanning tunneling spectroscopic measurements of the spatially resolved electronic structure and find that the spatially straight—wirelike—conduction channels observed up to energies of order one electron volt below the Fermi level do not originate from the Au-induced states seen in the ARPES data. The former are rather more likely to be associated with bulk Ge states that are localized to the subsurface region. Despite our proof of the 2D (two-dimentional) nature of the Au

  11. Dinuclear and 1D iron(III) Schiff base complexes bridged by 4-salicylideneamino-1,2,4-triazolate: X-ray structures and magnetic properties.

    PubMed

    Herchel, Radovan; Pavelek, Lubomír; Trávníček, Zdeněk

    2011-11-28

    Four new iron(III) complexes were obtained by the reaction of 4-salicylideneamino-1,2,4-triazole (Hsaltrz) and selected dinuclear μ-oxo-bridged iron(III) Schiff base complexes [{FeL(4)}(2)(μ-O)], where L(4) represents a terminal tetradentate dianionic Schiff-base ligand. X-ray structural analysis revealed a novel bridging mode of κN,κO of the saltrz ligand to form dinuclear complexes [{Fe(salen)(μ-saltrz)}(2)]·CH(3)OH (1) (H(2)salen = N,N'-ethylenebis(salicylimine)) and [{Fe(salpn)(μ-saltrz)}(2)] (2) (H(2)salpn = N,N'-1,2-propylenbis(salicylimine)), whereas one-dimensional (1D) zig-zag chains were formed in the case of [{Fe(salch)(μ-saltrz)}·0.5CH(3)OH](n) (3) (H(2)salch = N,N'-cyclohexanebis(salicylimine)) and [Fe(salophen)(μ-saltrz)](n) (4) (H(2)salophen = N,N'-o-phenylenebis(salicylimine)). It was also shown that the rigidity of the terminal ligand L(4) can be considered as the key factor for the molecular dimensionality of the products. The thorough magnetic analysis based on SQUID experiments, including the isotropic exchange and the zero-field splitting of both temperature and field dependent data, was performed for dimeric (1 and 2) and also for polymeric compounds (3 and 4) and revealed weak antiferromagnetic exchange mediated by the saltrz anions with much larger D-parameter (|D|≫|J|).

  12. Stabilization of Ca1-dFe2-xMnxO4 (0.44 lt x lt 2) with CaFe2O4-type Structure and Ca2plus Defects in 1D Channels

    SciTech Connect

    T Yang; M Croft; A Ignatov; I Nowik; R Cong; M Greenblatt

    2011-12-31

    Solid solutions of Ca{sub 1-{delta}}Fe{sub 2-x}Mn{sub x}O{sub 4} (0.45 {<=} x {<=} 2) were synthesized from CaCl{sub 2} as flux at 850 C in air. The entire series, even with x = 2, crystallizes in the CaFe{sub 2}O{sub 4}-type structure (Pnma), rather than in the CaMn{sub 2}O{sub 4}-type structure (Pbcm). Rietveld refinements confirmed mixed-valency Mn{sup 3+}/Mn{sup 4+} and a substantial level of Ca{sup 2+} deficiency ({delta} {approx} 0.25) at high x. With increasing x, the unit-cell dimensions a and b decrease, while that of c increases. Detailed structural analyses, together with Mn K-edge X-ray absorption and {sup 57}Fe Moessbauer spectroscopy studies, revealed that the stabilization of CaFe{sub 2}O{sub 4}-type structure, even at high values of x, is due to the existence of non-Jahn-Teller active Mn{sup 4+} (and Fe{sup 3+}), which is compensated by the formation of the Ca{sup 2+} deficiencies in the one-dimensional (1D) channels of Ca{sub 1-{delta}}Fe{sub 2-x}Mn{sub x}O{sub 4} during the flux synthesis. Antiferromagnetic (AFM) long-range ordering is achieved for all compounds at low temperature, because of strong AFM interactions between Mn{sup 3+}/Mn{sup 4+} and Fe{sup 3+}. In addition, a spin (or cluster) glass component was also observed, as expected, because of the extensive Mn/Fe structural and Mn{sup 3+}/Mn{sup 4+} charge disordering.

  13. From 2D graphene to 1D graphene nanoribbons: dimensional crossover signals in the structural thermal fluctuations

    NASA Astrophysics Data System (ADS)

    Dobry, Ariel; Costamagna, Sebastián

    2011-03-01

    I this work, by analyzing the thermal excited rippling in the graphene honeycomb lattice, we find clear signals of an existing dimensional crossover from 2D to 1D while reducing one of the dimensions of the graphene layer. Trough a joint study, using montecarlo atomistic simulations and analytical calculation based, we find that the normal-normal correlation function G (q) does not change the power law behavior valid on the long wavelength limit, however the system size dependency of the quadratic out of plane displacement h2 shows a breakdown of its corresponding scaling law. In this case we show that a new scaling law appear which correspond to a truly 1D system. On the basis of these results, and having explored a wide number of realistic systems size, we conclude that narrow nanoribbons presents strongest corrugations than the square graphene sheets. This result could have important consequences on the electron transport properties of freestanding graphene systems.

  14. Nuclear structure notes on element 115 decay chains

    SciTech Connect

    Rudolph, D. Sarmiento, L. G.; Forsberg, U.

    2015-10-15

    Hitherto collected data on more than hundred α-decay chains stemming from element 115 are combined to probe some aspects of the underlying nuclear structure of the heaviest atomic nuclei yet created in the laboratory.

  15. On constitutive functions for hindered settling velocity in 1-D settler models: Selection of appropriate model structure.

    PubMed

    Torfs, Elena; Balemans, Sophie; Locatelli, Florent; Diehl, Stefan; Bürger, Raimund; Laurent, Julien; François, Pierre; Nopens, Ingmar

    2017-03-01

    Advanced 1-D models for Secondary Settling Tanks (SSTs) explicitly account for several phenomena that influence the settling process (such as hindered settling and compression settling). For each of these phenomena a valid mathematical expression needs to be selected and its parameters calibrated to obtain a model that can be used for operation and control. This is, however, a challenging task as these phenomena may occur simultaneously. Therefore, the presented work evaluates several available expressions for hindered settling based on long-term batch settling data. Specific attention is paid to the behaviour of these hindered settling functions in the compression region in order to evaluate how the modelling of sludge compression is influenced by the choice of a certain hindered settling function. The analysis shows that the exponential hindered settling forms, which are most commonly used in traditional SST models, not only account for hindered settling but partly lump other phenomena (compression) as well. This makes them unsuitable for advanced 1-D models that explicitly include each phenomenon in a modular way. A power-law function is shown to be more appropriate to describe the hindered settling velocity in advanced 1-D SST models.

  16. Dynamics and supramolecular organization of the 1D spin transition polymeric chain compound [Fe(NH2trz)3](NO3)2. Muon spin relaxation.

    PubMed

    Garcia, Yann; Campbell, Stewart J; Lord, James S; Boland, Yves; Ksenofontov, Vadim; Gütlich, Philipp

    2007-09-27

    The thermal spin transition that occurs in the polymeric chain compound [Fe(NH(2)trz)3](NO3)2 above room temperature has been investigated by zero-field muon spin relaxation (microSR) over the temperature range approximately 8-402 K. The depolarization curves are best described by a Lorentzian and a Gaussian line that represent fast and slow components, respectively. The spin transition is associated with a hysteresis loop of width DeltaT = 34 K (T1/2 upward arrow = 346 K and T1/2 downward arrow = 312 K) that has been delineated by the temperature variation of the initial asymmetry parameter, in good agreement with previously published magnetic measurements. Zero-field and applied field (20-2000 Oe) microSR measurements show the presence of diamagnetic muon species and paramagnetic muonium radical species (A = 753 +/- 77 MHz) over the entire temperature range. Fast dynamics have been revealed in the high-spin state of [Fe(NH(2)trz)3](NO3)2 with the presence of a Gaussian relaxation mode that is mostly due to the dipolar interaction with static nuclear moments. This situation, where the muonium radicals are totally decoupled and not able to sense paramagnetic fluctuations, implies that the high-spin dynamics fall outside the muon time scale. Insights to the origin of the cooperative effects associated with the spin transition of [Fe(NH(2)trz)3](NO3)2 through muon implantation are presented.

  17. 1D μ-glycine-briged copper (II) chain in complex [Cu(μ-Gly)Im(ClO4)]n and ferromagnetic interactions among copper (II)

    NASA Astrophysics Data System (ADS)

    Pan, Lu; Lv, Xue-Chuan; Luo, Guan-Hua; Gao, Xiao-Han; Tan, Zhi-Cheng

    2016-12-01

    Complex [Cu(μ-Gly)Im(ClO4)]n(Im = imidazole, and Gly = glycine) with μ-glycine-briged copper (II) chain, containing six-coordination distorted elongated octahedron, was synthesized and characterized. The complex belongs to space group P 21/c measured by X-ray single crystal diffraction. In the cluster, each Cu2+ ion are six-coordination by one nitrogen atom and two oxygen atoms of glycine, one nitrogen atoms of imidazole, and two of oxygen atoms of two perchlorate. Each Cu2+ ion has an N2O4 donor set, which forms the distorted elongated octahedron due to the Jahn-Teller (JT) effect. The magnetic and thermodynamic properties were researched. Magnetic susceptibilities of the complex showed that ferromagnetic interactions occurred between the Cu (II) atoms. The Curie-Weiss constant C = 0.565 cm3 K·mol-1 and the Weiss constant θ = 1.0585 K were given by the Curie-Weiss law The ferromagnetic nature of the interaction could be deduced as the exchange pathway of Cusbnd Osbnd Csbnd Osbnd Cu, which involved an equatorial position at one copper (II) ion and an axial position of the nearest copper (II). The complex decomposed from 511 to 538 K as two steps.

  18. Structural insight for chain selection and stagger control in collagen

    PubMed Central

    Boudko, Sergei P.; Bächinger, Hans Peter

    2016-01-01

    Collagen plays a fundamental role in all known metazoans. In collagens three polypeptides form a unique triple-helical structure with a one-residue stagger to fit every third glycine residue in the inner core without disturbing the poly-proline type II helical conformation of each chain. There are homo- and hetero-trimeric types of collagen consisting of one, two or three distinct chains. Thus there must be mechanisms that control composition and stagger during collagen folding. Here, we uncover the structural basis for both chain selection and stagger formation of a collagen molecule. Three distinct chains (α1, α2 and α3) of the non-collagenous domain 2 (NC2) of type IX collagen are assembled to guide triple-helical sequences in the leading, middle and trailing positions. This unique domain opens the door for generating any fragment of collagen in its native composition and stagger. PMID:27897211

  19. 3-D imaging of large scale buried structure by 1-D inversion of very early time electromagnetic (VETEM) data

    USGS Publications Warehouse

    Aydmer, A.A.; Chew, W.C.; Cui, T.J.; Wright, D.L.; Smith, D.V.; Abraham, J.D.

    2001-01-01

    A simple and efficient method for large scale three-dimensional (3-D) subsurface imaging of inhomogeneous background is presented. One-dimensional (1-D) multifrequency distorted Born iterative method (DBIM) is employed in the inversion. Simulation results utilizing synthetic scattering data are given. Calibration of the very early time electromagnetic (VETEM) experimental waveforms is detailed along with major problems encountered in practice and their solutions. This discussion is followed by the results of a large scale application of the method to the experimental data provided by the VETEM system of the U.S. Geological Survey. The method is shown to have a computational complexity that is promising for on-site inversion.

  20. Forward waveform modelling procedure for 1-D crustal velocity structure and its application to the southern Korean Peninsula

    NASA Astrophysics Data System (ADS)

    Kim, Seongryong; Rhie, Junkee; Kim, Geunyoung

    2011-04-01

    We propose a full-grid search procedure for broad-band waveform modelling to determine a 1-D crustal velocity model. The velocity model can be more constrained because of the use of broad-band waveforms instead of traveltimes for the crustal phases, although only a small number of event-station pairs were employed. Despite the time-consuming nature of the full-grid search method to search the whole model parameter space, the use of an empirical relationship between the P- and S-wave velocities can significantly reduce computation time. The proposed method was applied to a case in the southern Korean Peninsula. Broad-band waveforms obtained from two inland earthquakes that occurred on 2007 January 20 (Mw 4.6) and 2004 April 26 (Mw 3.6) were used to test the method. The three-layers over half-space crustal velocity model of the P- and S-wave velocities was estimated. Comparisons of waveform fitness between the final model and previously published models demonstrate advancements in the average value of waveform fitness for the inland earthquakes. In addition, 1-D velocity models were determined for three distinct tectonic regions, namely, the Gyonggi Massif, the Okcheon Belt and the Gyeongsang Basin, which are all located inside the study area. A comparison between the three models demonstrates that the crustal thickness of the southern Korean Peninsula increases from NW to SE and that the lower crustal composition of the Okcheon belt differs from that of the other tectonic regions.

  1. Topological and geometric measurements of force-chain structure

    NASA Astrophysics Data System (ADS)

    Giusti, Chad; Papadopoulos, Lia; Owens, Eli T.; Daniels, Karen E.; Bassett, Danielle S.

    2016-09-01

    Developing quantitative methods for characterizing structural properties of force chains in densely packed granular media is an important step toward understanding or predicting large-scale physical properties of a packing. A promising framework in which to develop such methods is network science, which can be used to translate particle locations and force contacts into a graph in which particles are represented by nodes and forces between particles are represented by weighted edges. Recent work applying network-based community-detection techniques to extract force chains opens the door to developing statistics of force-chain structure, with the goal of identifying geometric and topological differences across packings, and providing a foundation on which to build predictions of bulk material properties from mesoscale network features. Here we discuss a trio of related but fundamentally distinct measurements of the mesoscale structure of force chains in two-dimensional (2D) packings, including a statistic derived using tools from algebraic topology, which together provide a tool set for the analysis of force chain architecture. We demonstrate the utility of this tool set by detecting variations in force-chain architecture with pressure. Collectively, these techniques can be generalized to 3D packings, and to the assessment of continuous deformations of packings under stress or strain.

  2. Topological and geometric measurements of force-chain structure.

    PubMed

    Giusti, Chad; Papadopoulos, Lia; Owens, Eli T; Daniels, Karen E; Bassett, Danielle S

    2016-09-01

    Developing quantitative methods for characterizing structural properties of force chains in densely packed granular media is an important step toward understanding or predicting large-scale physical properties of a packing. A promising framework in which to develop such methods is network science, which can be used to translate particle locations and force contacts into a graph in which particles are represented by nodes and forces between particles are represented by weighted edges. Recent work applying network-based community-detection techniques to extract force chains opens the door to developing statistics of force-chain structure, with the goal of identifying geometric and topological differences across packings, and providing a foundation on which to build predictions of bulk material properties from mesoscale network features. Here we discuss a trio of related but fundamentally distinct measurements of the mesoscale structure of force chains in two-dimensional (2D) packings, including a statistic derived using tools from algebraic topology, which together provide a tool set for the analysis of force chain architecture. We demonstrate the utility of this tool set by detecting variations in force-chain architecture with pressure. Collectively, these techniques can be generalized to 3D packings, and to the assessment of continuous deformations of packings under stress or strain.

  3. Interpolatory fixed-point algorithm for an efficient computation of TE and TM modes in arbitrary 1D structures at oblique incidence

    NASA Astrophysics Data System (ADS)

    Pérez Molina, Manuel; Francés Monllor, Jorge; Álvarez López, Mariela; Neipp López, Cristian; Carretero López, Luis

    2010-05-01

    We develop the Interpolatory Fixed-Point Algorithm (IFPA) to compute efficiently the TE and TM reflectance and transmittance coefficients for arbitrary 1D structures at oblique incidence. For this purpose, we demonstrate that the semi-analytical solutions of the Helmholtz equation provided by the fixed-point method have a polynomial dependence on variables that are related to the essential electromagnetic parameters -incidence angle and wavelength-, which allows a drastic simplification of the required calculations taking the advantage of interpolation for a few parameter values. The first step to develop the IFPA consists of stating the Helmholtz equation and boundary conditions for TE and TM plane incident waves on a 1D finite slab with an arbitrary permittivity profile surrounded by two homogeneous media. The Helmholtz equation and boundary conditions are then transformed into a second-order initial value problem which is written in terms of transfer matrices. By applying the fixed-point method, the coefficients of such transfer matrices are obtained as polynomials on several variables that can be characterized by a reduced set of interpolating parameters. We apply the IFPA to specific examples of 1D diffraction gratings, optical rugate filters and quasi-periodic structures, for which precise solutions for the TE and TM modes are efficiently obtained by computing less than 20 interpolating parameters.

  4. Sequence and structure of VH domain from naturally occurring camel heavy chain immunoglobulins lacking light chains.

    PubMed

    Muyldermans, S; Atarhouch, T; Saldanha, J; Barbosa, J A; Hamers, R

    1994-09-01

    We cloned 17 different PCR fragments encoding VH genes of camel (Camelus dromedarius). These clones were derived from the camel heavy chain immunoglobulins lacking the light chain counterpart of normal immunoglobulins. Insight into the camel VH sequences and structure may help the development of single domain antibodies. The most remarkable difference in the camel VH, consistent with the absence of the VL interaction, is the substitution of the conserved Leu45 by an Arg or Cys. Another noteworthy substitution is the Leu11 to Ser. This amino acid normally interacts with the CH1 domain, a domain missing in the camel heavy chain immunoglobulins. The nature of these substitutions agrees with the increased solubility behavior of an isolated camel VH domain. The VH domains of the camels are also characterized by a long CDR3, possibly compensating for the absence of the VL contacts with the antigen. The CDR3 lacks the salt bridge between Arg94 and Asp101. However, the frequent occurrence of additional Cys residues in both the CDR1 and CDR3 might lead to the formation of a second internal disulfide bridge, thereby stabilizing the CDR structure as in the DAW antibody. Within CDRs of the camel VH domains we observe a broad size distribution and a different amino acid pattern compared with the mouse or human VH. Therefore the camel hypervariable regions might adopt structures which differ substantially from the known canonical structures, thereby increasing the repertoire of the camel antigen binding sites within a VH.

  5. The dependence of lipid asymmetry upon phosphatidylcholine acyl chain structure[S

    PubMed Central

    Son, Mijin; London, Erwin

    2013-01-01

    Lipid asymmetry, the difference in inner and outer leaflet lipid composition, is an important feature of biomembranes. By utilizing our recently developed MβCD-catalyzed exchange method, the effect of lipid acyl chain structure upon the ability to form asymmetric membranes was investigated. Using this approach, SM was efficiently introduced into the outer leaflet of vesicles containing various phosphatidylcholines (PC), but whether the resulting vesicles were asymmetric (SM outside/PC inside) depended upon PC acyl chain structure. Vesicles exhibited asymmetry using PC with two monounsaturated chains of >14 carbons; PC with one saturated and one unsaturated chain; and PC with phytanoyl chains. Vesicles were most weakly asymmetric using PC with two 14 carbon monounsaturated chains or with two polyunsaturated chains. To define the origin of this behavior, transverse diffusion (flip-flop) of lipids in vesicles containing various PCs was compared. A correlation between asymmetry and transverse diffusion was observed, with slower transverse diffusion in vesicles containing PCs that supported lipid asymmetry. Thus, asymmetric vesicles can be prepared using a wide range of acyl chain structures, but fast transverse diffusion destroys lipid asymmetry. These properties may constrain acyl chain structure in asymmetric natural membranes to avoid short or overly polyunsaturated acyl chains. PMID:23093551

  6. Crystal Structure of Human Liver delta {4}-3-Ketosteroid 5 beta-Reductase (AKR1D1) and Implications for Substrate Binding and Catalysis

    SciTech Connect

    Di Costanzo,L.; Drury, J.; Penning, T.; Christianson, D.

    2008-01-01

    AKR1D1 (steroid 5{beta}-reductase) reduces all 4-3-ketosteroids to form 5{beta}-dihydrosteroids, a first step in the clearance of steroid hormones and an essential step in the synthesis of all bile acids. The reduction of the carbon-carbon double bond in an a,{beta}-unsaturated ketone by 5{beta}-reductase is a unique reaction in steroid enzymology because hydride transfer from NADPH to the {beta}-face of a 4-3-ketosteroid yields a cis-A/B-ring configuration with an {approx}90 bend in steroid structure. Here, we report the first x-ray crystal structure of a mammalian steroid hormone carbon-carbon double bond reductase, human 4-3-ketosteroid 5{beta}-reductase (AKR1D1), and its complexes with intact substrates. We have determined the structures of AKR1D1 complexes with NADP+ at 1.79- and 1.35- Angstroms resolution (HEPES bound in the active site), NADP+ and cortisone at 1.90- Angstroms resolution, NADP+ and progesterone at 2.03- Angstroms resolution, and NADP+ and testosterone at 1.62- Angstroms resolution. Complexes with cortisone and progesterone reveal productive substrate binding orientations based on the proximity of each steroid carbon-carbon double bond to the re-face of the nicotinamide ring of NADP+. This orientation would permit 4-pro-(R)-hydride transfer from NADPH. Each steroid carbonyl accepts hydrogen bonds from catalytic residues Tyr58 and Glu120. The Y58F and E120A mutants are devoid of activity, supporting a role for this dyad in the catalytic mechanism. Intriguingly, testosterone binds nonproductively, thereby rationalizing the substrate inhibition observed with this particular steroid. The locations of disease-linked mutations thought to be responsible for bile acid deficiency are also revealed.

  7. From 1D and 2D ZnO nanostructures to 3D hierarchical structures with enhanced gas sensing properties.

    PubMed

    Alenezi, Mohammad R; Henley, Simon J; Emerson, Neil G; Silva, S Ravi P

    2014-01-07

    Facile and low cost hydrothermal routes are developed to fabricate three-dimensional (3D) hierarchical ZnO structures with high surface-to-volume ratios and an increased fraction of (0001) polar surfaces. Hierarchical ZnO nanowires (ZNWs) and nanodisks (ZNDs) assembled from initial ZnO nanostructures are prepared from sequential nucleation and growth following a hydrothermal process. These hierarchical ZnO structures display an enhancement of gas sensing performance and exhibit significantly improved sensitivity and fast response to acetone in comparison to other mono-morphological ZnO, such as nanoparticles, NWs, or NDs. In addition to the high surface-to-volume ratio due to its small size, the nanowire building blocks show the enhanced gas sensing properties mainly ascribed to the increased proportion of exposed active (0001) planes, and the formation of many nanojunctions at the interface between the initial ZnO nanostructure and secondary NWs. This work provides the route for structure induced enhancement of gas sensing performance by designing a desirable nanostructure, which could also be extended to synthesize other metal oxide nanostructures with superior gas sensing performance.

  8. Tailoring the spin waves band structure of 1D magnonic crystals consisting of L-shaped iron/permalloy nanowires

    NASA Astrophysics Data System (ADS)

    Gubbiotti, G.; Silvani, R.; Tacchi, S.; Madami, M.; Carlotti, G.; Yang, Z.; Adeyeye, A. O.; Kostylev, M.

    2017-03-01

    We have investigated both experimentally and numerically the magnonic band structure of arrays of closely spaced Fe/permalloy nanowires (NWs) with an L-shape cross-section using the Brillouin light scattering technique and GPU-based micromagnetic simulations. NWs consist of a 340 nm wide and 10 nm thick permalloy layer covered by a 170 nm wide Fe overlayer. The thickness of the latter was varied in the range from 0 to 10 nm in order to analyze its influence on the magnonic band structure. We found that both the frequency and the spatial profile of the most intense and dispersive mode, can be efficiently tuned by the presence of the thin Fe NW overlayer. In particular, by increasing the Fe thickness, one observes a substantial frequency increase, while the spatial profile of the mode narrows and moves to the permalloy NW portion not covered by Fe. In addition, the presence of the Fe overlayer causes a significant increase of the number of detected modes and a change of their intensity in the Brillouin spectra as a function of the Bloch wave number. These results show that it is possible to engineer the band structure of magnonic crystals consisting of bi-layered, L-shaped, NWs by a careful control of the overlayer thickness.

  9. Propagation of the Ultra-Short Laser Pulses Through the Helical 1D Photonic Crystal Structure with Twist Defect

    NASA Astrophysics Data System (ADS)

    Antonov, Dmitrii V.; Iegorov, Roman

    2016-02-01

    The presence of the photonic band-gap is a featured property of the cholesteric liquid crystals (CLC). It can be practically realized for almost any reasonable wavelengths with very high degree of tunability. We have investigated theoretically the influence of the twist defect of the CLC helical structure onto the bandwidth-limited ultra-short laser pulse propagating inside the photonic band-gap. The changes of both pulse duration and peak power with defect angle were observed together with pulse acceleration and retardation for a case of normal incidence of the light.

  10. A Comparison of Long-Period SKS Datasets And What They Reveal About 1D Outer Core Structure

    NASA Astrophysics Data System (ADS)

    Houser, C. T.; Ritsema, J. E.; Grand, S.

    2010-12-01

    Seismology is the most direct tool for documenting the presences or absence of outer core stratification. The outermost core is most effectively sampled by SKS, S2KS, S3KS, S4KS, etc.) which have bottoming depths at the top of the outermost core. In order to incorporate modern data sets (e.g., USArray, Europe, China, etc), we need to sift through massive amounts of seismic data to identify the smaller portion of quality signals in a time-efficient manner. We evaluate the application of a cluster analysis technique (Houser et al., 2008) toward identifying and evaluating the SKS phases that traverse the outer core. Cluster analysis is a semi-automated method for interrogating large datasets by processing all the data for an earthquake while allowing the user to graphically interact with the data to remove low quality records. The Houser et al. (2008) cluster analysis method has already been applied to diffracted S waves (Manners et al., 2004), and here we will expand the cluster analysis to the radial component core phases. These newly measured SKS arrival times will be compared with SKS arrival time measurements used in previous mantle tomographic models, namely, S20RTS (Ritsema and van Heist, 2002) using a purely automated method and TXBW (Grand, 2002) using a purely manual method. We find that the arrival times collected by the three methods (automated, clustered, and manual) during overlapping time frames are in agreement within the measurement error bars. Therefore, the SKS data from these studies can be combined to constrain the radial structure of the outermost core. Thus, cluster analysis is an ideal tool for developing a large compilation of SKS arrival times from modern global seismic data, while simultaneously providing a measure of data quality.

  11. Study of the electronic structure of short chain oligothiophenes

    NASA Astrophysics Data System (ADS)

    Grazioli, C.; Baseggio, O.; Stener, M.; Fronzoni, G.; de Simone, M.; Coreno, M.; Guarnaccio, A.; Santagata, A.; D'Auria, M.

    2017-02-01

    The electronic structure of short-chain thiophenes (thiophene, 2,2'-bithiophene, and 2,2':5',2″-terthiophene) in the gas phase has been investigated by combining the outcomes of Near-Edge X-ray-Absorption Fine-Structure (NEXAFS) and X-ray Photoemission Spectroscopy (XPS) at the C K-edge with those of density functional theory (DFT) calculations. The calculated NEXAFS spectra provide a comprehensive description of the main experimental features and allow their attribution. The evolution of the C1s NEXAFS spectral features is analyzed as a function of the number of thiophene rings; a tendency to stabilization for increasing chain length is found. The computation of the binding energy allows to assign the experimental XPS peaks to the different carbon sites on the basis of both the inductive effects generated by the presence of the S atom as well as of the differential aromaticity effects.

  12. Assembly of 1D, 2D and 3D lanthanum(iii) coordination polymers with perchlorinated benzenedicarboxylates: positional isomeric effect, structural transformation and ring-opening polymerisation of glycolide.

    PubMed

    Chen, Sheng-Chun; Dai, An-Qi; Huang, Kun-Lin; Zhang, Zhi-Hui; Cui, Ai-Jun; He, Ming-Yang; Chen, Qun

    2016-02-28

    Utilizing a series of positional isomers of tetrachlorinated benzenedicarboxylic acid ligands, seven La(iii)-based coordination polymers were solvothermally synthesized and structurally characterized. Their structural dimensionalities varying from 1D double chains, to the 2D 3,4,5-connected network, to 3D 6-connected pcu topological nets are only governed by the positions of carboxyl groups on the tetrachlorinated benzene ring. A comprehensive analysis and comparison reveals that the size of the carbonyl solvent molecules (DMF, DEF, DMA, and NMP) can affect the coordination geometries around the La(iii) ions, the coordination modes of carboxylate groups, the packing arrangements, and the void volumes of the overall crystal lattices. One as-synthesized framework further shows an unprecedented structural transformation from a 3D 6-connected network to a 3D 4,5-connected net through the dissolution and reformation pathway in water, suggesting that these easily hydrolyzed lanthanide complexes may serve as precursors to produce new high-dimensional frameworks. The bulk solvent-free melt polymerisation of glycolide utilizing these La(iii) complexes as initiators has been reported herein for the first time. All complexes were found to promote the polymerization of glycolide over a temperature range of 200 to 220 °C, producing poly(glycolic acid) (PGA) with a molecular weight up to 93,280. Under the same experimental conditions, the different catalytic activities for these complexes may result from their structural discrepancy.

  13. Tertiary structure of human {Lambda}6 light chains.

    SciTech Connect

    Pokkuluri, P. R.; Solomon, A.; Weiss, D. T.; Stevens, F. J.; Schiffer, M.; Center for Mechanistic Biology and Biotechnology; Univ. of Tennessee Medical Center /Graduate School of Medicine

    1999-01-01

    AL amyloidosis is a disease process characterized by the pathologic deposition of monoclonal light chains in tissue. To date, only limited information has been obtained on the molecular features that render such light chains amyloidogenic. Although protein products of the major human V kappa and V lambda gene families have been identified in AL deposits, one particular subgroup--lambda 6--has been found to be preferentially associated with this disease. Notably, the variable region of lambda 6 proteins (V lambda 6) has distinctive primary structural features including the presence in the third framework region (FR3) of two additional amino acid residues that distinguish members of this subgroup from other types of light chains. However, the structural consequences of these alterations have not been elucidated. To determine if lambda 6 proteins possess unique tertiary structural features, as compared to light chains of other V lambda subgroups, we have obtained x-ray diffraction data on crystals prepared from two recombinant V lambda 6 molecules. These components, isolated from a bacterial expression system, were generated from lambda 6-related cDNAs cloned from bone marrow-derived plasma cells from a patient (Wil) who had documented AL amyloidosis and another (Jto) with multiple myeloma and tubular cast nephropathy, but no evident fibrillar deposits. The x-ray crystallographic analyses revealed that the two-residue insertion located between positions 68 and 69 (not between 66 and 67 as previously surmised) extended an existing loop region that effectively increased the surface area adjacent to the first complementarity determining region (CDR1). Further, an unusual interaction between the Arg 25 and Phe 2 residues commonly found in lambda 6 molecules was noted. However, the structures of V lambda 6 Wil and Jto also differed from each other, as evidenced by the presence in the latter of certain ionic and hydrophobic interactions that we posit increased protein

  14. Structure and Phase Transitions of Alkylammonium Chains on Mica

    NASA Astrophysics Data System (ADS)

    Heinz, Hendrik; Suter, Ulrich W.

    2004-03-01

    The properties of organically modified silicate minerals determine essentially the properties of polymer-clay nanocomposites. We investigate mica sheets with octadecyltrimethylammonium (C_18) ions or dioctadecyldimethylammonium (2C_18) ions, respectively, with periodicity in the xy plane by NVT molecular dynamics simulation at different temperatures (100 % alkali exchange). With increasing temperature, we find rearrangements of C_18 ions on the mica surface (not for 2C_18 ions due to geometric restraints), compute basal-plane spacings, tilt angles and gauche-trans ratios in the alkyl chains, as well as density and pressure profiles [1, 2]. Agreement with available experimental data is very good (AFM, DSC, IR, NMR, XRD) and we explain the phase transitions of the systems on heating. We also investigate shorter chains down to 2C_12 with only 80 % alkali exchange. Using a relation between basal-plane spacing and surface structure (alkylammonium-islands vs homogeneous mixtures with alkali ions), we discuss the preferred self-assembly pattern on the mica surface as a function of surface saturation with alkyl chains and the chain length [3]. [1] H. Heinz, H.-J. Castelijns, U. W. Suter, J. Am. Chem. Soc. 125, 9500 (2003). [2] H. Heinz, W. Paul, U. W. Suter, K. Binder, J. Chem. Phys., in press. [3] H. Heinz, U. W. Suter, Angew. Chem. Int. Ed., accepted for publication.

  15. Crystal Structure of Human Liver [delta][superscript 4]-3-Ketosteroid 5[beta]-Reductase (AKR1D1) and Implications for Substrate Binding and Catalysis

    SciTech Connect

    Di Costanzo, Luigi; Drury, Jason E.; Penning, Trevor M.; Christianson, David W.

    2008-07-15

    AKR1D1 (steroid 5{beta}-reductase) reduces all {Delta}{sup 4}-3-ketosteroids to form 5{beta}-dihydrosteroids, a first step in the clearance of steroid hormones and an essential step in the synthesis of all bile acids. The reduction of the carbon-carbon double bond in an {alpha}{beta}-unsaturated ketone by 5{beta}-reductase is a unique reaction in steroid enzymology because hydride transfer from NADPH to the {beta}-face of a {Delta}{sup 4}-3-ketosteroid yields a cis-A/B-ring configuration with an {approx}90{sup o} bend in steroid structure. Here, we report the first x-ray crystal structure of a mammalian steroid hormone carbon-carbon double bond reductase, human {Delta}{sup 4}-3-ketosteroid 5{beta}-reductase (AKR1D1), and its complexes with intact substrates. We have determined the structures of AKR1D1 complexes with NADP{sup +} at 1.79- and 1.35-{angstrom} resolution (HEPES bound in the active site), NADP{sup +} and cortisone at 1.90-{angstrom} resolution, NADP{sup +} and progesterone at 2.03-{angstrom} resolution, and NADP{sup +} and testosterone at 1.62-{angstrom} resolution. Complexes with cortisone and progesterone reveal productive substrate binding orientations based on the proximity of each steroid carbon-carbon double bond to the re-face of the nicotinamide ring of NADP{sup +}. This orientation would permit 4-pro-(R)-hydride transfer from NADPH. Each steroid carbonyl accepts hydrogen bonds from catalytic residues Tyr{sup 58} and Glu{sup 120}. The Y58F and E120A mutants are devoid of activity, supporting a role for this dyad in the catalytic mechanism. Intriguingly, testosterone binds nonproductively, thereby rationalizing the substrate inhibition observed with this particular steroid. The locations of disease-linked mutations thought to be responsible for bile acid deficiency are also revealed.

  16. Simple synthesis of PbSe nanocrystals and their self-assembly into 2D ‘flakes’ and 1D ‘ribbons’ structures

    SciTech Connect

    Díaz-Torres, E.; Ortega-López, M.; Matsumoto, Y.; Santoyo-Salazar, J.

    2016-08-15

    Highlights: • PbSe is obtained in a simple way by the co-precipitation method at low-temperature. • The structural, morphological and optical properties of PbSe were studied. • Adding NH{sub 4}OH to the precursor solutions influences on the morphology. • 2D- and 1D-PbSe structures assemble by oriented attachment. • PbSe can be a potential candidate for thermoelectric applications. - Abstract: This work presents a simple and low-temperature method to prepare a variety of Lead selenide (PbSe) nanostructures, using aqueous solutions of Pb(NO{sub 3}){sub 2} and NaHSe. Nanostructures with different morphology were obtained by varying the Pb:Se molar ratio, as well as the mixing sequence of NH{sub 4}OH with either Pb(NO{sub 3}){sub 2} or NaHSe. Nanoparticles with different shapes (spherical and octahedral), and self-assembled structures (flakes and ribbons) were observed by Transmission Electron Microscopy. X-ray results confirmed that the PbSe rock-salt crystalline structure was obtained for all of the prepared samples. The crystal size is in the order of 7.3 to 8.9 nm for single nanocrystals. The absorption spectra of the samples show exciton absorption bands at 1395 nm and 1660 nm. This material could be used to develop more advanced structures for thermoelectric generators.

  17. Structure of electrorheological fluids: a dielectric study of chain formation.

    PubMed

    Horváth, B; Szalai, I

    2012-12-01

    A dielectric measurement method has been proposed to apply to the study of the microstructure of electrorheological (ER) fluids. To test our measurement method the dielectric permittivity increment caused by pair and chain formation was measured in dilute Brownian ER fluids composed of silicone oil and nanosized silica particles. The critical values of the electric field required to induce structure formation were experimentally determined from the electric field dependence of the measured permittivity increment. From the electric field induced time evolution of the relative permittivity of ER fluids, the characteristic times of the pair and chain formation were calculated. Our experimental results for the time constants are in good agreement with the corresponding theoretical data obtained from the Eyring theory.

  18. Structural Transition in Atomic Chains Driven by Transient Doping

    NASA Astrophysics Data System (ADS)

    Polei, S.; Snijders, P. C.; Erwin, S. C.; Himpsel, F. J.; Meiwes-Broer, K.-H.; Barke, I.

    2013-10-01

    A reversible structural transition is observed on Si(553)-Au by scanning tunneling microscopy, triggered by electrons injected from the tip into the surface. The periodicity of atomic chains near the step edges changes from the 1×3 ground state to a 1×2 excited state with increasing tunneling current. The threshold current for this transition is reduced at lower temperatures. In conjunction with first-principles density-functional calculations it is shown that the 1×2 phase is created by temporary doping of the atom chains. Random telegraph fluctuations between two levels of the tunneling current provide direct access to the dynamics of the phase transition, revealing lifetimes in the millisecond range.

  19. Structural, Electronic, and Mechanical Properties of Chains of Silicon Clusters with Trigonal Bipiramidal Structures

    NASA Astrophysics Data System (ADS)

    Tchernatinsky, Alex; Jayanthi, C. S.; Wu, S. Y.

    2002-03-01

    We report here our investigation of structural, electronic, and mechanical properties of non-trivial silicon chains. These chains are built from elementary blocks of clusters of 5 and 8 silicon atoms, arranged into trigonal bipiramidal structures and periodically continued along the axial direction. The initial configurations are constructed such that there are no dangling bonds associated with any atom along the chains. The stable configurations of the chains are determined by molecular dynamics simulations based on the first-principles method of Sankey and Niklewski [1] using the self-consistency scheme given in Ref. [2]. Mechanical and electronic properties of the resulting stable chains will be presented. 1. O.F.Sankey, and D.J.Niklewski, Phys. Rev. B 40 3979(1989). 2. P.Ordejon, E.Artacho, and J.M.Soler, Phys.Rev. B 53,10441 (1996).

  20. Spontaneous nucleation of structural defects in inhomogeneous ion chains

    NASA Astrophysics Data System (ADS)

    De Chiara, Gabriele; del Campo, Adolfo; Morigi, Giovanna; Plenio, Martin B.; Retzker, Alex

    2010-11-01

    Structural defects in ion crystals can be formed during a linear quench of the transverse trapping frequency across the mechanical instability from a linear chain to a zigzag structure. The density of defects after the sweep can be conveniently described by the Kibble-Zurek mechanism (KZM). In particular, the number of kinks in the zigzag ordering can be derived from a time-dependent Ginzburg-Landau equation for the order parameter, here the zigzag transverse size, under the assumption that the ions are continuously laser cooled. In a linear Paul trap, the transition becomes inhomogeneous, since the charge density is larger in the center and more rarefied at the edges. During the linear quench, the mechanical instability is first crossed in the center of the chain, and a front, at which the mechanical instability is crossed during the quench, is identified that propagates along the chain from the center to the edges. If the velocity of this front is smaller than the sound velocity, the dynamics become adiabatic even in the thermodynamic limit and no defect is produced. Otherwise, the nucleation of kinks is reduced with respect to the case in which the charges are homogeneously distributed, leading to a new scaling of the density of kinks with the quenching rate. The analytical predictions are verified numerically by integrating the Langevin equations of motion of the ions, in the presence of a time-dependent transverse confinement. We argue that the non-equilibrium dynamics of an ion chain in a Paul trap constitutes an ideal scenario to test the inhomogeneous extension of the KZM, which lacks experimental evidence to date.

  1. Mononuclear, dinuclear and 1-D polymeric complexes of Cd(II) of a pyridyl pyrazole ligand: Syntheses, crystal structures and photoluminescence studies

    NASA Astrophysics Data System (ADS)

    Das, Kinsuk; Konar, Saugata; Jana, Atanu; Barik, Anil Kumar; Roy, Sangita; Kar, Susanta Kumar

    2013-03-01

    The syntheses, crystal structures and photoluminescence properties of four new Cd(II) complexes are reported using strongly coordinating ligand 3,5-dimethyl-1-(2'-pyridyl) pyrazole (L) in presence of anionic ancillary bridging ligands as nitrite, chloride and dicyanamide. Among the complexes two (1 and 2) are monomeric, 3 is μ2 - chloro bridged dimer and the last one (4) is a mixed alternate chloro - end to end (EE) dicyanamide bridged 1D polymer. All the four complexes have been X-ray crystallographically characterized. The ligand L behaves as a potent bidentate neutral N, N donor. Geometrical diversity of Cd(II) complexes is due to no loss or gain of crystal field stability with the variation of geometry. Consequently the stability of a structure depends on steric requirements. The ligand L shows considerable fluorescence and all four complexes in methanol exhibit interesting photoluminescence properties with different emission intensities. The band maxima and fluorescence efficiency (in methanol) are found to be dependent on the coordination chromophore and structural rigidity induced by the incorporated Cd(II) ion. Among the synthesized complexes 1 exhibits the highest fluorescence intensity in methanol.

  2. K2Ca4[(UO2)(Si2O7)2]: A Uranyl Silicate with a One-Dimensional Chain Structure.

    PubMed

    Liu, Chia-Lin; Liu, Hsin-Kuan; Chang, Wen-Jung; Lii, Kwang-Hwa

    2015-09-08

    A new uranyl silicate, K2Ca4[(UO2)(Si2O7)2], with a 1D chain structure has been synthesized from a solution of mixed alkali- and alkaline-earth-metal cations under hydrothermal conditions at 550 °C and 1400 bar and characterized by single-crystal X-ray diffraction and photoluminescence spectroscopy. It crystallizes in the triclinic space group P1̅ (No. 2) with a = 6.6354(2) Å, b = 6.6791(2) Å, c = 9.6987(3) Å, α = 98.324(2)°, β = 93.624(2)°, γ = 112.310(2)°, and Z = 1. Its crystal structure consists of a 1D chain of uranyl disilicate formed of corner-sharing UO6 tetragonal bipyramids and Si2O7 double groups. The adjacent chains are separated by K(+) and Ca(2+) cations. It is the first example of uranyl silicate with a 1D chain structure.

  3. Mechanically interlocked daisy-chain-like structures as multidimensional molecular muscles

    NASA Astrophysics Data System (ADS)

    Chang, Jia-Cheng; Tseng, Shin-Han; Lai, Chien-Chen; Liu, Yi-Hung; Peng, Shie-Ming; Chiu, Sheng-Hsien

    2016-09-01

    Daisy chains (DCs) are garlands of flowers that can be worn as bracelets and necklaces. As a result of their beautiful interlocked structures and possible muscle-like motions, cyclic molecular DCs ([cn]DCs, where n is the number of repeating units) have long been attractive synthetic targets for supramolecular chemists. Herein we report artificial molecular muscles that—unlike one-dimensional (1D) biological muscles—contract and stretch in 2D or 3D. These systems have the structures of [c3]- and [c4]DCs with subcomponents that operate as molecular switches, powered through the addition or removal of Zn2+ ions to impart muscle-like behaviour. We assembled these [c3]- and [c4]DCs selectively by exploiting structural rigidity, coordination geometries and bond rotational barriers that disfavoured the formation of smaller homologues. The switching phenomena of our [c3]- and [c4]DCs resulted in the contracted molecular muscles stretching by approximately 23 and 36%, respectively, comparable to the value (27%) for linear biological muscles.

  4. MR Elastography Studies of the 3D Force Chain Structure in Dense Granular Media: Distribution of Chain Lengths

    NASA Astrophysics Data System (ADS)

    Sanfratello, L.; Fukushima, E.

    2009-06-01

    We recently developed a novel extension of MR Elastograpy (MRE) to image the force chain structure within a dense 3D quasi-static granular assembly. Subsequently, computer codes and algorithms to determine the distribution of the force chain lengths, where a chain is taken to be a relatively straight section between branching points, were developed. Similar tools were used previously to analyze 2D photoelastic data and now have been expanded to analyze our most current 3D MRE force chain data. These investigations reveal that the distribution of the chain lengths in 3D decays exponentially, as was observed in 2D. The exponential decay of the length distribution is consistent with DEM simulation results of Peters, et al. We conclude that the decay length of this distribution is a meaningful quantitative measure that characterizes granular assemblies.

  5. Correlation Between Chain Architecture and Hydration Water Structure in Polysaccharides

    NASA Astrophysics Data System (ADS)

    Grossutti, Michael; Dutcher, John

    The physical properties of confined water can differ dramatically from those of bulk water. Hydration water associated with polysaccharides provides a particularly important example of confined water, with differences in polysaccharide structure providing different spatially confined environments for water adsorption. We have used attenuated total reflection infrared (ATR-IR) spectroscopy to investigate the structure of hydration water in films of three different polysaccharides under controlled relative humidity (RH) conditions. We compare the results obtained for films of highly branched, monodisperse phytoglycogen nanoparticles to those obtained for two unbranched polysaccharides, hyaluronic acid (HA) and chitosan. We find similarities between water structuring in the two linear polysaccharides, and significant differences for phytoglycogen. In particular, the phytoglycogen nanoparticles exhibited high network water connectivity, and a large increase in the fraction of multimer water clusters with increasing RH, whereas the water structure for HA and chitosan was found to be insensitive to changes in RH. These measurements provide unique insight into the relationship between the chain architecture and hydration of polysaccharides.

  6. A pure inorganic 1D chain based on {Mo8O28} clusters and Mn(II) ions: [Mn(H2O)2Mo8O28 ] n 6 n -

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaofen; Yan, Yonghong; Wu, Lizhou; Yu, Chengxin; Dong, Xinbo; Hu, Huaiming; Xue, Ganglin

    2016-01-01

    A new pure inorganic polymer, (NH4)6n[Mn(H2O)2Mo8O28)]n(H2O)2n(1), has been synthesized and characterized by elemental analyses, IR spectrum, UV-vis absorption spectra, TG-DSC and electrochemical studies. In 1, [Mo8O28]8- anions act as tetradentate ligands and are alternately linked by Mn(H2O)2 2 + ions into a one-dimensional chain structure. It is interesting that 1 represents the first example of pure inorganic-inorganic hybrid based on octamolybdate and transition metal ions. Moreover, it was indicated that 1 had definite catalytic activities on the probe reaction of benzyl alcohol oxidation to benzaldehyde with H2O2.

  7. Structure and Dynamics of Asymmetric Poly(styrene-b-1,4-isoprene) Diblock Copolymer under 1D and 2D Nanoconfinement.

    PubMed

    Kipnusu, Wycliffe K; Elmahdy, Mahdy M; Mapesa, Emmanuel U; Zhang, Jianqi; Böhlmann, Winfried; Smilgies, Detlef-M; Papadakis, Christine M; Kremer, Friedrich

    2015-06-17

    The impact of 1- and 2-dimensional (2D) confinement on the structure and dynamics of poly(styrene-b-1,4-isoprene) P(S-b-I) diblock copolymer is investigated by a combination of Scanning Electron Microscopy (SEM), Atomic Force Microscopy (AFM), Grazing-Incidence Small-Angle X-ray Scattering (GISAXS), and Broadband Dielectric Spectroscopy (BDS). 1D confinement is achieved by spin coating the P(S-b-I) to form nanometric thin films on silicon substrates, while in the 2D confinement, the copolymer is infiltrated into cylindrical anodized aluminum oxide (AAO) nanopores. After dissolving the AAO matrix having mean pore diameter of 150 nm, the SEM images of the exposed P(S-b-I) show straight nanorods. For the thin films, GISAXS and AFM reveal hexagonally packed cylinders of PS in a PI matrix. Three dielectrically active relaxation modes assigned to the two segmental modes of the styrene and isoprene blocks and the normal mode of the latter are studied selectively by BDS. The dynamic glass transition, related to the segmental modes of the styrene and isoprene blocks, is independent of the dimensionality and the finite sizes (down to 18 nm) of confinement, but the normal mode is influenced by both factors with 2D geometrical constraints exerting greater impact. This reflects the considerable difference in the length scales on which the two kinds of fluctuations take place.

  8. Forest-atmosphere BVOC exchange in diverse and structurally complex canopies: 1-D modeling of a mid-successional forest in northern Michigan

    NASA Astrophysics Data System (ADS)

    Bryan, Alexander M.; Cheng, Susan J.; Ashworth, Kirsti; Guenther, Alex B.; Hardiman, Brady S.; Bohrer, Gil; Steiner, Allison L.

    2015-11-01

    Foliar emissions of biogenic volatile organic compounds (BVOC)-important precursors of tropospheric ozone and secondary organic aerosols-vary widely by vegetation type. Modeling studies to date typically represent the canopy as a single dominant tree type or a blend of tree types, yet many forests are diverse with trees of varying height. To assess the sensitivity of biogenic emissions to tree height variation, we compare two 1-D canopy model simulations in which BVOC emission potentials are homogeneous or heterogeneous with canopy depth. The heterogeneous canopy emulates the mid-successional forest at the University of Michigan Biological Station (UMBS). In this case, high-isoprene-emitting foliage (e.g., aspen and oak) is constrained to the upper canopy, where higher sunlight availability increases the light-dependent isoprene emission, leading to 34% more isoprene and its oxidation products as compared to the homogeneous simulation. Isoprene declines from aspen mortality are 10% larger when heterogeneity is considered. Overall, our results highlight the importance of adequately representing complexities of forest canopy structure when simulating light-dependent BVOC emissions and chemistry.

  9. Forest-atmosphere BVOC exchange in diverse and structurally complex canopies: 1-D modeling of a mid-successional forest in northern Michigan

    SciTech Connect

    Bryan, Alexander M.; Cheng, Susan J.; Ashworth, Kirsti; Guenther, Alex B.; Hardiman, Brady; Bohrer, Gil; Steiner, A. L.

    2015-11-01

    Foliar emissions of biogenic volatile organic compounds (BVOC)dimportant precursors of tropospheric ozone and secondary organic aerosolsdvary widely by vegetation type. Modeling studies to date typi-cally represent the canopy as a single dominant tree type or a blend of tree types, yet many forests are diverse with trees of varying height. To assess the sensitivity of biogenic emissions to tree height vari-ation, we compare two 1-D canopy model simulations in which BVOC emission potentials are homo-geneous or heterogeneous with canopy depth. The heterogeneous canopy emulates the mid-successional forest at the University of Michigan Biological Station (UMBS). In this case, high-isoprene-emitting fo-liage (e.g., aspen and oak) is constrained to the upper canopy, where higher sunlight availability increases the light-dependent isoprene emission, leading to 34% more isoprene and its oxidation products as compared to the homogeneous simulation. Isoprene declines from aspen mortality are 10% larger when heterogeneity is considered. Overall, our results highlight the importance of adequately representing complexities of forest canopy structure when simulating light-dependent BVOC emissions and chemistry.

  10. Beta 1D integrin displaces the beta 1A isoform in striated muscles: localization at junctional structures and signaling potential in nonmuscle cells.

    PubMed

    Belkin, A M; Zhidkova, N I; Balzac, F; Altruda, F; Tomatis, D; Maier, A; Tarone, G; Koteliansky, V E; Burridge, K

    1996-01-01

    The cytoplasmic domains of integrins provide attachment of these extracellular matrix receptors to the cytoskeleton and play a critical role in integrin-mediated signal transduction. In this report we describe the identification, expression, localization, and initial functional characterization of a novel form of beta 1 integrin, termed beta 1D. This isoform contains a unique alternatively spliced cytoplasmic domain of 50 amino acids, with the last 24 amino acids encoded by an additional exon. Of these 24 amino acids, 11 are conserved when compared to the beta 1A isoform, but 13 are unique (Zhidkova, N. I., A. M. Belkin, and R. Mayne. 1995. Biochem. Biophys. Res. Commun. 214:279-285; van der Flier, A., I. Kuikman, C. Baudoin, R, van der Neuf, and A. Sonnenberg. 1995. FEBS Lett. 369:340-344). Using an anti-peptide antibody against the beta 1D integrin subunit, we demonstrated that the beta 1D isoform is synthesized only in skeletal and cardiac muscles, while very low amounts of beta 1A were detected by immunoblot in striated muscles. Whereas beta 1A could not be detected in adult skeletal muscle fibers and cardiomyocytes by immunofluorescence, beta 1D was localized to the sarcolemma of both cell types. In skeletal muscle, beta 1D was concentrated in costameres, myotendinous, and neuromuscular junctions. In cardiac muscle this beta 1 isoform was found in costamers and intercalated discs. beta 1D was associated with alpha 7A and alpha 7B in adult skeletal muscle. In cardiomyocytes of adult heart, alpha 7B was the major partner for the beta 1D isoform. beta 1D could not be detected in proliferating C2C12 myoblasts, but it appeared immediately after myoblast fusion and its amount continued to rise during myotube growth and maturation. In contrast, expression of the beta 1A isoform was downregulated during myodifferentiation in culture and it was completely displaced by beta 1D in mature differentiated myotubes. We also analyzed some functional properties of the beta 1D

  11. Chaining sequence/structure seeds for computing RNA similarity.

    PubMed

    Bourgeade, Laetitia; Chauve, Cédric; Allali, Julien

    2015-03-01

    We describe a new method to compare a query RNA with a static set of target RNAs. Our method is based on (i) a static indexing of the sequence/structure seeds of the target RNAs; (ii) searching the target RNAs by detecting seeds of the query present in the target, chaining these seeds in promising candidate homologs; and then (iii) completing the alignment using an anchor-based exact alignment algorithm. We apply our method on the benchmark Bralibase2.1 and compare its accuracy and efficiency with the exact method LocARNA and its recent seeds-based speed-up ExpLoc-P. Our pipeline RNA-unchained greatly improves computation time of LocARNA and is comparable to the one of ExpLoc-P, while improving the overall accuracy of the final alignments.

  12. 1-D "Platinum Wire" Stacking Structure Built of Platinum(II) Diimine Bis(σ-acetylide) Units with Luminescence in the NIR Region.

    PubMed

    Kang, Jiajia; Zhang, Xiaoxin; Zhou, Huajun; Gai, Xuqiao; Jia, Ting; Xu, Liang; Zhang, Jianjun; Li, Yanqin; Ni, Jun

    2016-10-17

    A square-planar platinum(II) complex, Pt(DiBrbpy)(C≡CC6H4Et-4)2 (1) (DiBrbpy = 4,4-dibromo-2,2'-bipyridine), and crystals of its three solvated forms, namely, 1·DMSO, 1·1/2(CH3CN), and 1·1/8(CH2Cl2), were developed and characterized. 1·DMSO and 1·1/2(CH3CN) contain quasi-dimeric and dimeric structures with luminescence in the visible range, whereas 1·1/8(CH2Cl2) exhibits NIR luminescence at 1022 nm due to its intrinsic 1-D "platinum wire" stacking structure with strong Pt-Pt interactions. 1·1/8(CH2Cl2) represents the first compound based on platinum(II) diimine bis(σ-acetylide) molecular units with the NIR luminescence beyond 1000 nm. 1 selectively responds to DMSO and CH3CN by changing its color and luminescence property and the three solvated forms can be reversibly converted to each other upon exposure to corresponding solvent vapors. Their desolvated forms, namely 1a, 1b, and 1c, obtained after heating 1·DMSO, 1·1/2(CH3CN), and 1·1/8(CH2Cl2), respectively, can also be restored to the original solvated forms upon exposure to corresponding solvent vapors. 1a and 1b emit NIR luminescence peaked at 998 and 1018 nm respectively, suggesting indirect synthetic methods as powerful alternatives to achieve NIR luminescence with long wavelength. In contrast, 1c exhibits a red luminescence with a broad unstructured emission band centered at 667 nm. All the responses to organic solvent vapors and heating are due to the structural transformations which result in the conversion of the lowest energy excited states between (3)MLCT/(3)LLCT and (3)MMLCT in solid-state as supported by time-dependent density functional theory (TD-DFT) calculations.

  13. Electronic, bonding, and optical properties of 1d [CuCN]n (n = 1-10) chains, 2d [CuCN]n (n = 2-10) nanorings, and 3d [Cun (CN)n ]m (n = 4, m = 2, 3; n = 10, m = 2) tubes studied by DFT/TD-DFT methods.

    PubMed

    Tsipis, Athanassios C; Stalikas, Alexandros V

    2015-06-30

    The electronic, bonding, and photophysical properties of one-dimensional [CuCN](n) (n = 1-10) chains, 2-D [CuCN](n) (n = 2-10) nanorings, and 3-D [Cu(n)(CN)(n)](m) (n = 4, m = 2, 3; n = 10, m = 2) tubes are investigated by means of a multitude of computational methodologies using density functional theory (DFT) and time-dependent-density-functional theory (TD-DFT) methods. The calculations revealed that the 2-D [CuCN](n) (n = 2-10) nanorings are more stable than the respective 1-D [CuCN](n) (n = 2-10) linear chains. The 2-D [CuCN](n) (n = 2-10) nanorings are predicted to form 3-D [Cun (CN)(n)](m) (n = 4, m = 2, 3; n = 10, m = 2) tubes supported by weak stacking interactions, which are clearly visualized as broad regions in real space by the 3D plots of the reduced density gradient. The bonding mechanism in the 1-D [CuCN](n) (n = 1-10) chains, 2-D [CuCN](n) (n = 2-10) nanorings, and 3-D [Cu(n)(CN)(n)](m) (n = 4, m = 2, 3; n = 10, m = 2) tubes are easily recognized by a multitude of electronic structure calculation approaches. Particular emphasis was given on the photophysical properties (absorption and emission spectra) of the [CuCN](n) chains, nanorings, and tubes which were simulated by TD-DFT calculations. The absorption and emission bands in the simulated TD-DFT absorption and emission spectra have thoroughly been analyzed and assignments of the contributing principal electronic transitions associated to individual excitations have been made.

  14. Synthesis, characterization and crystal structure determination of Mn (II) ion based 1D polymer constructed from 2, 2‧ bipyridyl and azide group, its thermal stability, magnetic properties and Hirshfeld surface analysis

    NASA Astrophysics Data System (ADS)

    Mudsainiyan, R. K.; Jassal, Amanpreet Kaur; Chawla, S. K.

    2015-05-01

    The 1-D polymeric complex (I) is having formula [Mn(2,2‧-BP).(N3)2]n, which has been crystallized in distilled water and characterized by elemental analyses, FT-IR spectrum, powder X-ray diffraction analyses and single-crystal diffraction analysis. This polymer possesses 1D helical chains or coils where Mn-azide-Mn forms the base of the coil which is alternatively garlanded by rigid bi-pyridine rings, where coordinates are in anti-fashion. The Mn (II) ions in the repeating units are linked by two end-on azide groups which extend through the two end-to-end azide ligands to the next unit forming a 1-D polymeric chain. The present study suggests that the use of this rigid and neutral building block leads to give better arrangement of the polymeric motif with [010] chains in 2-c uninodal net. During investigation of strong or weak intermolecular interactions, X-ray diffraction analysis and Hirshfeld surface analysis give rise to comparable results but in Hirshfeld surface analysis, two-third times more results of close contacts are obtained. The fingerprint plots demonstrate that these weak non-bonding interactions are important for stabilizing the crystal packing. Magnetic properties of the complex (I) were analyzed on the basis of an alternating ferro- and antiferromagnetic Heisenberg chain of Mn (II) ions. The J-exchange parameters found are J1=64.3 K (45.3 cm-1), and J2=-75.7 K (-53.3 cm-1). Magnetic properties are discussed in comparison with those of other similar molecular magnets of [Mn(L-L)(N3)2]n type.

  15. Low-Dimensional Systems: Structures of Interfaces and Magnetic Chains

    NASA Astrophysics Data System (ADS)

    Shen, Qing

    The solid-solid metal oxide(MO) interface in (100) orientation was modeled and its properties were investigated by molecular Dynamics(MD). MD was used to model temperature dependent geometry in the interface region, using standard interatomic potentials. The lattice structure across the MO-MO interface is found to change continually from one crystal to another. The radial distribution function, average potential energy for each layer, the average interplanar spacing, mean square displacement of the ions and spectrum of the autocorrelation function of velocity were calculated. Results for (100) MgO-CoO and NiO-CoO interfaces are compared with solid-solution and pure-phase data. The solid-solid metal oxide interface of rock -salt structure in (100) orientation was modeled and its properties were investigated by Local Density(LD) theory. Starting with molecular dynamics determined time-average atomic configurations at the interface, self-consistent LD calculations were made to determine electronic structure, spectroscopic and energetic properties of interface atoms. Spectral distributions, bonding mechanisms, charge densities and consequences for the optical band gap were determined. Results are given for (100) MgO-CoO interfaces, rm Mg_{x}Co_{1-x}O alloy and NiO-CoO interface. The magnetic properties of transition-metal based quasi-one dimensional molecular metals show unusual concentration and temperature dependence. Ion magnetization in the one dimensional rm Cu_{1-c}Ni _{c} chain of rm Cu_{1-c}Ni_{c}(pc)I was modeled by Monte Carlo methods, using indirect exchange interaction potentials of variable range. The effects of dilution of Cu spin moments by diamagnetic Ni ions and impurity scattering effects on the electron gas polarization are determined. Results are compared with NMR T-dependent magnetization data for this molecular metal.

  16. Structural changes upon excitation of D1-D2-Cyt b559 photosystem II reaction centers depend on the beta-carotene content.

    PubMed

    Losi, Aba; Yruela, Inmaculada; Reus, Michael; Holzwarth, Alfred R; Braslavsky, Silvia E

    2003-07-01

    Different preparations of D1-D2-Cyt b559 complexes from spinach with different beta-carotene (Car) content [on average from <0.5 to 2 per reaction center (RC)] were studied by means of laser-induced optoacoustic spectroscopy. phiP680(+)Pheo(-) does not depend on the preparation (or on the Car content) inasmuch as the magnitude of the prompt heat (produced within 20 ns) does not vary for the different samples upon excitation at 675 and 620 nm. The energy level of the primary charge-separated state, P680(+)Pheo(-), was determined as EP680(+)Pheo(-) = 1.55 eV. Thus, an enthalpy change accompanying charge separation from excited P680 of deltaH*P680Pheo-->P680(+)Pheo(-) = -0.27 eV is obtained. Calculations using the heat evolved during the time-resolved decay of P680(+)Pheo(-) (< or = 100 ns) affords a triplet (3[P680Pheo]) quantum yield phi3[P680Pheo] = 0.5 +/- 0.14. The structural volume change, deltaV1, corresponding to the formation of P680(+)Pheo(-), strongly depends on the Car content; it is ca. -2.5 A3 molecule(-1) for samples with <0.5 Car on average, decreases (in absolute value) to -0.5 +/- 0.2 A3 for samples with an average of 1 Car, and remains the same for samples with two Cars per RC. This suggests that the Car molecules induce changes in the ground-state RC conformation, an idea which was confirmed by preferential excitation of Car with blue light, which produced different carotene triplet lifetimes in samples with 2 Car compared to those containing less carotene. We conclude that the two beta-carotenes are not structurally equivalent. Upon blue-light excitation (480 nm, preferential carotene absorption) the fraction of energy stored is ca. 60% for the 9Chl-2Car sample, whereas it is 40% for the preparations with one or less Cars on average, indicating different paths of energy distribution after Car excitation in these RCs with remaining chlorophyll antennae.

  17. The structures and properties of the new two-dimensional inorganic–organic hybrid materials based on the molybdate chains

    SciTech Connect

    Li, Na; Mu, Bao; Cao, Xinyu; Huang, Rudan

    2014-09-15

    A series of inorganic organic hybrid materials based on polyoxometalates(POMs), namely, [M{sup II}(HL){sub 2}(H{sub 2}O){sub 2}][Mo{sup VI}{sub 6}O{sub 20}] [M=Co (1), Ni (2), Cu (3), Zn (4)], [Mn{sup IV}L{sub 2}(H{sub 2}O){sub 2}][Mo{sup VI}{sub 6}O{sub 20}] (5), and (HL){sub 3}PMO{sub 12}O{sub 40} (6) [L=3-(4-pyridyl)pyrazole], have been synthesized. The compounds have been characterized by elemental analysis, powder X-ray diffraction (PXRD) and single-crystal X-ray diffraction. The results from single-crystal X-ray diffraction indicate that 1–5 are isostructural. It is worth noting that the polyanions are bridged by Mo–O–Mo to form 1D inorganic chains, which are further connected via M ions to form 2D nets. In compound 6, the ligands are used as the positive ions to balance the charge of the compound. Moreover, the magnetic properties of compound 5 have also been investigated in detail. - Graphical abstract: In complex 1, The Co ion is six coordinated by four oxygen atoms from two Mo{sub 6}O{sub 20} and two water molecules, and two N atoms from two different ligand. It is noticeable that there is an one-dimensional chain molybdate, which is combined by O–Mo–O, then the chain parallel with each other, the Mo{sub 6} anion acts as a bidentate ligand providing O7 atoms to bridge CoII ions to form a 2D inorganic layer. Finally every nets become 3D structure by hydrogen bond. - Highlights: • Novel inorganic–organic hybrid materials have been prepared. • Compounds 1–5 contain the 1D molybdate chains composed of (MoO{sub 6}) octahedra. • The 1D chains parallel with each other to form a 2D inorganic layer.

  18. Structure of self-assembled Mn atom chains on Si(001)

    NASA Astrophysics Data System (ADS)

    Villarreal, Renan; Longobardi, Maria; Koester, Sigrun A.; Kirkham, Christopher J.; Bowler, David; Renner, Christoph

    Mn has been found to self-assemble into atomic chains running perpendicular to the surface dimer reconstruction on Si(001). They differ from other atomic chains by a striking asymmetric appearance in filled state scanning tunneling microscopy (STM) images. This has prompted complicated structural models involving up to three Mn atoms per chain unit. Combining STM, atomic force microscopy and density functional theory we find that a simple necklace-like chain of single Mn atoms reproduces all their prominent features, including their asymmetry not captured by current models. The upshot is a remarkably simpler structure for modelling the electronic and magnetic properties of Mn atom chains on Si(001).

  19. Structure of Self-Assembled Mn Atom Chains on Si(001)

    NASA Astrophysics Data System (ADS)

    Villarreal, R.; Longobardi, M.; Köster, S. A.; Kirkham, Ch. J.; Bowler, D.; Renner, Ch.

    2015-12-01

    Mn has been found to self-assemble into atomic chains running perpendicular to the surface dimer reconstruction on Si(001). They differ from other atomic chains by a striking asymmetric appearance in filled state scanning tunneling microscopy (STM) images. This has prompted complicated structural models involving up to three Mn atoms per chain unit. Combining STM, atomic force microscopy, and density functional theory we find that a simple necklacelike chain of single Mn atoms reproduces all their prominent features, including their asymmetry not captured by current models. The upshot is a remarkably simpler structure for modeling the electronic and magnetic properties of Mn atom chains on Si(001).

  20. First principles calculation of the structural, electronic, and magnetic properties of Au-Pd atomic chains

    SciTech Connect

    Dave, Mudra R.; Sharma, A. C.

    2015-06-24

    The structural, electronic and magnetic properties of free standing Au-Pd bimetallic atomic chain is studied using ab-initio method. It is found that electronic and magnetic properties of chains depend on position of atoms and number of atoms. Spin polarization factor for different atomic configuration of atomic chain is calculated predicting a half metallic behavior. It suggests a total spin polarised transport in these chains.

  1. The role of cellular structure on increasing the detonability limits of three-step chain-branching detonations

    SciTech Connect

    Short, Mark; Kiyanda, Charles B; Quirk, James J; Sharpe, Gary J

    2011-01-27

    In [1], the dynamics of a pulsating three-step chain-branching detonation were studied. The reaction model consists of, sequentially, chain-initiation, chain-branching and chain-termination steps. The chain-initiation and chain-branching steps are taken to be thermally neutral, with chemical energy release occuring in the chain-termination stage. The purpose of the present study is to examine whether cellular detonation structure can increase the value of the chain-branching cross-over temperature T{sub b} at which fully coupled detonation solutions are observed over those in 1 D. The basic concept is straightforward and has been discussed in [1] and [3]; if T{sub s} drops below T{sub b} at the lead shock, the passage of a transverse shock can increase both the lead shock temperature and the temperature behind the transverse wave back above T{sub b}, thus sustaining an unstable cellular detonation for values of T{sub b} for which a one-dimensional pulsating detonation will fail. Experiments potentially supporting this hypothesis with irregular detonations have been shown in [3] in a shock tube with acoustically absorbing walls. Removal of the transverse waves results in detonation failure, giving way to a decoupled shock-flame complex. A number of questions remain to be addressed regarding the possibility of such a mechanism, and, if so, about the precise mechanisms driving the cellular structure for large T{sub b}. For instance, one might ask what sets the cell size in a chain-branching detonation, particularly could the characteristic cell size be set by the chain-branching cross-over temperature T{sub b}: after a transverse wave shock collision, the strength of the transverse wave weakens as it propagates along the front. If the spacing between shock collisions is too large (cell size), then the transverse shocks may weaken to the extent that the lead shock temperature or that behind the transverse waves is not raised above T{sub b}, losing chemical energy to

  2. Singularities of the dynamical structure factors of the spin-1/2 XXX chain at finite magnetic field

    NASA Astrophysics Data System (ADS)

    Carmelo, J. M. P.; Sacramento, P. D.; Machado, J. D. P.; Campbell, D. K.

    2015-10-01

    We study the longitudinal and transverse spin dynamical structure factors of the spin-1/2 XXX chain at finite magnetic field h, focusing in particular on the singularities at excitation energies in the vicinity of the lower thresholds. While the static properties of the model can be studied within a Fermi-liquid like description in terms of pseudoparticles, our derivation of the dynamical properties relies on the introduction of a form of the ‘pseudofermion dynamical theory’ (PDT) of the 1D Hubbard model suitably modified for the spin-only XXX chain and other models with two pseudoparticle Fermi points. Specifically, we derive the exact momentum and spin-density dependences of the exponents {{\\zeta}τ}(k) controlling the singularities for both the longitudinal ≤ft(τ =l\\right) and transverse ≤ft(τ =t\\right) dynamical structure factors for the whole momentum range k\\in ]0,π[ , in the thermodynamic limit. This requires the numerical solution of the integral equations that define the phase shifts in these exponents expressions. We discuss the relation to neutron scattering and suggest new experiments on spin-chain compounds using a carefully oriented crystal to test our predictions.

  3. Singularities of the dynamical structure factors of the spin-1/2 XXX chain at finite magnetic field.

    PubMed

    Carmelo, J M P; Sacramento, P D; Machado, J D P; Campbell, D K

    2015-10-14

    We study the longitudinal and transverse spin dynamical structure factors of the spin-1/2 XXX chain at finite magnetic field h, focusing in particular on the singularities at excitation energies in the vicinity of the lower thresholds. While the static properties of the model can be studied within a Fermi-liquid like description in terms of pseudoparticles, our derivation of the dynamical properties relies on the introduction of a form of the 'pseudofermion dynamical theory' (PDT) of the 1D Hubbard model suitably modified for the spin-only XXX chain and other models with two pseudoparticle Fermi points. Specifically, we derive the exact momentum and spin-density dependences of the exponents ζ(τ)(k) controlling the singularities for both the longitudinal (τ = l) and transverse (τ = t) dynamical structure factors for the whole momentum range k ∈ ]0,π[, in the thermodynamic limit. This requires the numerical solution of the integral equations that define the phase shifts in these exponents expressions. We discuss the relation to neutron scattering and suggest new experiments on spin-chain compounds using a carefully oriented crystal to test our predictions.

  4. Ammonia detection of 1-D ZnO/polypyrrole nanocomposite: Effect of CSA doping and their structural, chemical, thermal and gas sensing behavior

    NASA Astrophysics Data System (ADS)

    Jain, Shilpa; Karmakar, Narayan; Shah, Akshara; Kothari, D. C.; Mishra, Satyendra; Shimpi, Navinchandra G.

    2017-02-01

    Nanocomposites of polypyrrole (PPy) with varying concentration of ZnO nanorods (ZnO NRs) were synthesized using in-situ oxidative polymerization technique. The prepared nanocomposites (PPy, PPy-ZnO and CSA doped PPy-ZnO) were studied for various oxidizing and reducing gases at room temperature and found to be more selective towards ammonia gas. Various concentrations of ZnO NRs in Ppy matrix were studied and 15% was found to be optimum in terms of sensor response (66% towards 120 ppm NH3). Further, with 15% doping of camphor sulphonic acid (CSA) in PPy-ZnO nanocomposite for 15% ZnO NRs in Ppy matrix, sensor response increased from 66 to 79% towards 120 ppm of NH3. Structural, Optical and thermal behavior of nanocomposites were studied using powder X-ray diffraction (XRD), Fourier Transform Infra-Red (FTIR) spectroscopy, X-ray Photoelectron Spectroscopy (XPS), UV-vis (UV-vis) absorption spectroscopy, room temperature Photoluminescence (PL) Spectroscopy, Thermo-gravimetric analysis (TGA) and Field Emission Scanning Electron Microscopy (FESEM). ZnO has been completely embedded inside the polymeric chains as observed from in SEM. Meanwhile, FT-IR spectra indicate better conjugation and interaction in nanocomposites. With CSA doping interaction grows stronger due to extended delocalization over π electrons leading to higher sensor response and with response time and recovery time of 24 s and 34 s respectively. CSA doped PPy-ZnO (15%) nanocomposites observed to be a potential candidate for ammonia detection at lower ppm level.

  5. Synthesis, characterization and crystal structure determination of Mn (II) ion based 1D polymer constructed from 2, 2′ bipyridyl and azide group, its thermal stability, magnetic properties and Hirshfeld surface analysis

    SciTech Connect

    Mudsainiyan, R.K. Jassal, Amanpreet Kaur; Chawla, S.K.

    2015-05-15

    The 1-D polymeric complex (I) is having formula [Mn(2,2′-BP).(N{sub 3}){sub 2}]{sub n}, which has been crystallized in distilled water and characterized by elemental analyses, FT-IR spectrum, powder X-ray diffraction analyses and single-crystal diffraction analysis. This polymer possesses 1D helical chains or coils where Mn–azide–Mn forms the base of the coil which is alternatively garlanded by rigid bi-pyridine rings, where coordinates are in anti-fashion. The Mn (II) ions in the repeating units are linked by two end-on azide groups which extend through the two end-to-end azide ligands to the next unit forming a 1-D polymeric chain. The present study suggests that the use of this rigid and neutral building block leads to give better arrangement of the polymeric motif with [010] chains in 2-c uninodal net. During investigation of strong or weak intermolecular interactions, X-ray diffraction analysis and Hirshfeld surface analysis give rise to comparable results but in Hirshfeld surface analysis, two-third times more results of close contacts are obtained. The fingerprint plots demonstrate that these weak non-bonding interactions are important for stabilizing the crystal packing. Magnetic properties of the complex (I) were analyzed on the basis of an alternating ferro- and antiferromagnetic Heisenberg chain of Mn (II) ions. The J-exchange parameters found are J{sub 1}=64.3 K (45.3 cm{sup −1}), and J{sub 2}=−75.7 K (−53.3 cm{sup −1}). Magnetic properties are discussed in comparison with those of other similar molecular magnets of [Mn(L–L)(N{sub 3}){sub 2}]{sub n} type. - - Highlights: • Synthesized 1-D polymeric complex of Mn (II) ions with 2, 2′ bipyridyl and azide group. • X-ray data of complex (I) is in a good agreement with TGA and other spectroscopic techniques. • DFT calculations were done and compared with the parameter of experimental and theoretical data. • Intermolecular interactions calculated by Hirshfeld surface analysis

  6. Structurally driven magnetic state transition of biatomic Fe chains on Ir(001)

    NASA Astrophysics Data System (ADS)

    Mokrousov, Yuriy; Thiess, Alexander; Heinze, Stefan

    2009-11-01

    Using first-principles calculations, we demonstrate that the magnetic exchange interaction and the magnetocrystalline anisotropy of biatomic Fe chains grown in the trenches of the (5×1) reconstructed Ir(001) surface depend sensitively on the atomic arrangement of the Fe atoms. Two structural configurations have been considered which are suggested from recent experiments. They differ by the local symmetry and the spacing between the two strands of the biatomic Fe chain. Since both configurations are very close in total energy they may coexist in experiment. We have investigated collinear ferro- and antiferromagnetic solutions as well as a collinear state with two moments in one direction and one in the opposite direction ( ↑↓↑ -state). For the structure with a small interchain spacing, there is a strong exchange interaction between the strands and the ferromagnetic state is energetically favorable. In the structure with larger spacing, the two strands are magnetically nearly decoupled and exhibit antiferromagnetic order along the chain. In both cases, due to hybridization with the Ir substrate the exchange interaction along the chain axis is relatively small compared to free-standing biatomic iron chains. The easy magnetization axis of the Fe chains also switches with the structural configuration and is out-of-plane for the ferromagnetic chains with small spacing and along the chain axis for the antiferromagnetic chains with large spacing between the two strands. Calculated scanning tunneling microscopy images and spectra suggest the possibility to experimentally distinguish between the two structural and magnetic configurations.

  7. Synthesis and characterization of 1D iron(II) spin crossover coordination polymers with hysteresis.

    PubMed

    Bauer, Wolfgang; Lochenie, Charles; Weber, Birgit

    2014-02-07

    Purposeful ligand design was used for the synthesis of eight new 1D iron(II) spin crossover coordination polymers aiming for cooperative spin transitions with hysteresis. The results from magnetic measurements and X-ray structure analysis show that the combination of rigid linkers and a hydrogen bond network between the 1D chains is a promising tool to reach this goal. Five of the eight new samples show a cooperative spin transition with hysteresis with up to 43 K wide hysteresis loops.

  8. The study of the structure factor of a wormlike chain in an orientational external field

    NASA Astrophysics Data System (ADS)

    Jiang, Ying; Zhang, Xinghua; Miao, Bing; Yan, Dadong

    2015-04-01

    A precise representation of the structure factor of a wormlike chain for the arbitrary chain flexibility in an orientational external field is obtained by virtue of the numerical solution to the modified diffusion equation satisfied by the Green's function. The model is built from a standard wormlike chain formalism in a continuous version which crossovers from the rigid-rod limit to the flexible chain limit and the Maier-Saupe interaction which describes the orientational effects from the nematic field. The behaviors of the structure factor in the distinct wavevector k regimes are numerically investigated as functions of chain flexibility and tilt angle between the directors of the nematic field and k. The radius of gyration extracted from the structure factor in small-k regime is also carefully analysed in both the directions along and perpendicular to the nematic axis. Our calculations exactly recover the prediction of the structure factor undergoing an orientational field in the rigid rod limit.

  9. Naturally occurring branched-chain polyamines induce a crosslinked meshwork structure in a giant DNA

    NASA Astrophysics Data System (ADS)

    Muramatsu, Akira; Shimizu, Yuta; Yoshikawa, Yuko; Fukuda, Wakao; Umezawa, Naoki; Horai, Yuhei; Higuchi, Tsunehiko; Fujiwara, Shinsuke; Imanaka, Tadayuki; Yoshikawa, Kenichi

    2016-12-01

    We studied the effect of branched-chain polyamines on the folding transition of genome-sized DNA molecules in aqueous solution by the use of single-molecule observation with fluorescence microcopy. Detailed morphological features of polyamine/DNA complexes were characterized by atomic force microscopy (AFM). The AFM observations indicated that branched-chain polyamines tend to induce a characteristic change in the higher-order structure of DNA by forming bridges or crosslinks between the segments of a DNA molecule. In contrast, natural linear-chain polyamines cause a parallel alignment between DNA segments. Circular dichroism measurements revealed that branched-chain polyamines induce the A-form in the secondary structure of DNA, while linear-chain polyamines have only a minimum effect. This large difference in the effects of branched- and linear-chain polyamines is discussed in relation to the difference in the manner of binding of these polyamines to negatively charged double-stranded DNA.

  10. The magnetization curve of spin chains with superlattice structure

    NASA Astrophysics Data System (ADS)

    Silva-Valencia, J.; Franco, R.

    2006-10-01

    The magnetization curve of the spin superlattices composed of repeat pattern of two spin- {1}/{2} XXZ chains with different anisotropy parameters was calculated using density matrix renormalization group. We observe a nontrivial plateau with magnetization value given by the relative sizes of the subchains.

  11. Organizing Defense Logistics: What Strategic Structures Should Exist for the Defense Supply Chain

    DTIC Science & Technology

    2007-11-02

    within the Department of Defense to facilitate further integration of the defense supply chain ? To answer this question, this thesis analyzed...successful strategies from three supply chain paradigms: Academic, Military, and Corporate. A research model was developed to evaluate and compare the three...paradigms according to six criteria. Each criterion represented a strategic structural requirement for an organization integrating its supply chain . Based

  12. Induction of gamma-turn-like structure in ferrocene bearing dipeptide chains via conformational control.

    PubMed

    Moriuchi, Toshiyuki; Nagai, Takayoshi; Hirao, Toshikazu

    2006-01-05

    [structure: see text] A combination of the ferrocene scaffold as a central reverse-turn unit with the dipeptide chains (-L-Pro-L-Ala-NHPy) was demonstrated to induce both inverse gamma-turn-like and antiparallel beta-sheet-like structures. Only the antiparallel beta-sheet-like structure was formed in the ferrocene bearing the heterochiral dipeptide chains (-L-Pro-D-Ala-NHPy), in which highly organized self-assembly was achieved through a network of intermolecular hydrogen bonds.

  13. Amylopectin small chain glucans form structure fingerprint that determines botanical origin of starch.

    PubMed

    Jaiswal, Sarita; Chibbar, Ravindra N

    2017-02-20

    Starch granule size, shape and structure of amylopectin are species specific and influence starch properties and end-use of starch. Amylopectin glucan chain structure was used to predict the starch botanical sources. Mathematical probability for accumulation of small glucan chains DP 6-10 reveal exponential fit curve with maximum R(2) in smallest granule size starches (Chlamydomonas, quinoa, buckwheat). Cereal and cassava showed R(2) of 0.81-0.96 while in pulses and tubers it was less than 0.7. The amylopectin small glucan chains form a unique 'finger print region' that identified starch botanical source. Differential amylopectin chain length distribution (APCLD) graphs between DP 6-80 of all species from Chlamydomonas starch distinguished five structural groups that clustered the 31 analyzed starches into four major patterns. APCLD analyses of amylopectin combined with characteristic pattern of small linear DP (6-9) glucan chains predicted the starch botanical source.

  14. Synthesis and structures of ligand-dominated one-dimensional silver(I)-bis(pyridylmethyl)amine coordination chains

    NASA Astrophysics Data System (ADS)

    Lin, Hung-Jui; Liu, Yu-Chiao; Tseng, Yu-Jui; Wu, Jing-Yun

    2016-10-01

    Reactants slow diffusion of Ag(I) salts with 3,4‧-bis(pyridylmethyl)amine (3,4‧-bpma), an unsymmetric bis-pyridyl ligand equipped with a non-innocent amine backbone, afforded polymeric coordination adducts 1-5 having a general formula {[Ag(3,4‧-bpma)(solv)]X}n (solv = H2O, CH3OH, and none; X= CF3CO2-, BF4-, ClO4-, CF3SO3-, and SbF6-). Single-crystal X-ray diffraction (SCXRD) analyses reveal that colorless crystals of Ag(I) coordination polymers (CPs) 1-5 have very similar one-dimensional (1D) non-flat chain structures, which are preferentially depicted as a "zipper-like" rather than a ladder-like or a double-stranded chain topologies. The 3,4‧-bpma ligand in these Ag(I) CPs displays a μ3-bridging mode with a gauche-trans (1,4, and 5) and a trans-trans (2 and 3) conformations. Noteworthy, anions do not show strong influence on structural modulation of Ag(I) CPs in the solid state, but really affect CP conformations and packing fashions, indicative of a ligand-dominated assembly process for such a Ag(I)-3,4‧-bpma system. Thermal stabilities and solid-state photoluminescence properties of crystalline materials 1-5 were investigated.

  15. Design, synthesis, and functional activity of labeled CD1d glycolipid agonists.

    PubMed

    Jervis, Peter J; Polzella, Paolo; Wojno, Justyna; Jukes, John-Paul; Ghadbane, Hemza; Garcia Diaz, Yoel R; Besra, Gurdyal S; Cerundolo, Vincenzo; Cox, Liam R

    2013-04-17

    Invariant natural killer T cells (iNKT cells) are restricted by CD1d molecules and activated upon CD1d-mediated presentation of glycolipids to T cell receptors (TCRs) located on the surface of the cell. Because the cytokine response profile is governed by the structure of the glycolipid, we sought a method for labeling various glycolipids to study their in vivo behavior. The prototypical CD1d agonist, α-galactosyl ceramide (α-GalCer) 1, instigates a powerful immune response and the generation of a wide range of cytokines when it is presented to iNKT cell TCRs by CD1d molecules. Analysis of crystal structures of the TCR-α-GalCer-CD1d ternary complex identified the α-methylene unit in the fatty acid side chain, and more specifically the pro-S hydrogen at this position, as a site for incorporating a label. We postulated that modifying the glycolipid in this way would exert a minimal impact on the TCR-glycolipid-CD1d ternary complex, allowing the labeled molecule to function as a good mimic for the CD1d agonist under investigation. To test this hypothesis, the synthesis of a biotinylated version of the CD1d agonist threitol ceramide (ThrCer) was targeted. Both diastereoisomers, epimeric at the label tethering site, were prepared, and functional experiments confirmed the importance of substituting the pro-S, and not the pro-R, hydrogen with the label for optimal activity. Significantly, functional experiments revealed that biotinylated ThrCer (S)-10 displayed behavior comparable to that of ThrCer 5 itself and also confirmed that the biotin residue is available for streptavidin and antibiotin antibody recognition. A second CD1d agonist, namely α-GalCer C20:2 4, was modified in a similar way, this time with a fluorescent label. The labeled α-GalCer C20:2 analogue (11) again displayed functional behavior comparable to that of its unlabeled substrate, supporting the notion that the α-methylene unit in the fatty acid amide chain should be a suitable site for attaching

  16. Design, Synthesis, and Functional Activity of Labeled CD1d Glycolipid Agonists

    PubMed Central

    2013-01-01

    Invariant natural killer T cells (iNKT cells) are restricted by CD1d molecules and activated upon CD1d-mediated presentation of glycolipids to T cell receptors (TCRs) located on the surface of the cell. Because the cytokine response profile is governed by the structure of the glycolipid, we sought a method for labeling various glycolipids to study their in vivo behavior. The prototypical CD1d agonist, α-galactosyl ceramide (α-GalCer) 1, instigates a powerful immune response and the generation of a wide range of cytokines when it is presented to iNKT cell TCRs by CD1d molecules. Analysis of crystal structures of the TCR−α-GalCer–CD1d ternary complex identified the α-methylene unit in the fatty acid side chain, and more specifically the pro-S hydrogen at this position, as a site for incorporating a label. We postulated that modifying the glycolipid in this way would exert a minimal impact on the TCR–glycolipid–CD1d ternary complex, allowing the labeled molecule to function as a good mimic for the CD1d agonist under investigation. To test this hypothesis, the synthesis of a biotinylated version of the CD1d agonist threitol ceramide (ThrCer) was targeted. Both diastereoisomers, epimeric at the label tethering site, were prepared, and functional experiments confirmed the importance of substituting the pro-S, and not the pro-R, hydrogen with the label for optimal activity. Significantly, functional experiments revealed that biotinylated ThrCer (S)-10 displayed behavior comparable to that of ThrCer 5 itself and also confirmed that the biotin residue is available for streptavidin and antibiotin antibody recognition. A second CD1d agonist, namely α-GalCer C20:2 4, was modified in a similar way, this time with a fluorescent label. The labeled α-GalCer C20:2 analogue (11) again displayed functional behavior comparable to that of its unlabeled substrate, supporting the notion that the α-methylene unit in the fatty acid amide chain should be a suitable site for

  17. Suspended chains damp wind-induced oscillations of tall flexible structures

    NASA Technical Reports Server (NTRS)

    Reed, W. H., III

    1968-01-01

    Hanging-chain system, which is a form of impact damper, suppresses wind-induced bending oscillations of tall cylindrical antenna masts. A cluster of chains enclosed in a neoprene shroud is suspended inside the tip of the antenna mast, forming a simple method of damping structural vibrations.

  18. Novel 1D coordination polymer {l_brace}Tm(Piv){sub 3{r_brace}n}: Synthesis, structure, magnetic properties and thermal behavior

    SciTech Connect

    Fomina, Irina; Dobrokhotova, Zhanna; Aleksandrov, Grygory; Emelina, Anna; Bykov, Mikhail; Bogomyakov, Artem; Puntus, Lada; Novotortsev, Vladimir; Eremenko, Igor

    2012-01-15

    The new 1D coordination polymer {l_brace}Tm(Piv){sub 3{r_brace}n} (1), where Piv=OOCBu{sup t-}, was synthesized in high yield (>95%) by the reaction of thulium acetate with pivalic acid in air at 100 Degree-Sign S. According to the X-ray diffraction data, the metal atoms in compound 1 are in an octahedral ligand environment unusual for lanthanides. The magnetic and luminescence properties of polymer 1, it's the solid-phase thermal decomposition in air and under argon, and the thermal behavior in the temperature range of -50 Horizontal-Ellipsis +50 Degree-Sign S were investigated. The vaporization process of complex 1 was studied by the Knudsen effusion method combined with mass-spectrometric analysis of the gas-phase composition in the temperature range of 570-680 K. - Graphical Abstract: Novel 1D coordination polymer {l_brace}Tm(Piv){sub 3{r_brace}n} was synthesized and studied by X-ray diffraction. The magnetic, luminescence properties, the thermal behavior and the volatility for the compound {l_brace}Tm(Piv){sub 3{r_brace}n} were investigated. Black-Small-Square Highlights: Black-Right-Pointing-Pointer We synthesized the coordination polymer {l_brace}Tm(Piv){sub 3{r_brace}n}. Black-Right-Pointing-Pointer Tm atoms in polymer have the coordination number 6. Black-Right-Pointing-Pointer Polymer exhibits blue-color emission at room temperature. Black-Right-Pointing-Pointer Polymer shows high thermal stability and volatility. Black-Right-Pointing-Pointer Polymer has no phase transitions in the range of -50 Horizontal-Ellipsis +50 Degree-Sign S.

  19. Analysis of the rotational structure in the high-resolution infrared spectra of cis,cis- and trans,trans-1,4-difluorobutadiene-1-d1 and trans,trans-1,4-difluorobutadiene-1,4-d2

    SciTech Connect

    Craig, Norman C.; Chen, Yihui; Lu, Yuhua; Neese, Christopher F.; Nemchick, Deacon J.; Blake, Thomas A.

    2013-06-01

    Samples of cis,cis- and trans,trans-1,4-difluorobutadiene-1- d1 and of trans,trans-1,4-difluorobutadiene-1,4-d2 have been synthesized, and high-resolution (≤0.0018 cm-1) infrared spectra of these substances have been recorded in the gas phase. Analysis of the rotational structure, mostly in C-type bands, has yielded ground state rotational constants. For the two 1-d1 species more than one band has been analyzed. For the 1,4-d2 species only one band was available for analysis. However, good agreement between the experimental centrifugal distortion constants and those predicted with a B3LYP/cc-pVTZ model give strong support to the analysis of the very dense spectrum. The ground state rotational constants are a contribution to finding semiexperimental equilibrium structures of the two nonpolar isomers of 1,4- difluorobutadiene.

  20. Dual character of the electronic structure in YBa2Cu4O8: conduction bands of CuO2 planes and CuO chains

    NASA Astrophysics Data System (ADS)

    Kaminski, A.; Kondo, T.; Khasanov, R.; Karpinski, J.; Kazakov, S. M.; Zhigadlo, N. D.; Ohta, T.; Fretwell, H. M.; Palczewski, A. D.; Koll, J. D.; Mesot, J.; Rotenberg, E.; Keller, H.

    2007-03-01

    We use microprobe Angle-Resolved Photoemission Spectroscopy (μARPES) to separately investigate the electronic properties of CuO2 planes and CuO chains in the high temperature superconductor, YBa2Cu4O8. In the CuO2 planes, a two dimensional (2D) electronic structure with nearly momentum independent bilayer splitting is observed. The splitting energy is 150 meV at (π,0), almost 50% larger than in Bi2Sr2CaCu2O8+δ and the electron scattering at the Fermi level in the bonding band is about 1.5 times stronger than in the antibonding band. The CuO chains have a quasi one dimensional (1D) electronic structure. We observe two 1D bands separated by ˜ 550meV: a conducting band and an insulating band with an energy gap of ˜240meV. We find that the conduction electrons are well confined within the planes and chains with a non-trivial hybridization.

  1. An experimental disturbance alters fish size structure but not food chain length in streams.

    PubMed

    Walters, Annika W; Post, David M

    2008-12-01

    Streams experience frequent natural disturbance and are undergoing considerable anthropogenic disturbance due to dam construction and water diversion. Disturbance is known to impact community structure, but its effect on food chain length is still a matter of considerable debate. Theoretical models show that longer food chains are less resilient to disturbance, so food chain length is predicted to be shorter following a disturbance event. Here we experimentally test the effect of disturbance on food chain length in streams by diverting stream flow. We found that our experimental low-flow disturbance did not alter food chain length. We did see an effect on body-size structure in our food webs suggesting that food chain length may be an insensitive indicator of disturbance. We suggest that habitat heterogeneity and food web complexity buffer the effect of disturbance on food chain length. The theoretical predictions of disturbance on food chain length are only likely to be seen in homogeneous systems that closely approximate the linear food chains the models are based upon.

  2. Thermodynamic and structure investigations of new side-chain liquid crystal polymer

    NASA Astrophysics Data System (ADS)

    Danch, A.; Laggner, Peter; Degovics, G.; Sek, D.; Stelzer, F.

    1998-01-01

    Bis [((omega) -(4'-cyanobiphenyl)-4-yl)oxy-n- alkyl]norborn-5-ene-2,3-dicarboxylate was polymerized via ring opening metathesis polymerization. Two distributed polynorbornene derivatives, both of cis configuration, with different length of side-chain were studied. The influence of thermal history on the smectic phase stabilization, position and shape of the glass transition with temperature and on the relaxation process is shown. Glass transition temperatures enthalpies of isotropization and average layer spacing were calculated. Although, the rather flexible spacer between the mesogenic group and the main chain seems to be sufficient to partially decouple the mobility of the main chain from that of the mesogenic group, the influence of a backbone chain structure is still significant for polymer properties, especially in bulk. The measured layer spacing doe not correspond to double length of the side chain which suggests that either the side chains are not fully extended or some overlapping of CN tails occurs.

  3. Crystal structure of 7,8,9,10-tetra­hydro­benzo[b]naphtho­[2,1-d]furan

    PubMed Central

    Wu, Zhongyuan; Reetz, Manfred T.; Harms, Klaus

    2016-01-01

    In the title compound, C16H14O, the cyclo­hexene ring has a half-chair conformation. The mean plane, calculated through all non-H atoms of the mol­ecule, except for the central CH2 atoms of the cyclo­hexene ring, which deviate by 0.340 (3) and −0.369 (3) Å from this mean plane, has an r.m.s. deviation of 0.012 Å. In the crystal, there are C—H⋯π contacts present, resulting in the formation of zigzag chains propagating along the [010] direction. PMID:26870597

  4. 3D coordination networks based on supramolecular chains as building units: synthesis and crystal structures of two silver(I) pyridyldiethynides.

    PubMed

    Zhang, Tianle; Kong, Jianxi; Hu, Yuejie; Meng, Xianggao; Yin, Hongbing; Hu, Dongshuang; Ji, Changpeng

    2008-04-21

    Two silver(I) pyridyldiethynides, [Ag2(3,5-C2PyC2).4CF3CO2Ag.4H2O] ( A) and [Ag 2(3,5-C2PyC2).3AgNO3.H2O](B), were synthesized by reactions of 3,5-diethynylpyridine with silver trifluoroacetate and silver nitrate in high yield, respectively. X-ray crystallographic studies revealed that in A pyridyldiethynide groups connect Ag 11 cluster units to generate 1D supramolecular chains as bridging ligands, where each ethynide group interacts with four silver atoms. These supramolecular chains bearing pyridyl groups are linked by silver ions to form wavelike layers, which are further connected by trifluoroacetate ligands to afford a 3D coordination network. However, B exhibits a different structural feature, where two ethynide groups in one pyridyldiethynide ligand coordinate to three and four silver atoms, respectively. These silver ethynide cluster units are linked through silver-ethynide and argentophilic interactions, leading to a double silver chain by sharing silver atoms in these units. In B, the silver double chains are further connected by bridging pyridyldiethynide groups to generate 2D networks, which interact through the Ag-N coordination bonds between silver atoms and pyridyl groups in the adjacent layers to generate a 3D coordination network. In these two compounds, trifluoroacetate and nitrate groups exhibit different bonding modes, indicating that the counterion is an important factor influencing the structures of supramolecular chains and coordination networks.

  5. Effect of the band structure in a rigorous two-body model with long-range interactions in 1D optical lattices

    NASA Astrophysics Data System (ADS)

    Kristensen, Tom; Simoni, Andrea; Launay, Jean-Michel

    2016-05-01

    We compute scattering and bound state properties for two ultracold molecules in a pure 1D optical lattice. We introduce reference functions with complex quasi-momentum that naturally account for the effect of excited energy bands. Our exact results for a short-range interaction are first compared with the simplest version of the standard Bose-Hubbard (BH) model. Such comparison allows us to highlight the effect of the excited bands, of the non-on-site interaction and of tunneling with distant neighbor, that are not taken into account in the BH model. The effective interaction can depend strongly on the particle quasi-momenta and can present a resonant behavior even in a deep lattice. As a second step, we study scattering of two polar particles in the optical lattice. Peculiar Wigner threshold laws stem from the interplay of the long range dipolar interaction and the presence of the energy bands. We finally assess the validity of an extended Bose-Hubbard model for dipolar gases based on our exact two-body calculations. This work was supported by the Agence Nationale de la Recherche (Contract No. ANR-12-BS04-0020-01).

  6. Quantitation and structures of oligosaccharide chains in human trachea mucin glycoproteins.

    PubMed

    Sangadala, S; Bhat, U R; Mendicino, J

    1992-12-02

    Human respiratory mucin glycoproteins from patients with cystic fibrosis were purified and oligosaccharide chains were released by treatment with alkaline borohydride. A neutral oligosaccharide alditol fraction was isolated from mucin obtained from a patient with A blood group determinant by chromatography on DEAE-cellulose and individual oligosaccharide chains were then isolated by gel filtration on BioGel P-6 columns and high performance liquid chromatography with gradient and isocratic solvent systems. The structures of the purified oligosaccharides were determined by methylation analysis, sequential glycosidase digestion and 'H-NMR spectroscopy. The amount of each chain was determined by compositional analysis. A wide array of discrete branched oligosaccharide structures that contain from 3 to 22 sugar residues were found. Many of the oligosaccharides are related and appear to be precursors of larger chains. The predominant branched oligosaccharides which accumulate contain terminal blood group H (Fuc alpha 2Ga1 beta 4) or blood group A (Fuc alpha 2(Ga1NAc alpha 3) (Ga1 beta 4) determinants which stop further branching and chain elongation. The elongation of oligosaccharide chains in respiratory mucins occurs on the beta 3-linked G1cNAc at branch points, whereas the beta 6-linked G1cNAc residue ultimately forms short side chains with a Fuc alpha 2(Ga1NAc alpha 3) Ga1 beta 4 G1cNAc beta 6 structure in individuals with A blood group determinant. The results obtained in the current studies further suggest that even higher molecular weight oligosaccharide chains with analogous branched structures are present in some human respiratory mucin glycoproteins. Increasing numbers of the repeating sequence shown in the oligosaccharide below is present in the higher molecular weight chains. [formula: see text] This data in conjunction with our earlier observations on the extensive branching of these oligosaccharide chains helps to define and explain the enormous range of

  7. Glass-based 1-D dielectric microcavities

    NASA Astrophysics Data System (ADS)

    Chiasera, Alessandro; Scotognella, Francesco; Valligatla, Sreeramulu; Varas, Stefano; Jasieniak, Jacek; Criante, Luigino; Lukowiak, Anna; Ristic, Davor; Gonçalves, Rogeria Rocha; Taccheo, Stefano; Ivanda, Mile; Righini, Giancarlo C.; Ramponi, Roberta; Martucci, Alessandro; Ferrari, Maurizio

    2016-11-01

    We have developed a reliable RF sputtering techniques allowing to fabricate glass-based one dimensional microcavities, with high quality factor. This property is strongly related to the modification of the density of states due to the confinement of the gain medium in a photonic band gap structure. In this short review we present some of the more recent results obtained by our team exploiting these 1D microcavities. In particular we present: (1) Er3+ luminescence enhancement of the 4I13/2 → 4I15/2 transition; (2) broad band filters based on disordered 1-D photonic structures; (3) threshold defect-mode lasing action in a hybrid structure.

  8. Discrete hexamer water clusters and 2D water layer trapped in three luminescent Ag/tetramethylpyrazine/benzene-dicarboxylate hosts: 1D chain, 2D layer and 3D network

    NASA Astrophysics Data System (ADS)

    Mei, Hong-Xin; Zhang, Ting; Huang, Hua-Qi; Huang, Rong-Bin; Zheng, Lan-Sun

    2016-03-01

    Three mix-ligand Ag(I) coordination compounds, namely, {[Ag10(tpyz) 5(L1) 5(H2 O)2].(H2 O)4}n (1, tpyz = 2,3,4,5-tetramethylpyrazine, H2 L1 = phthalic acid), [Ag4(tpyz) 2(L2) 2(H2 O)].(H2 O)5}n (2, H2 L2 = isophthalic acid) {[Ag2(tpyz) 2(L3) (H2 O)4].(H2 O)8}n (3, H2 L3 = terephthalic acid), have been synthesized and characterized by elemental analysis, IR, PXRD and X-ray single-crystal diffraction. 1 exhibits a 2D layer which can be simplified as a (4,4) net. 2 is a 3D network which can be simplified as a (3,3)-connected 2-nodal net with a point symbol of {102.12}{102}. 3 consists of linear [Ag(tpyz) (H2 O)2]n chain. Of particular interest, discrete hexamer water clusters were observed in 1 and 2, while a 2D L10(6) water layer exists in 3. The results suggest that the benzene dicarboxylates play pivotal roles in the formation of the different host architectures as well as different water aggregations. Moreover, thermogravimetric analysis (TGA) and emissive behaviors of these compounds were investigated.

  9. Probing atomic structure and Majorana wavefunctions in mono-atomic Fe chains on superconducting Pb surface

    NASA Astrophysics Data System (ADS)

    Pawlak, Rémy; Kisiel, Marcin; Klinovaja, Jelena; Meier, Tobias; Kawai, Shigeki; Glatzel, Thilo; Loss, Daniel; Meyer, Ernst

    2016-11-01

    Motivated by the striking promise of quantum computation, Majorana bound states (MBSs) in solid-state systems have attracted wide attention in recent years. In particular, the wavefunction localisation of MBSs is a key feature and is crucial for their future implementation as qubits. Here we investigate the spatial and electronic characteristics of topological superconducting chains of iron atoms on the surface of Pb(110) by combining scanning tunnelling microscopy and atomic force microscopy. We demonstrate that the Fe chains are mono-atomic, structured in a linear manner and exhibit zero-bias conductance peaks at their ends, which we interpret as signature for a MBS. Spatially resolved conductance maps of the atomic chains reveal that the MBSs are well localised at the chain ends (≲25 nm), with two localisation lengths as predicted by theory. Our observation lends strong support to use MBSs in Fe chains as qubits for quantum-computing devices.

  10. [Study of the antigenic structure of human immunoglobulin lambda-chain using monoclonal antibodies].

    PubMed

    Arsen'eva, E L; Bogacheva, G T; Solomon, A; Weiss, D; Ibragimov, A R; Rokhlin, O V

    1990-01-01

    Nine monoclonals against human Ig lambda chains were produced, 4 antibodies react with C-domain, 5--with V-domain of the lambda chain. Anti-C lambda domain antibodies recognize not less than 3 epitopes and one of them is expressed only on the isolated chain. Anti-V lambda antibodies bind both isolated lambda chain and intact IgG, IgM, IgA. Four epitopes are expressed by few lambda Bence Jones proteins of the III subgroup, the immunogen possessing the same isotype. The 4 mentioned epitopes represent private idiotypic determinants. The epitope 3E10 is characteristic of 50% Bence Jones proteins of the II and III V lambda-subgroups thus representing a common idiotypic determinant. Using anti-V lambda antibodies germ line variability of V lambda III proteins was analysed and the similarity of antigenic structure of normal and myeloma human Ig lambda chains was demonstrated.

  11. Magnetic properties of cubic FeCo nanoparticles with anisotropic long chain structure

    NASA Astrophysics Data System (ADS)

    Liu, Jinming; Wu, Kai; Wang, Jian-Ping

    2016-05-01

    Cubic FeCo alloy nanoparticles (NPs) with body-centered cubic (bcc) phase were prepared using sputter based gas-condensation method. When the NPs formed long chain assemblies, the magnetic properties were quite different from that of well-dispersed NPs. Most of the well-dispersed NPs were superparamagnetic at room temperature while the long chain NP assemblies were ferromagnetic with coercivities around 765 Oe, which displayed quite different magnetic properties. The ferromagnetism of long chain NPs was from the exchange coupling between NPs, which eventually led to the transition from superparamagnetism (SPM) to superferromagetism (SFM). Zero-field-cooled (ZFC) and field-cooled (FC) curves were obtained and long chain NP assemblies displayed ferromagnetism at the temperature ranging from 10 K to 400 K. Time-dependent remanent magnetic moment curves also indicated that the long chain structure had better thermal stability due to the strong exchange coupling.

  12. Structural and optical properties of self-assembled chains of plasmonic nanocubes

    SciTech Connect

    Klinkova, Anna; Gang, Oleg; Therien-Aubin, Heloise; Ahmed, Aftab; Nykypanchuk, Dmytro; Choueiri, Rachelle M.; Gagnon, Brandon; Muntyanu, Anastasiya; Walker, Gilbert C.; Kumacheva, Eugenia

    2014-10-10

    Solution-based linear self-assembly of metal nanoparticles offers a powerful strategy for creating plasmonic polymers, which, so far, have been formed from spherical nanoparticles and nanorods. Here, we report linear solution-based self-assembly of metal nanocubes (NCs), examine the structural characteristics of the NC chains and demonstrate their advanced optical characteristics. Predominant face-to-face assembly of large NCs coated with short polymer ligands led to a larger volume of hot spots in the chains, a nearly uniform E-field enhancement in the gaps between co-linear NCs and a new coupling mode for NC chains, in comparison with chains of nanospheres with similar dimensions, composition and surface chemistry. The NC chains exhibited a stronger surface enhanced Raman scattering (SERS) signal, in comparison with linear assemblies of nanospheres. The experimental results were in agreement with finite difference time domain (FDTD) simulations.

  13. Structural and optical properties of self-assembled chains of plasmonic nanocubes

    DOE PAGES

    Klinkova, Anna; Gang, Oleg; Therien-Aubin, Heloise; ...

    2014-10-10

    Solution-based linear self-assembly of metal nanoparticles offers a powerful strategy for creating plasmonic polymers, which, so far, have been formed from spherical nanoparticles and nanorods. Here, we report linear solution-based self-assembly of metal nanocubes (NCs), examine the structural characteristics of the NC chains and demonstrate their advanced optical characteristics. Predominant face-to-face assembly of large NCs coated with short polymer ligands led to a larger volume of hot spots in the chains, a nearly uniform E-field enhancement in the gaps between co-linear NCs and a new coupling mode for NC chains, in comparison with chains of nanospheres with similar dimensions, compositionmore » and surface chemistry. The NC chains exhibited a stronger surface enhanced Raman scattering (SERS) signal, in comparison with linear assemblies of nanospheres. The experimental results were in agreement with finite difference time domain (FDTD) simulations.« less

  14. Self-Organized Growth, Structure, and Magnetism of Monatomic Transition-Metal Oxide Chains

    NASA Astrophysics Data System (ADS)

    Ferstl, Pascal; Hammer, Lutz; Sobel, Christopher; Gubo, Matthias; Heinz, Klaus; Schneider, M. Alexander; Mittendorfer, Florian; Redinger, Josef

    2016-07-01

    We report on the self-organized growth of monatomic transition-metal oxide chains of (3 ×1 ) periodicity and unusual M O2 stoichiometry (M =Ni , Co, Fe, Mn) on Ir(100). We analyze their structural and magnetic properties by means of quantitative LEED, STM, and density functional theory (DFT) calculations. LEED analyses reveal a fascinating common atomic structure in which the transition-metal atoms sit above a missing-row structure of the surface and are coupled to the substrate only via oxygen atoms. This structure is confirmed by DFT calculations with structural parameters deviating by less than 1.7 pm. The DFT calculations predict that the NiO2 chains are nonmagnetic, CoO2 chains are ferromagnetic, while FeO2 and MnO2 are antiferromagnetic. All structures show only weak magnetic interchain coupling. Further, we demonstrate the growth of oxide chains of binary alloys of Co and Ni or Fe on Ir(100), which allows us to produce well-controlled ensembles of ferromagnetic chains of different lengths separated by nonmagnetic or antiferromagnetic segments.

  15. Fabrication and investigation of 1D and 2D structures in LiNbO 3 thin films by pulsed laser ablation

    NASA Astrophysics Data System (ADS)

    Meriche, F.; Boudrioua, A.; Kremer, R.; Dogheche, E.; Neiss-Clauss, E.; Mouras, R.; Fischer, A.; Beghoul, M.-R.; Fogarassy, E.; Boutaoui, N.

    2010-09-01

    Lithium niobate thin films were deposited on sapphire substrate by radio-frequency magnetron sputtering technique. One and two dimensional structures have been made using a KrF excimer laser at 248 nm and 6 ns pulse width, under various conditions of ablation, in order to assess the applicability of laser direct-writing of photonic waveguides. The optical and waveguiding properties of LiNbO 3 thin films were studied by prism-coupling technique, while micro-Raman spectroscopy was used for structural and composition characterization, as well as laser processing mechanism investigation. The surface morphology of the processed structures was obtained by a Nomarski optical microscope, an atomic force microscope and a White Light Interferometer Microscope.

  16. Self-similar spectral structures and edge-locking hierarchy in open-boundary spin chains

    SciTech Connect

    Haque, Masudul

    2010-07-15

    For an anisotropic Heisenberg (XXZ) spin chain, we show that an open boundary induces a series of approximately self-similar features at different energy scales, high up in the eigenvalue spectrum. We present a nonequilibrium phenomenon related to this fractal structure, involving states in which a connected block near the edge is polarized oppositely to the rest of the chain. We show that such oppositely polarized blocks can be 'locked' to the edge of the spin chain and that there is a hierarchy of edge-locking effects at various orders of the anisotropy. The phenomenon enables dramatic control of quantum-state transmission and magnetization control.

  17. An Innovative Supply Chain Management Programme Structure: Broadening the SCM Skill Set

    ERIC Educational Resources Information Center

    Okongwu, Uche

    2007-01-01

    This paper proposes a matrix structure for training Supply Chain Management (SCM) professionals. It is an innovative programme structure that combines two approaches: cross-border and inter-organisational. It enables the students to comprehend complex and specific business environments and to understand the diverse nature of SCM systems in both…

  18. Bone marrow lambda-type light chain crystalline structures associated with multiple myeloma.

    PubMed

    Schvartz, H; Bonhomme, P; Caulet, S; Beorchia, A; Patey, M; Caulet, T

    1985-01-01

    A 58-year-old man showed bone marrow crystalline structures associated with a lambda light chain producing multiple myeloma. Analysis and processing of electron images clearly displayed the periodic structure of the crystals. Immunochemistry suggested that they contained the whole or a fragmented constant portion of immunoglobulin.

  19. Structural determination of prunusins A and B, new C-alkylated flavonoids from Prunus domestica, by 1D and 2D NMR spectroscopy.

    PubMed

    Mahmood, Azhar; Fatima, Itrat; Kosar, Shaheen; Ahmed, Rehana; Malik, Abdul

    2010-02-01

    Prunusins A (1) and B (2), the new C-alkylated flavonoids, have been isolated from the seed kernels of Prunus domestica. Their structures were assigned from (1)H and (13)C nuclear magnetic resonating spectra, DEPT and by correlation spectroscopy, HMQC and HMBC experiments. 3, 5, 7, 4'-Tetrahydroxyflavone (3) and 3, 5, 7-trihydroxy-8, 4'-dimethoxyflavone (4) have also been reported from this species. Both compounds (1) and (2) showed significant antifungal activity against pathogenic fungus Trichophyton simmi.

  20. Synthesis, Structure, and Magnetic Properties of A2Cu5(TeO3)(SO4)3(OH)4 (A = Na, K): The First Compounds with a 1D Kagomé Strip Lattice.

    PubMed

    Tang, Yingying; Guo, Wenbin; Xiang, Hongping; Zhang, Suyun; Yang, Ming; Cui, Meiyan; Wang, Nannan; He, Zhangzhen

    2016-01-19

    Two new tellurite-sulfates A2Cu5(TeO3)(SO4)3(OH)4 (A = Na, K) have been synthesized by a conventional hydrothermal method. Both compounds feature 1D kagomé strip structure built by distorted CuO6 octahedra, which can be regarded as the dimensional reduction of kagomé lattice. Magnetic measurements confirmed that the titled compounds possess antiferromagnetic ordering at low temperature, while a field-induced magnetic transition can be observed at critical field. To the best of our knowledge, this is the first time to obtain distorted kagomé strip compounds.

  1. Quantification of transition dipole strengths using 1D and 2D spectroscopy for the identification of molecular structures via exciton delocalization: Application to α-helices

    PubMed Central

    Grechko, Maksim; Zanni, Martin T.

    2012-01-01

    Vibrational and electronic transition dipole strengths are often good probes of molecular structures, especially in excitonically coupled systems of chromophores. One cannot determine transition dipole strengths using linear spectroscopy unless the concentration is known, which in many cases it is not. In this paper, we report a simple method for measuring transition dipole moments from linear absorption and 2D IR spectra that does not require knowledge of concentrations. Our method is tested on several model compounds and applied to the amide I′ band of a polypeptide in its random coil and α-helical conformation as modulated by the solution temperature. It is often difficult to confidently assign polypeptide and protein secondary structures to random coil or α-helix by linear spectroscopy alone, because they absorb in the same frequency range. We find that the transition dipole strength of the random coil state is 0.12 ± 0.013 D2, which is similar to a single peptide unit, indicating that the vibrational mode of random coil is localized on a single peptide unit. In an α-helix, the lower bound of transition dipole strength is 0.26 ± 0.03 D2. When taking into account the angle of the amide I′ transition dipole vector with respect to the helix axis, our measurements indicate that the amide I′ vibrational mode is delocalized across a minimum of 3.5 residues in an α-helix. Thus, one can confidently assign secondary structure based on exciton delocalization through its effect on the transition dipole strength. Our method will be especially useful for kinetically evolving systems, systems with overlapping molecular conformations, and other situations in which concentrations are difficult to determine. PMID:23163364

  2. Crystal Structures of T Cell Receptor (Beta) Chains Related to Rheumatoid Arthritis

    SciTech Connect

    Li,H.; van Vranken, S.; Zhao, Y.; Li, Z.; Guo, Y.; Eisele, L.; Li, Y.

    2005-01-01

    The crystal structures of the V{beta}17+ {beta} chains of two human T cell receptors (TCRs), originally derived from the synovial fluid (SF4) and tissue (C5-1) of a patient with rheumatoid arthritis (RA), have been determined in native (SF4) and mutant (C5-1{sub F104{yields}Y/C187{yields}S}) forms, respectively. These TCR {beta} chains form homo-dimers in solution and in crystals. Structural comparison reveals that the main-chain conformations in the CDR regions of the C5-1 and SF4 V{beta}17 closely resemble those of a V{beta}17 JM22 in a bound form; however, the CDR3 region shows different conformations among these three V{beta}17 structures. At the side-chain level, conformational differences were observed at the CDR2 regions between our two ligand-free forms and the bound JM22 form. Other significant differences were observed at the V{beta} regions 8-12, 40-44, and 82-88 between C5-1/SF4 and JM22 V{beta}17, implying that there is considerable variability in the structures of very similar {beta} chains. Structural alignments also reveal a considerable variation in the V{beta}-C{beta} associations, and this may affect ligand recognition. The crystal structures also provide insights into the structure basis of T cell recognition of Mycoplasma arthritidis mitogen (MAM), a superantigen that may be implicated in the development of human RA. Structural comparisons of the V{beta} domains of known TCR structures indicate that there are significant similarities among V{beta} regions that are MAM-reactive, whereas there appear to be significant structural differences among those V{beta} regions that lack MAM-reactivity. It further reveals that CDR2 and framework region (FR) 3 are likely to account for the binding of TCR to MAM.

  3. Control globular structure formation of a copolymer chain through inverse design.

    PubMed

    Yang, Xi; Lu, Zhong-Yuan

    2016-06-14

    A copolymer chain in dilute solution can exhibit various globular structures with characteristic morphologies, which makes it a potentially useful candidate for artificial materials design. However, the chain has a huge conformation space and may not naturally form the globular structure we desire. An ideal way to control globular structure formation should be inverse design, i.e., starting from the target structure and finding out what kind of polymers can effectively generate it. To accomplish this, we propose an inverse design procedure, which is combined with Wang-Landau Monte Carlo to fully and precisely explore the huge conformation space of the chain. Starting from a desired target structure, all the geometrically possible sequences are exactly enumerated. Interestingly, reasonable interaction strengths are obtained and found to be not specified for only one sequence. Instead, they can be combined with many other sequences and also achieve a relatively high yield for target structure, although these sequences may be rather different. These results confirm the possibility of controlling globular structure formation of a copolymer chain through inverse design and pave the way for targeted materials design.

  4. Control globular structure formation of a copolymer chain through inverse design

    NASA Astrophysics Data System (ADS)

    Yang, Xi; Lu, Zhong-Yuan

    2016-06-01

    A copolymer chain in dilute solution can exhibit various globular structures with characteristic morphologies, which makes it a potentially useful candidate for artificial materials design. However, the chain has a huge conformation space and may not naturally form the globular structure we desire. An ideal way to control globular structure formation should be inverse design, i.e., starting from the target structure and finding out what kind of polymers can effectively generate it. To accomplish this, we propose an inverse design procedure, which is combined with Wang-Landau Monte Carlo to fully and precisely explore the huge conformation space of the chain. Starting from a desired target structure, all the geometrically possible sequences are exactly enumerated. Interestingly, reasonable interaction strengths are obtained and found to be not specified for only one sequence. Instead, they can be combined with many other sequences and also achieve a relatively high yield for target structure, although these sequences may be rather different. These results confirm the possibility of controlling globular structure formation of a copolymer chain through inverse design and pave the way for targeted materials design.

  5. Quasi-1D physics in metal-organic frameworks: MIL-47(V) from first principles

    PubMed Central

    Jaeken, Jan W; De Baerdemacker, Stijn; Lejaeghere, Kurt; Van Speybroeck, Veronique

    2014-01-01

    Summary The geometric and electronic structure of the MIL-47(V) metal-organic framework (MOF) is investigated by using ab initio density functional theory (DFT) calculations. Special focus is placed on the relation between the spin configuration and the properties of the MOF. The ground state is found to be antiferromagnetic, with an equilibrium volume of 1554.70 Å3. The transition pressure of the pressure-induced large-pore-to-narrow-pore phase transition is calculated to be 82 MPa and 124 MPa for systems with ferromagnetic and antiferromagnetic chains, respectively. For a mixed system, the transition pressure is found to be a weighted average of the ferromagnetic and antiferromagnetic transition pressures. Mapping DFT energies onto a simple-spin Hamiltonian shows both the intra- and inter-chain coupling to be antiferromagnetic, with the latter coupling constant being two orders of magnitude smaller than the former, suggesting the MIL-47(V) to present quasi-1D behavior. The electronic structure of the different spin configurations is investigated and it shows that the band gap position varies strongly with the spin configuration. The valence and conduction bands show a clear V d-character. In addition, these bands are flat in directions orthogonal to VO6 chains, while showing dispersion along the the direction of the VO6 chains, similar as for other quasi-1D materials. PMID:25383285

  6. Phase Behavior of a Single Structured Ionomer Chain in Solution

    SciTech Connect

    Aryal, Dipak; Etampawala, Thusitha; Perahia, Dvora; Grest, Gary S.

    2014-08-14

    Structured polymers offer a means to tailor transport pathways within mechanically stable manifolds. Here we examine the building block of such a membrane, namely a single large pentablock co-polymer that consist of a center block of a randomly sulfonated polystyrene, designed for transport, tethered to poly-ethylene-r-propylene and end-capped by poly-t-butyl styrene, for mechanical stability,using molecular dynamics simulations. The polymer structure in a cyclohexane-heptane mixture, a technologically viable solvent, and in water, a poor solvent for all segments and a ubiquitous substance is extracted. In all solvents the pentablock collapsed into nearly spherical aggregates where the ionic block is segregated. In hydrophobic solvents, the ionic block resides in the center, surrounded by swollen intermix of flexible and end blocks. In water all blocks are collapsed with the sulfonated block residing on the surface. Our results demonstrate that solvents drive different local nano-segregation, providing a gateway to assemble membranes with controlled topology.

  7. Phase Behavior of a Single Structured Ionomer Chain in Solution

    DOE PAGES

    Aryal, Dipak; Etampawala, Thusitha; Perahia, Dvora; ...

    2014-08-14

    Structured polymers offer a means to tailor transport pathways within mechanically stable manifolds. Here we examine the building block of such a membrane, namely a single large pentablock co-polymer that consist of a center block of a randomly sulfonated polystyrene, designed for transport, tethered to poly-ethylene-r-propylene and end-capped by poly-t-butyl styrene, for mechanical stability,using molecular dynamics simulations. The polymer structure in a cyclohexane-heptane mixture, a technologically viable solvent, and in water, a poor solvent for all segments and a ubiquitous substance is extracted. In all solvents the pentablock collapsed into nearly spherical aggregates where the ionic block is segregated. Inmore » hydrophobic solvents, the ionic block resides in the center, surrounded by swollen intermix of flexible and end blocks. In water all blocks are collapsed with the sulfonated block residing on the surface. Our results demonstrate that solvents drive different local nano-segregation, providing a gateway to assemble membranes with controlled topology.« less

  8. Harnessing graphical structure in Markov chain Monte Carlo learning

    SciTech Connect

    Stolorz, P.E.; Chew P.C.

    1996-12-31

    The Monte Carlo method is recognized as a useful tool in learning and probabilistic inference methods common to many datamining problems. Generalized Hidden Markov Models and Bayes nets are especially popular applications. However, the presence of multiple modes in many relevant integrands and summands often renders the method slow and cumbersome. Recent mean field alternatives designed to speed things up have been inspired by experience gleaned from physics. The current work adopts an approach very similar to this in spirit, but focusses instead upon dynamic programming notions as a basis for producing systematic Monte Carlo improvements. The idea is to approximate a given model by a dynamic programming-style decomposition, which then forms a scaffold upon which to build successively more accurate Monte Carlo approximations. Dynamic programming ideas alone fail to account for non-local structure, while standard Monte Carlo methods essentially ignore all structure. However, suitably-crafted hybrids can successfully exploit the strengths of each method, resulting in algorithms that combine speed with accuracy. The approach relies on the presence of significant {open_quotes}local{close_quotes} information in the problem at hand. This turns out to be a plausible assumption for many important applications. Example calculations are presented, and the overall strengths and weaknesses of the approach are discussed.

  9. Structure and Active Stie Residues of Pg1D, an N-Acetyltransferase from the Bacillosamine Synthetic Pathway Required for N-Glycan Synthesis in Campylobacter jejuni

    SciTech Connect

    Rangarajan,E.; Ruane, K.; Sulea, T.; Watson, D.; Proteau, A.; Leclerc, S.; Cygler, M.; Matte, A.; Young, N.

    2008-01-01

    Campylobacter jejuni is highly unusual among bacteria in forming N-linked glycoproteins. The heptasaccharide produced by its pgl system is attached to protein Asn through its terminal 2, 4-diacetamido-2, 4,6-trideoxy-d-Glc (QuiNAc4NAc or N, N'-diacetylbacillosamine) moiety. The crucial, last part of this sugar's synthesis is the acetylation of UDP-2-acetamido-4-amino-2, 4,6-trideoxy-d-Glc by the enzyme PglD, with acetyl-CoA as a cosubstrate. We have determined the crystal structures of PglD in CoA-bound and unbound forms, refined to 1.8 and 1.75 Angstroms resolution, respectively. PglD is a trimer of subunits each comprised of two domains, an N-terminal {alpha}/{beta}-domain and a C-terminal left-handed {beta}-helix. Few structural differences accompany CoA binding, except in the C-terminal region following the {beta}-helix (residues 189-195), which adopts an extended structure in the unbound form and folds to extend the {beta}-helix upon binding CoA. Computational molecular docking suggests a different mode of nucleotide-sugar binding with respect to the acetyl-CoA donor, with the molecules arranged in an 'L-shape', compared with the 'in-line' orientation in related enzymes. Modeling indicates that the oxyanion intermediate would be stabilized by the NH group of Gly143', with His125' the most likely residue to function as a general base, removing H+ from the amino group prior to nucleophilic attack at the carbonyl carbon of acetyl-CoA. Site-specific mutations of active site residues confirmed the importance of His125', Glu124', and Asn118. We conclude that Asn118 exerts its function by stabilizing the intricate hydrogen bonding network within the active site and that Glu124' may function to increase the pKa of the putative general base, His125'.

  10. Carbohydrate Conformation and Lipid Condensation in Monolayers Containing Glycosphingolipid Gb3: Influence of Acyl Chain Structure

    PubMed Central

    Watkins, Erik B.; Gao, Haifei; Dennison, Andrew J.C.; Chopin, Nathalie; Struth, Bernd; Arnold, Thomas; Florent, Jean-Claude; Johannes, Ludger

    2014-01-01

    Globotriaosylceramide (Gb3), a glycosphingolipid found in the plasma membrane of animal cells, is the endocytic receptor of the bacterial Shiga toxin. Using x-ray reflectivity (XR) and grazing incidence x-ray diffraction (GIXD), lipid monolayers containing Gb3 were investigated at the air-water interface. XR probed Gb3 carbohydrate conformation normal to the interface, whereas GIXD precisely characterized Gb3’s influence on acyl chain in-plane packing and area per molecule (APM). Two phospholipids, 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) and 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine (DPPE), were used to study Gb3 packing in different lipid environments. Furthermore, the impact on monolayer structure of a naturally extracted Gb3 mixture was compared to synthetic Gb3 species with uniquely defined acyl chain structures. XR results showed that lipid environment and Gb3 acyl chain structure impact carbohydrate conformation with greater solvent accessibility observed for smaller phospholipid headgroups and long Gb3 acyl chains. In general, GIXD showed that Gb3 condensed phospholipid packing resulting in smaller APM than predicted by ideal mixing. Gb3’s capacity to condense APM was larger for DSPC monolayers and exhibited different dependencies on acyl chain structure depending on the lipid environment. The interplay between Gb3-induced changes in lipid packing and the lipid environment’s impact on carbohydrate conformation has broad implications for glycosphingolipid macromolecule recognition and ligand binding. PMID:25185550

  11. Helix-like structure formation of a semi-flexible chain confined in a cylinder channel

    NASA Astrophysics Data System (ADS)

    Wen, Xiaohui; Sun, Tieyu; Zhang, Wei-Bing; Lam, Chi-Hang; Zhang, Linxi; Zang, Huaping

    2016-09-01

    Molecular dynamics method is used to study the conformation behavior of a semi-flexible polymer chain confined in a cylinder channel. A novel helix-like structure is found to form during the simulation. Moreover, the detailed characteristic parameters and formation probability of these helix-like structures under moderate conditions are investigated. We find that the structure is not a perfect helix, but a bundle of elliptical turns. In addition, we conduct a statistical analysis for the chain monomer distribution along the radial direction. This research contributes to our understanding of the microscopic conformation of polymer chains in confined environments filled with a solvent. Project supported by the National Natural Science Foundation of China (Grant Nos. 11504033 and 11404290) and the General Research Fund of Hong Kong Research Council of China (Grant No. 15301014).

  12. Tetrel Bonds in Infinite Molecular Chains by Electronic Structure Theory and Their Role for Crystal Stabilization.

    PubMed

    George, Janine; Dronskowski, Richard

    2017-02-16

    Intermolecular bonds play a crucial role in the rational design of crystal structures, dubbed crystal engineering. The relatively new term tetrel bonds (TBs) describes a long-known type of such interactions presently in the focus of quantum chemical cluster calculations. Here, we energetically explore the strengths and cooperativity of these interactions in infinite chains, a possible arrangement of such tetrel bonds in extended crystals, by periodic density functional theory. In the chains, the TBs are amplified due to cooperativity by up to 60%. Moreover, we computationally take apart crystals stabilized by infinite tetrel-bonded chains and assess the importance of the TBs for the crystal stabilization. Tetrel bonds can amount to 70% of the overall interaction energy within some crystals, and they can also be energetically decisive for the taken crystal structure; their individual strengths also compete with the collective packing within the crystal structures.

  13. Demonstration of structural polymorphism among MB3 light chains by two-dimensional gel electrophoresis.

    PubMed

    Ishikawa, N; Kasahara, M; Ikeda, H; Ogasawara, K; Hawkin, S; Takenouchi, T; Wakisaka, A; Kikuchi, Y; Aizawa, M

    1985-01-01

    The heavy and light chain subunits of MB3 molecules were isolated from KT2 (DKT2, DR4, MB3 homozygous), ER (Dw4, DR4, MB3 homozygous), JMe (Dw5, DR5, MB3 homozygous), EBV-Sh (DSh, DRw6.2, MB3 homozygous), and EBV-Ky (DKy, DRw9, MB3 homozygous) cells and were compared with one another by two-dimensional gel electrophoresis. The MB3 light chains from KT2, ER, and EBV-Ky cells were clearly different in terms of their isoelectric points, whereas those from ER, JMe, and EBV-Sh cells were indistinguishable. No differences in charge or m.w. were noted for the MB3 heavy chains from the five cell lines. Thus, three out of the five MB3-positive, D/DR-disparate cell lines were found to express structurally distinct MB3 molecules, demonstrating that MB3 is a public serologic specificity shared by at least three structurally distinct MB (human I-A-like) molecules. Because the DR light chain subunits isolated from EBV-Wa, KT2, ER, JMe, EBV-Sh, and EBV-Ky cells differed from one another in their isoelectric points, the DR light chains were apparently more polymorphic than the MB3 light chains.

  14. Differential Recognition of CD1d-[alpha]-Galactosyl Ceramide by the V[beta]8.2 and V[beta]7 Semi-invariant NKT T Cell Receptors

    SciTech Connect

    Pellicci, Daniel G.; Patel, Onisha; Kjer-Nielsen, Lars; Pang, Siew Siew; Sullivan, Lucy C.; Kyparissoudis, Konstantinos; Brooks, Andrew G.; Reid, Hugh H.; Gras, Stephanie; Lucet, Isabelle S.; Koh, Ruide; Smyth, Mark J.; Mallevaey, Thierry; Matsuda, Jennifer L.; Gapin, Laurent; McCluskey, James; Godfrey, Dale I.; Rossjohn, Jamie; PMCI-A; Monash; UCHSC; Melbourne

    2009-09-02

    The semi-invariant natural killer T cell receptor (NKT TCR) recognizes CD1d-lipid antigens. Although the TCR{alpha} chain is typically invariant, the {beta} chain expression is more diverse, where three V{beta} chains are commonly expressed in mice. We report the structures of V{alpha}14-V{beta}8.2 and V{alpha}14-V{beta}7 NKT TCRs in complex with CD1d-{alpha}-galactosylceramide ({alpha}-GalCer) and the 2.5 {angstrom} structure of the human NKT TCR-CD1d-{alpha}-GalCer complex. Both V{beta}8.2 and V{beta}7 NKT TCRs and the human NKT TCR ligated CD1d-{alpha}-GalCer in a similar manner, highlighting the evolutionarily conserved interaction. However, differences within the V{beta} domains of the V{beta}8.2 and V{beta}7 NKT TCR-CD1d complexes resulted in altered TCR{beta}-CD1d-mediated contacts and modulated recognition mediated by the invariant {alpha} chain. Mutagenesis studies revealed the differing contributions of V{beta}8.2 and V{beta}7 residues within the CDR2{beta} loop in mediating contacts with CD1d. Collectively we provide a structural basis for the differential NKT TCR V{beta} usage in NKT cells.

  15. The 2012 Ferrara seismic sequence: from a 1D reliable crustal structure for moment tensor solutions to strong implications for seismic hazard

    NASA Astrophysics Data System (ADS)

    Buttinelli, M.; Malagnini, L.; Herrmann, R. B.; Munafò, I.; Anselmi, M.; Akinci, A.; Boschi, E.

    2012-12-01

    On May 20 2012, an event of ML 5.9 (MW 5.6) struck the southern edge of the Po river plain (Pianura Padana). The earthquake was preceded by a foreshock of ML 4.1 (MW 3.8), less than 3 hours before the MW 5.6 main. Hypocentral depths were 6.3 km for both events. Centroid depths were 5 and 6 km, respectively. The activated fault was a reverse one, dipping to the south. Then a complex seismic sequence started, in which more than six earthquakes with ML greater than 5 struck the area, the last one on June 3, 2012. Aftershocks delineated a 50 km-long and 10-15 km-wide zone, approximately elongated in the WE direction. More than 2100 events were located between May 19 and June 25 2012 by the INGV National Seismic Network, 80 of them with ML greater than 3.5. The damage due to the ML 5+ earthquakes was widespread, as they severely hit historical towns and industrial infrastructures. However, a striking inconsistency exists between the relatively small moment magnitudes and the corresponding high level of damage. In order to define a velocity structure for the crust beneath the Pianura Padana, to be used for waveform inversion of moment tensors, we gathered all the geophysical and geological information available for the area. The model is characterized by very thick and shallow Quaternary sediments, to be used for the inversion of broadband waveforms for moment tensor (MT) solutions, in the frequency band between 0.02-0.1 Hz. We calculated moment tensors for 20 events down to MW~3.2. We demonstrate how surface waves dominate the seismograms in the region, which may have played a major role in enhancing the damage to industrial structures observed in the epicentral area. Synthetic seismograms computed using the developed model well reproduced the anomalous durations of the ground motion observed in Pianura Padana, also highlighting important implications for the seismic hazard in the entire area. The present seismic hazard assessment as well as the size of the historical

  16. Tuning heat transport in trapped-ion chains across a structural phase transition

    NASA Astrophysics Data System (ADS)

    Ruiz, A.; Alonso, D.; Plenio, M. B.; del Campo, A.

    2014-06-01

    We analyze the heat transport in an ion chain that is confined in a strongly anisotropic Paul trap. To drive a heat current across the chain different pairs of counterpropagating laser beams are applied to the ions on the edges. The lasers behave as heat reservoirs operating at different temperatures, and a nonequilibrium heat flow can be sustained. The control of the spatial distribution of the ions in the chain by variation of the trapping frequencies makes ion chains an ideal testbed to study heat transport properties in finite open systems of low dimensionality with tunable nonlinearities. We explore heat transport across a structural phase transition between the linear and zigzag configurations, identifying the condition for optimal heat transport.

  17. Moments of the Spin Structure Functions g1p and g1d for 0.05 < Q2 < 3.0 GeV2

    SciTech Connect

    Prok, Yelena; Bosted, Peter; Burkert, Volker; Deur, Alexandre; Dharmawardane, Kahanawita; Dodge, Gail; Griffioen, Keith; Kuhn, Sebastian; Minehart, Ralph; Adams, Gary; Amaryan, Moscov; Amaryan, Moskov; Anghinolfi, Marco; Asryan, G.; Audit, Gerard; Avagyan, Harutyun; Baghdasaryan, Hovhannes; Baillie, Nathan; Ball, J.P.; Ball, Jacques; Baltzell, Nathan; Barrow, Steve; Battaglieri, Marco; Beard, Kevin; Bedlinskiy, Ivan; Bektasoglu, Mehmet; Bellis, Matthew; Benmouna, Nawal; Berman, Barry; Biselli, Angela; Blaszczyk, Lukasz; Boyarinov, Sergey; Bonner, Billy; Bouchigny, Sylvain; Bradford, Robert; Branford, Derek; Briscoe, William; Brooks, William; Bultmann, S.; Bueltmann, Stephen; Butuceanu, Cornel; Calarco, John; Careccia, Sharon; Carman, Daniel; Casey, Liam; Cazes, Antoine; Chen, Shifeng; Cheng, Lu; Cole, Philip; Collins, Patrick; Coltharp, Philip; Cords, Dieter; Corvisiero, Pietro; Crabb, Donald; Crede, Volker; Cummings, John; Dale, Daniel; Dashyan, Natalya; De Masi, Rita; De Vita, Raffaella; De Sanctis, Enzo; Degtiarenko, Pavel; Denizli, Haluk; Dennis, Lawrence; Dhuga, Kalvir; Dickson, Richard; Djalali, Chaden; Doughty, David; Dugger, Michael; Dytman, Steven; Dzyubak, Oleksandr; Egiyan, Hovanes; Egiyan, Kim; Elfassi, Lamiaa; Elouadrhiri, Latifa; Eugenio, Paul; Fatemi, Renee; Fedotov, Gleb; Feldman, Gerald; Fersch, Robert; Feuerbach, Robert; Forest, Tony; Fradi, Ahmed; Funsten, Herbert; Garcon, Michel; Gavalian, Gagik; Gevorgyan, Nerses; Gilfoyle, Gerard; Giovanetti, Kevin; Girod, Francois-Xavier; Goetz, John; Golovach, Evgeny; Gothe, Ralf; Guidal, Michel; Guillo, Matthieu; Guler, Nevzat; Guo, Lei; Gyurjyan, Vardan; Hadjidakis, Cynthia; Hafidi, Kawtar; Hakobyan, Hayk; Hanretty, Charles; Hardie, John; Hassall, Neil; Heddle, David; Hersman, F.; Hicks, Kenneth; Hleiqawi, Ishaq; Holtrop, Maurik; Huertas, Marco; Hyde, Charles; Ilieva, Yordanka; Ireland, David; Ishkhanov, Boris; Isupov, Evgeny; Ito, Mark; Jenkins, David; Jo, Hyon-Suk; Johnstone, John; Joo, Kyungseon; Juengst, Henry; Kalantarians, Narbe; Keith, Christopher; Kellie, James; Khandaker, Mahbubul; Kim, Kui; Kim, Kyungmo; Kim, Wooyoung; Klein, Andreas; Klein, Franz; Klusman, Mike; Kossov, Mikhail; Krahn, Zebulun; Kramer, Laird; Kubarovsky, Valery; Kuhn, Joachim; Kuleshov, Sergey; Kuznetsov, Viacheslav; Lachniet, Jeff; Laget, Jean; Langheinrich, Jorn; Lawrence, Dave; Lima, Ana; Livingston, Kenneth; Lu, Haiyun; Lukashin, K.; MacCormick, Marion; Marchand, Claude; Markov, Nikolai; Mattione, Paul; McAleer, Simeon; McKinnon, Bryan; McNabb, John; Mecking, Bernhard; Mestayer, Mac; Meyer, Curtis; Mibe, Tsutomu; Mikhaylov, Konstantin; Mirazita, Marco; Miskimen, Rory; Mokeev, Viktor; Morand, Ludyvine; Moreno, Brahim; Moriya, Kei; Morrow, Steven; Moteabbed, Maryam; Mueller, James; Munevar Espitia, Edwin; Mutchler, Gordon; Nadel-Turonski, Pawel; Nasseripour, Rakhsha; Niccolai, Silvia; Niculescu, Gabriel; Niculescu, Maria-Ioana; Niczyporuk, Bogdan; Niroula, Megh; Niyazov, Rustam; Nozar, Mina; O'Rielly, Grant; Osipenko, Mikhail; Ostrovidov, Alexander; Park, Kijun; Pasyuk, Evgueni; Paterson, Craig; Anefalos Pereira, S.; Philips, Sasha; Pierce, J.; Pivnyuk, Nikolay; Pocanic, Dinko; Pogorelko, Oleg; Popa, Iulian; Pozdnyakov, Sergey; Preedom, Barry; Price, John; Procureur, Sebastien; Protopopescu, Dan; Qin, Liming; Raue, Brian; Riccardi, Gregory; Ricco, Giovanni; Ripani, Marco; Ritchie, Barry; Rosner, Guenther; Rossi, Patrizia; Rowntree, David; Rubin, Philip; Sabatie, Franck; Salamanca, Julian; Salgado, Carlos; Santoro, Joseph; Sapunenko, Vladimir; Schumacher, Reinhard; Seely, Mikell; Serov, Vladimir; Sharabian, Youri; Sharov, Dmitri; Shaw, Jeffrey; Shvedunov, Nikolay; Skabelin, Alexander; Smith, Elton; Smith, Lee; Sober, Daniel; Sokhan, Daria; Stavinskiy, Aleksey; Stepanyan, Samuel; Stepanyan, Stepan; Stokes, Burnham; Stoler, Paul; Strakovski, Igor; Strauch, Steffen; Suleiman, Riad; Taiuti, Mauro; Tedeschi, David; Tkabladze, Avtandil; Tkachenko, Svyatoslav; Todor, Luminita; Ungaro, Maurizio; V

    2009-02-01

    The spin structure functions $g_1$ for the proton and the deuteron have been measured over a wide kinematic range in $x$ and \\Q2 using 1.6 and 5.7 GeV longitudinally polarized electrons incident upon polarized NH$_3$ and ND$_3$ targets at Jefferson Lab. Scattered electrons were detected in the CEBAF Large Acceptance Spectrometer, for $0.05 < Q^2 < 5 $\\ GeV$^2$ and $W < 3$ GeV. The first moments of $g_1$ for the proton and deuteron are presented -- both have a negative slope at low \\Q2, as predicted by the extended Gerasimov-Drell-Hearn sum rule. The first result for the generalized forward spin polarizability of the proton $\\gamma_0^p$ is also reported, and shows evidence of scaling above $Q^2$ = 1.5 GeV$^2$. Although the first moments of $g_1$ are consistent with Chiral Perturbation Theory (\\ChPT) calculations up to approximately $Q^2 = 0.06$ GeV$^2$, a significant discrepancy is observed between the $\\gamma_0^p$ data and \\ChPT\\ for $\\gamma_0^p$,even at the lowest \\Q2.

  18. Chirality organization of ferrocenes bearing podand dipeptide chains: synthesis and structural characterization.

    PubMed

    Moriuchi, T; Nomoto, A; Yoshida, K; Ogawa, A; Hirao, T

    2001-01-10

    A variety of ferrocenes bearing podand dipeptide chains have been synthesized to form an ordered structure in both solid and solution states and have been investigated by 1H NMR, FT-IR, CD, and X-ray crystallographic analyses. Conformational enantiomerization through chirality organization was achieved by the intramolecular hydrogen bondings between the podand dipeptide chains. The single-crystal X-ray structure determination of the ferrocene 2 bearing the podand dipeptide chains (-D-Ala-D-Pro-OEt) revealed two C2-symmetric intramolecular hydrogen bondings between CO (Ala) and NH (another Ala) of each podand dipeptide chain to induce the chirality-organized structure. The molecular structures of the ferrocene 1 composed of the podand L-dipeptide chains (-L-Ala-L-Pro-OEt) and 2 are in a good mirror image relationship, indicating that they are conformational enantiomers. An opposite helically ordered molecular arrangement was formed in the crystal packing of 2 as compared with 1. The ferrocene 2 exhibited induced circular dichroism (CD), which appeared at the absorbance of the ferrocene moiety. The mirror image of the CD signals between 1 and 2 was observed, suggesting that the chirality-organized structure via intramolecular hydrogen bondings is present even in solution. The ferrocene 4 bearing the podand dipeptide chains (-Gly-L-Leu-OEt) also showed an ordered structure in the crystal based on two intramolecular hydrogen bondings between CO (Gly) and NH (another Gly) of each podand dipeptide chain, together with intermolecular hydrogen bondings between CO adjacent to the ferrocene unit and NH (neighboring Leu) to create the highly organized self-assembly. A different self-assembly was observed in the crystal of the ferrocene 5 composed of the podand dipeptide chains (-Gly-L-Phe-OEt), wherein each molecule is bonded to two neighboring molecules through two pairs of symmetrical intermolecular hydrogen bonds to form a 14-membered intermolecularly hydrogen-bonded ring

  19. Synthesis, crystal structure and magnetic properties of a novel heterobimetallic rhenium(IV)-dysprosium(III) chain.

    PubMed

    Pejo, Carolina; Guedes, Guilherme P; Novak, Miguel A; Speziali, Nivaldo L; Chiozzone, Raúl; Julve, Miguel; Lloret, Francesc; Vaz, Maria G F; González, Ricardo

    2015-06-08

    The use of the mononuclear rhenium(IV) precursor [ReBr5 (H2 pydc)](-) (H2 pydc=3,5-pyridinedicarboxylic acid) as a metalloligand towards dysprosium(III) afforded the first heterobimetallic Re(IV) -Dy(III) complex. Crystal structures and static and dynamic magnetic properties of both rhenium-containing species are reported herein. The 5d-4f compound shows an extended 1D structure and the AC magnetic measurements reveal frequency dependence at low temperature suggesting slow relaxation of the magnetization.

  20. Probing structure-induced optical behavior in a new class of self-activated luminescent 0D/1D CaWO₄ metal oxide – CdSe nanocrystal composite heterostructures

    SciTech Connect

    Han, Jinkyu; McBean, Coray; Wang, Lei; Hoy, Jessica; Jaye, Cherno; Liu, Haiqing; Li, Zhuo-Qun; Sfeir, Matthew Y.; Fischer, Daniel A.; Taylor, Gordon T.; Misewich, James A.; Wong, Stanislaus S.

    2015-01-30

    In this report, we synthesize and characterize the structural and optical properties of novel heterostructures composed of (i) semiconducting nanocrystalline CdSe quantum dot (QDs) coupled with (ii) both one and zero-dimensional (1D and 0D) motifs of self-activated luminescence CaWO₄ metal oxides. Specifically, ~4 nm CdSe QDs have been anchored onto (i) high-aspect ratio 1D nanowires, measuring ~230 nm in diameter and ~3 μm in length, as well as onto (ii) crystalline 0D nanoparticles (possessing an average diameter of ~ 80 nm) of CaWO₄ through the mediation of 3-mercaptopropionic acid (MPA) as a connecting linker. Composite formation was confirmed by complementary electron microscopy and spectroscopy (i.e. IR and Raman) data. In terms of luminescent properties, our results show that our 1D and 0D heterostructures evince photoluminescence (PL) quenching and shortened PL lifetimes of CaWO₄ as compared with unbound CaWO₄. We propose that a photo-induced electron transfer process occurs from CaWO₄ to CdSe QDs, a scenario which has been confirmed by NEXAFS measurements and which highlights a decrease in the number of unoccupied orbitals in the conduction bands of CdSe QDs. By contrast, the PL signature and lifetimes of MPA-capped CdSe QDs within these heterostructures do not exhibit noticeable changes as compared with unbound MPA-capped CdSe QDs. The striking difference in optical behavior between CaWO₄ nanostructures and CdSe QDs within our heterostructures can be correlated with the relative positions of their conduction and valence energy band levels. In addition, the PL quenching behaviors for CaWO₄ within the heterostructure configuration were examined by systematically varying (i) the quantities and coverage densities of CdSe QDs as well as (ii) the intrinsic morphology (and by extension, the inherent crystallite size) of CaWO₄ itself.

  1. Structural re-alignment in an immunologic surface region of ricin A chain

    SciTech Connect

    Zemla, A T; Zhou, C E

    2007-07-24

    We compared structure alignments generated by several protein structure comparison programs to determine whether existing methods would satisfactorily align residues at a highly conserved position within an immunogenic loop in ribosome inactivating proteins (RIPs). Using default settings, structure alignments generated by several programs (CE, DaliLite, FATCAT, LGA, MAMMOTH, MATRAS, SHEBA, SSM) failed to align the respective conserved residues, although LGA reported correct residue-residue (R-R) correspondences when the beta-carbon (Cb) position was used as the point of reference in the alignment calculations. Further tests using variable points of reference indicated that points distal from the beta carbon along a vector connecting the alpha and beta carbons yielded rigid structural alignments in which residues known to be highly conserved in RIPs were reported as corresponding residues in structural comparisons between ricin A chain, abrin-A, and other RIPs. Results suggest that approaches to structure alignment employing alternate point representations corresponding to side chain position may yield structure alignments that are more consistent with observed conservation of functional surface residues than do standard alignment programs, which apply uniform criteria for alignment (i.e., alpha carbon (Ca) as point of reference) along the entirety of the peptide chain. We present the results of tests that suggest the utility of allowing user-specified points of reference in generating alternate structural alignments, and we present a web server for automatically generating such alignments.

  2. Severe Hypertriglyceridemia in Glut1D on Ketogenic Diet.

    PubMed

    Klepper, Joerg; Leiendecker, Baerbel; Heussinger, Nicole; Lausch, Ekkehart; Bosch, Friedrich

    2016-04-01

    High-fat ketogenic diets are the only treatment available for Glut1 deficiency (Glut1D). Here, we describe an 8-year-old girl with classical Glut1D responsive to a 3:1 ketogenic diet and ethosuximide. After 3 years on the diet a gradual increase of blood lipids was followed by rapid, severe asymptomatic hypertriglyceridemia (1,910 mg/dL). Serum lipid apheresis was required to determine liver, renal, and pancreatic function. A combination of medium chain triglyceride-oil and a reduction of the ketogenic diet to 1:1 ratio normalized triglyceride levels within days but triggered severe myoclonic seizures requiring comedication with sultiam. Severe hypertriglyceridemia in children with Glut1D on ketogenic diets may be underdiagnosed and harmful. In contrast to congenital hypertriglyceridemias, children with Glut1D may be treated effectively by dietary adjustments alone.

  3. Synconset waves and chains: spiking onsets in synchronous populations predict and are predicted by network structure.

    PubMed

    Raghavan, Mohan; Amrutur, Bharadwaj; Narayanan, Rishikesh; Sikdar, Sujit Kumar

    2013-01-01

    Synfire waves are propagating spike packets in synfire chains, which are feedforward chains embedded in random networks. Although synfire waves have proved to be effective quantification for network activity with clear relations to network structure, their utilities are largely limited to feedforward networks with low background activity. To overcome these shortcomings, we describe a novel generalisation of synfire waves, and define 'synconset wave' as a cascade of first spikes within a synchronisation event. Synconset waves would occur in 'synconset chains', which are feedforward chains embedded in possibly heavily recurrent networks with heavy background activity. We probed the utility of synconset waves using simulation of single compartment neuron network models with biophysically realistic conductances, and demonstrated that the spread of synconset waves directly follows from the network connectivity matrix and is modulated by top-down inputs and the resultant oscillations. Such synconset profiles lend intuitive insights into network organisation in terms of connection probabilities between various network regions rather than an adjacency matrix. To test this intuition, we develop a Bayesian likelihood function that quantifies the probability that an observed synfire wave was caused by a given network. Further, we demonstrate it's utility in the inverse problem of identifying the network that caused a given synfire wave. This method was effective even in highly subsampled networks where only a small subset of neurons were accessible, thus showing it's utility in experimental estimation of connectomes in real neuronal-networks. Together, we propose synconset chains/waves as an effective framework for understanding the impact of network structure on function, and as a step towards developing physiology-driven network identification methods. Finally, as synconset chains extend the utilities of synfire chains to arbitrary networks, we suggest utilities of our

  4. Crystal Structures of Mouse CD1d-IGb3 Complex And Its Cognate Valpha14 T Cell Receptor Suggest a Model for Dual Recognition of Foreign And Self Glycolipids

    SciTech Connect

    Zajonc, D.M.; Saveage, P.B.; Bendelac, A.; Wilson, I.A.; Teyton, L.

    2009-05-28

    The semi-invariant Valpha14Jalpha18 T cell receptor (TCR) is expressed by regulatory NKT cells and has the unique ability to recognize chemically diverse ligands presented by CD1d. The crystal structure of CD1d complexed to a natural, endogenous ligand, isoglobotrihexosylceramide (iGb3), illustrates the extent of this diversity when compared to the binding of potent, exogenous ligands, such as alpha-galactosylceramide (alpha-GalCer). A single mode of recognition for these two classes of ligands would then appear problematic for a single T cell receptor. However, the Valpha14 TCR adopts two different conformations in the crystal where, in one configuration, the presence of a larger cavity between the two CDR3 regions could accommodate iGb3 and, in the other, a smaller cavity fits alpha-GalCer more snugly. Alternatively, the extended iGb3 headgroup could be 'squashed' upon docking of the TCR and accommodated between the CD1 and TCR surfaces. Thus, the same TCR may adopt alternative modes of recognition for these foreign and self-ligands for NKT cell activation.

  5. Beyond Donor-Acceptor (D-A) Approach: Structure-Optoelectronic Properties-Organic Photovoltaic Performance Correlation in New D-A1 -D-A2 Low-Bandgap Conjugated Polymers.

    PubMed

    Chochos, Christos L; Drakopoulou, Sofia; Katsouras, Athanasios; Squeo, Benedetta M; Sprau, Christian; Colsmann, Alexander; Gregoriou, Vasilis G; Cando, Alex-Palma; Allard, Sybille; Scherf, Ullrich; Gasparini, Nicola; Kazerouni, Negar; Ameri, Tayebeh; Brabec, Christoph J; Avgeropoulos, Apostolos

    2017-04-01

    Low-bandgap near-infrared polymers are usually synthesized using the common donor-acceptor (D-A) approach. However, recently polymer chemists are introducing more complex chemical concepts for better fine tuning of their optoelectronic properties. Usually these studies are limited to one or two polymer examples in each case study so far, though. In this study, the dependence of optoelectronic and macroscopic (device performance) properties in a series of six new D-A1 -D-A2 low bandgap semiconducting polymers is reported for the first time. Correlation between the chemical structure of single-component polymer films and their optoelectronic properties has been achieved in terms of absorption maxima, optical bandgap, ionization potential, and electron affinity. Preliminary organic photovoltaic results based on blends of the D-A1 -D-A2 polymers as the electron donor mixed with the fullerene derivative [6,6]-phenyl-C71 -butyric acid methyl ester demonstrate power conversion efficiencies close to 4% with short-circuit current densities (J sc ) of around 11 mA cm(-2) , high fill factors up to 0.70, and high open-circuit voltages (V oc s) of 0.70 V. All the devices are fabricated in an inverted architecture with the photoactive layer processed in air with doctor blade technique, showing the compatibility with roll-to-roll large-scale manufacturing processes.

  6. 1D polymeric copper(I) complex [Cu2(μ-(2,6-Cl-ba)2en)(μ-I)2]n with exceptionally short Cusbnd Cu distance: Synthesis, characterization, thermal study and crystal structure

    NASA Astrophysics Data System (ADS)

    Khalaji, Aliakbar Dehno; Peyghoun, Seyyed Javad; Akbari, Alireza; Feizi, Nourollah; Dusek, Michal; Eigner, Vaclav

    2017-01-01

    A new 1D polymeric three coordinated copper(I) complex, [Cu2(μ-(2,6-Cl-ba)2en)(μ-I)2]n, with the bidentate Schiff base ligand N,N‧-bis(2,6-dichlorobenzylidene)ethane-1,2-diamine containing a flexible spacer (dbnd NCH2sbnd CH2sbnd Ndbnd) was synthesized and characterized by elemental analyses, UV-Vis, FT-IR and 1H NMR spectroscopy and thermal analaysis. Its molecular structure was determined by single-crystal X-ray diffraction and shows the (2,6-Cl-ba)2en acts as a bis-monodentate bridging ligand forming the dinuclear [Cu2(μ-(2,6-Cl-ba)2en)] groups. Such dinuclear groups are bridged by two iodine anions [(μ-I)2] to form a 1D polymeric copper(I) complex. The copper(I) ions are coordinated in a distorted trigonal planar geometry by two I atoms and one nitrogen atom of Schiff base ligand (2,6-Cl-ba)2en.

  7. Absolute Side-chain Structure at Position 13 Is Required for the Inhibitory Activity of Bromein*

    PubMed Central

    Sawano, Yoriko; Hatano, Ken-ichi; Miyakawa, Takuya; Tanokura, Masaru

    2008-01-01

    Bromelain isoinhibitor (bromein), a cysteine proteinase inhibitor from pineapple stem, has a unique double-chain structure. The bromein precursor protein includes three homologous inhibitor domains, each containing an interchain peptide between the light and heavy chains. The interchain peptide in the single-chain precursor is immediately processed by bromelain, a target proteinase. In the present study, to clarify the essential inhibitory site of bromein, we constructed 44 kinds of site-directed and deletion mutants and investigated the inhibitory activity of each toward bromelain. As a result, the complete chemical structure of Leu13 in the light chain was revealed to be essential for inhibition. Pro12 prior to the leucine residue was also involved in the inhibitory activity and would control the location of the leucine side chain by the fixed φ dihedral angle of proline. Furthermore, the five-residue length of the interchain peptide was strictly required for the inhibitory activity. On the other hand, no inhibitory activity against bromelain was observed by the substitution of proline for the N terminus residue Thr15 of the interchain peptide. In summary, these mutational analyses of bromein demonstrated that the appropriate position and conformation of Leu13 are absolutely crucial for bromelain inhibition. PMID:18948264

  8. The Effect of Plate Structure on Intraplate Volcanism, Kodiak-Bowie Seamount Chain, Gulf of Alaska

    NASA Astrophysics Data System (ADS)

    Reece, R. S.; Christeson, G. L.; Gulick, S. S.; Barth, G. A.; Van Avendonk, H. J.

    2012-12-01

    Newly acquired ocean bottom seismometer (OBS) and multi-channel seismic (MCS) data in the vicinity of the Kodiak-Bowie Seamount Chain and Aja Fracture Zone reveal the character and structure of the Pacific Plate, overlying sediment, and seamounts in the Gulf of Alaska. Our data include two marine wide-angle OBS profiles, two coincident MCS profiles, and several nearby MCS profiles, including lines parallel to and crossing the Seamount Chain and Fracture Zone. This new data may help to reveal the character of the Kodiak-Bowie Seamount Chain and associated intraplate volcanism, much of which is concealed by the Surveyor and Baranof sedimentary fan systems. The Kodiak-Bowie Seamount Chain stretches over 1000 km across the Gulf of Alaska, from the Aleutian Trench in the northwest to offshore Queen Charlotte Islands in the southeast. The ages of the seamounts range from 24 Ma at Kodiak Seamount in the northwest to ≥0.7 Ma at Bowie Seamount in the southeast. Although the seamounts are largely age-progressive, some members of the chain are dated significantly out of sequence. Previous studies suggest the possibility that the majority of seamounts in the chain could be products of the Bowie plume. The Gulf-wide Aja Fracture Zone intersects the Kodiak-Bowie Seamount Chain in the central Gulf at the location of the seismic lines. Preliminary tomographic inversions of the seismic data reveal significant changes in crustal thickness across the Aja Fracture Zone, including at least a 3 km step up in the moho from south to north. Additionally, the region north of the Fracture Zone exhibits a 3 km thick low velocity zone in the upper crust, which is double the thickness of the same feature south of the fracture zone. This low velocity zone in the upper crust may be representative of intraplate volcanism associated with the Kodiak-Bowie Chain; several higher velocity perturbations within this zone are coincident with the locations of major seamounts. We will further refine

  9. SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures

    PubMed Central

    Nadzirin, Nurul; Gardiner, Eleanor J.; Willett, Peter; Artymiuk, Peter J.; Firdaus-Raih, Mohd

    2012-01-01

    Similarities in the 3D patterns of amino acid side chains can provide insights into their function despite the absence of any detectable sequence or fold similarities. Search for protein sites (SPRITE) and amino acid pattern search for substructures and motifs (ASSAM) are graph theoretical programs that can search for 3D amino side chain matches in protein structures, by representing the amino acid side chains as pseudo-atoms. The geometric relationship of the pseudo-atoms to each other as a pattern can be represented as a labeled graph where the pseudo-atoms are the graph's nodes while the edges are the inter-pseudo-atomic distances. Both programs require the input file to be in the PDB format. The objective of using SPRITE is to identify matches of side chains in a query structure to patterns with characterized function. In contrast, a 3D pattern of interest can be searched for existing occurrences in available PDB structures using ASSAM. Both programs are freely accessible without any login requirement. SPRITE is available at http://mfrlab.org/grafss/sprite/ while ASSAM can be accessed at http://mfrlab.org/grafss/assam/. PMID:22573174

  10. Structural Basis for Substrate Fatty Acyl Chain Specificity: Crystal Structure of Human Very-Long-Chain Acyl-CoA Dehydrogenase

    SciTech Connect

    McAndrew, Ryan P.; Wang, Yudong; Mohsen, Al-Walid; He, Miao; Vockley, Jerry; Kim, Jung-Ja P.

    2008-08-26

    Very-long-chain acyl-CoA dehydrogenase (VLCAD) is a member of the family of acyl-CoA dehydrogenases (ACADs). Unlike the other ACADs, which are soluble homotetramers, VLCAD is a homodimer associated with the mitochondrial membrane. VLCAD also possesses an additional 180 residues in the C terminus that are not present in the other ACADs. We have determined the crystal structure of VLCAD complexed with myristoyl-CoA, obtained by co-crystallization, to 1.91-{angstrom} resolution. The overall fold of the N-terminal {approx}400 residues of VLCAD is similar to that of the soluble ACADs including medium-chain acyl-CoA dehydrogenase (MCAD). The novel C-terminal domain forms an {alpha}-helical bundle that is positioned perpendicular to the two N-terminal helical domains. The fatty acyl moiety of the bound substrate/product is deeply imbedded inside the protein; however, the adenosine pyrophosphate portion of the C14-CoA ligand is disordered because of partial hydrolysis of the thioester bond and high mobility of the CoA moiety. The location of Glu-422 with respect to the C2-C3 of the bound ligand and FAD confirms Glu-422 to be the catalytic base. In MCAD, Gln-95 and Glu-99 form the base of the substrate binding cavity. In VLCAD, these residues are glycines (Gly-175 and Gly-178), allowing the binding channel to extend for an additional 12{angstrom} and permitting substrate acyl chain lengths as long as 24 carbons to bind. VLCAD deficiency is among the more common defects of mitochondrial {beta}-oxidation and, if left undiagnosed, can be fatal. This structure allows us to gain insight into how a variant VLCAD genotype results in a clinical phenotype.

  11. Correlation between morphology, electron band structure, and resistivity of Pb atomic chains on the Si(5 5 3)-Au surface.

    PubMed

    Jałochowski, M; Kwapiński, T; Łukasik, P; Nita, P; Kopciuszyński, M

    2016-07-20

    Structural and electron transport properties of multiple Pb atomic chains fabricated on the Si(5 5 3)-Au surface are investigated using scanning tunneling spectroscopy, reflection high electron energy diffraction, angular resolved photoemission electron spectroscopy and in situ electrical resistance. The study shows that Pb atomic chains growth modulates the electron band structure of pristine Si(5 5 3)-Au surface and hence changes its sheet resistivity. Strong correlation between chains morphology, electron band structure and electron transport properties is found. To explain experimental findings a theoretical tight-binding model of multiple atomic chains interacting on effective substrate is proposed.

  12. Magnetism and electronic structure of Fe chains and nano-wires

    NASA Astrophysics Data System (ADS)

    Yang, Tzong-Jer; Zhao, Yu-Jun; Freeman, A. J.

    2004-05-01

    The electronic and magnetic structures of an Fe linear chain and FCC and BCC nano-wires were determined by accurate first-principles self-consistent full potential linearized augmented plane wave calculations. The one-dimensional nature of the systems results in dramatic changes in their properties—as expected from the early predictions of Weinert and Freeman (J. Mag. Magn. Mater. 38 (1983) 23) for linear transition metal chains: a high density of states arising from van Hove singularities, large s-d-exchange splittings (larger in the chain than in the wires) and filled majority d bands (i.e., a "strong Stoner" ferromagnet) and strikingly enhanced Fe magnetic moments that depend on their coordination number. These unusual and distinctive properties are expected to invite somewhat unique experimental characterizations.

  13. Communication: Role of short chain branching in polymer structure and dynamics.

    PubMed

    Kim, Jun Mo; Baig, Chunggi

    2016-02-28

    A comprehensive understanding of chain-branching effects, essential for establishing general knowledge of the structure-property-phenomenon relationship in polymer science, has not yet been found, due to a critical lack of knowledge on the role of short-chain branches, the effects of which have mostly been neglected in favor of the standard entropic-based concepts of long polymers. Here, we show a significant effect of short-chain branching on the structural and dynamical properties of polymeric materials, and reveal the molecular origins behind the fundamental role of short branches, via atomistic nonequilibrium molecular dynamics and mesoscopic Brownian dynamics by systematically varying the strength of the mobility of short branches. We demonstrate that the fast random Brownian kinetics inherent to short branches plays a key role in governing the overall structure and dynamics of polymers, leading to a compact molecular structure and, under external fields, to a lesser degree of structural deformation of polymer, to a reduced shear-thinning behavior, and to a smaller elastic stress, compared with their linear analogues. Their fast dynamical nature being unaffected by practical flow fields owing to their very short characteristic time scale, short branches would substantially influence (i.e., facilitate) the overall relaxation behavior of polymeric materials under various flowing conditions.

  14. Helical structures in vertically aligned dust particle chains in a complex plasma.

    PubMed

    Hyde, Truell W; Kong, Jie; Matthews, Lorin S

    2013-05-01

    Self-assembly of structures from vertically aligned, charged dust particle bundles within a glass box placed on the lower, powered electrode of a Gaseous Electronics Conference rf reference cell were produced and examined experimentally. Self-organized formation of one-dimensional vertical chains, two-dimensional zigzag structures, and three-dimensional helical structures of triangular, quadrangular, pentagonal, hexagonal, and heptagonal symmetries are shown to occur. System evolution is shown to progress from a one-dimensional chain structure, through a zigzag transition to a two-dimensional, spindlelike structure, and then to various three-dimensional, helical structures exhibiting multiple symmetries. Stable configurations are found to be dependent upon the system confinement, γ(2)=(ω(0h)/ω(0v))(2) (where ω(0h,v) are the horizontal and vertical dust resonance frequencies), the total number of particles within a bundle, and the rf power. For clusters having fixed numbers of particles, the rf power at which structural phase transitions occur is repeatable and exhibits no observable hysteresis. The critical conditions for these structural phase transitions as well as the basic symmetry exhibited by the one-, two-, and three-dimensional structures that subsequently develop are in good agreement with the theoretically predicted configurations of minimum energy determined employing molecular dynamics simulations for charged dust particles confined in a prolate, spheroidal potential as presented theoretically by Kamimura and Ishihara [Kamimura and Ishihara, Phys. Rev. E 85, 016406 (2012)].

  15. Synconset Waves and Chains: Spiking Onsets in Synchronous Populations Predict and Are Predicted by Network Structure

    PubMed Central

    Raghavan, Mohan; Amrutur, Bharadwaj; Narayanan, Rishikesh; Sikdar, Sujit Kumar

    2013-01-01

    Synfire waves are propagating spike packets in synfire chains, which are feedforward chains embedded in random networks. Although synfire waves have proved to be effective quantification for network activity with clear relations to network structure, their utilities are largely limited to feedforward networks with low background activity. To overcome these shortcomings, we describe a novel generalisation of synfire waves, and define ‘synconset wave’ as a cascade of first spikes within a synchronisation event. Synconset waves would occur in ‘synconset chains’, which are feedforward chains embedded in possibly heavily recurrent networks with heavy background activity. We probed the utility of synconset waves using simulation of single compartment neuron network models with biophysically realistic conductances, and demonstrated that the spread of synconset waves directly follows from the network connectivity matrix and is modulated by top-down inputs and the resultant oscillations. Such synconset profiles lend intuitive insights into network organisation in terms of connection probabilities between various network regions rather than an adjacency matrix. To test this intuition, we develop a Bayesian likelihood function that quantifies the probability that an observed synfire wave was caused by a given network. Further, we demonstrate it's utility in the inverse problem of identifying the network that caused a given synfire wave. This method was effective even in highly subsampled networks where only a small subset of neurons were accessible, thus showing it's utility in experimental estimation of connectomes in real neuronal-networks. Together, we propose synconset chains/waves as an effective framework for understanding the impact of network structure on function, and as a step towards developing physiology-driven network identification methods. Finally, as synconset chains extend the utilities of synfire chains to arbitrary networks, we suggest utilities of

  16. Conceptual Model of Supply Chain Structure Mapping - A Case of Subsidized LPG Commodity in Yogyakarta

    NASA Astrophysics Data System (ADS)

    Sulistio, Joko; Thoif, Afifuddin; Fitri Alindira, Aulia

    2016-01-01

    — In 2007, the government launched a conversion program of kerosene to LPG by issuing a Presidential Regulation No. 104/2007 on Supply, Distribution and Pricing LPG 3 Kg. Article 2 on the regulation says that setting the supply, distribution, and pricing of LPG 3 Kg include planning an annual sales volume of enterprises, the reference price and the retail price and conditions of export and import of LPG 3 Kg in order to reduce subsidies Kerosene especially to divert the use of kerosene according to government policy. In principle, the purpose of this policy is to reduce energy subsidies on commodities, especially Kerosene. Although the government claimed the conversion program is success, there are few problems arising from conversion program. In 2014, many scarcity and high price of LPG 3 Kg were reported. In this case, Pertamina was given full authority to manage all supply chain and distribution. Because the root of the problem of scarcity that occurred in the supply chain system has not been explained, the proposed solutions will also be partial and not comprehensive. Thus, this research will build a structural map of the causes of supply chain system LPG 3 Kg, as well as providing a comprehensive picture of system dynamics of LPG 3 Kg supply chain system which applied in Indonesia. And the result is expected as in form of Causal Loop Diagram of supply chain system.

  17. Untangleing the effects of chain rigidity on the structure and dynamics of strongly adsorbed polymer melts

    DOE PAGES

    Carrillo, Jan-Michael Y.; Cheng, Shiwang; Kumar, Rajeev; ...

    2015-06-11

    Here, we present a detailed analysis of coarse-grained molecular dynamics simulations of semiflexible polymer melts in contact with a strongly adsorbing substrate. We have characterized the segments in the interfacial layer by counting the number of trains, loops, tails and unadsorbed segments. For more rigid chains, a tail and an adsorbed segment (a train) dominate while loops are more prevalent in more flexible chains. The tails exhibit a non-uniformly stretched conformation akin to the polydispersed pseudobrush envisioned by Guiselin. To probe the dynamics of the segments we computed the layer z-resolved intermediate coherent collective dynamics structure factor, S(q, t, z),more » mean-square displacement of segments, and the 2nd Legendre polynomial of the time-autocorrelation of unit bond vectors, 2[ni(t,z)•ni(0,z)]>. Our results show that segmental dynamics is slower for stiffer chains and there is a strong correlation between the structure and dynamics in the interfacial layer. There is no glassy layer, and the slowing down in dynamics of stiffer chains in the adsorbed region can be attributed to the densification and the more persistent layering of segments.« less

  18. Ubiquitin Ser65 phosphorylation affects ubiquitin structure, chain assembly and hydrolysis.

    PubMed

    Wauer, Tobias; Swatek, Kirby N; Wagstaff, Jane L; Gladkova, Christina; Pruneda, Jonathan N; Michel, Martin A; Gersch, Malte; Johnson, Christopher M; Freund, Stefan M V; Komander, David

    2015-02-03

    The protein kinase PINK1 was recently shown to phosphorylate ubiquitin (Ub) on Ser65, and phosphoUb activates the E3 ligase Parkin allosterically. Here, we show that PINK1 can phosphorylate every Ub in Ub chains. Moreover, Ser65 phosphorylation alters Ub structure, generating two conformations in solution. A crystal structure of the major conformation resembles Ub but has altered surface properties. NMR reveals a second phosphoUb conformation in which β5-strand slippage retracts the C-terminal tail by two residues into the Ub core. We further show that phosphoUb has no effect on E1-mediated E2 charging but can affect discharging of E2 enzymes to form polyUb chains. Notably, UBE2R1- (CDC34), UBE2N/UBE2V1- (UBC13/UEV1A), TRAF6- and HOIP-mediated chain assembly is inhibited by phosphoUb. While Lys63-linked poly-phosphoUb is recognized by the TAB2 NZF Ub binding domain (UBD), 10 out of 12 deubiquitinases (DUBs), including USP8, USP15 and USP30, are impaired in hydrolyzing phosphoUb chains. Hence, Ub phosphorylation has repercussions for ubiquitination and deubiquitination cascades beyond Parkin activation and may provide an independent layer of regulation in the Ub system.

  19. Conserved structure of amphibian T-cell antigen receptor beta chain.

    PubMed Central

    Fellah, J S; Kerfourn, F; Guillet, F; Charlemagne, J

    1993-01-01

    All jawed vertebrates possess well-differentiated thymuses and elicit T-cell-like cell-mediated responses; however, no surface T-cell receptor (TCR) molecules or TCR genes have been identified in ectothermic vertebrate species. Here we describe cDNA clones from an amphibian species, Ambystoma mexicanum (the Mexican axolotl), that have sequences highly homologous to the avian and mammalian TCR beta chains. The cloned amphibian beta chain variable region (V beta) shares most of the structural characteristics with the more evolved vertebrate V beta and presents approximately 56% amino acid identities with the murine V beta 14 and human V beta 18 families. The two different cloned axolotl beta chain joining regions (J beta) were found to have conserved all the invariant mammalian J beta residues, and in addition, the presence of a conserved glycine at the V beta-J beta junction suggests the existence of diversity elements. The extracellular domains of the two axolotl beta chain constant region isotypes C beta 1 and C beta 2 show an impressively high degree of identity, thus suggesting that a very efficient mechanism of gene correction has been in operation to preserve this structure at least from the early tetrapod evolution. The transmembrane axolotl C beta domains have been less well conserved when compared to the mammalian C beta but they do maintain the lysine residue that is thought to be involved in the charged interaction between the TCR alpha beta heterodimer and the CD3 complex. Images Fig. 1 PMID:8341702

  20. Quasiparticle band structure of infinite hydrogen fluoride and hydrogen chloride chains.

    PubMed

    Buth, Christian

    2006-10-21

    We study the quasiparticle band structure of isolated, infinite (HF)(infinity) and (HCl)(infinity) bent (zigzag) chains and examine the effect of the crystal field on the energy levels of the constituent monomers. The chains are one of the simplest but realistic models of the corresponding three-dimensional crystalline solids. To describe the isolated monomers and the chains, we set out from the Hartree-Fock approximation, harnessing the advanced Green's function methods local molecular orbital algebraic diagrammatic construction (ADC) scheme and local crystal orbital ADC (CO-ADC) in a strict second order approximation, ADC(2,2) and CO-ADC(2,2), respectively, to account for electron correlations. The configuration space of the periodic correlation calculations is found to converge rapidly only requiring nearest-neighbor contributions to be regarded. Although electron correlations cause a pronounced shift of the quasiparticle band structure of the chains with respect to the Hartree-Fock result, the bandwidth essentially remains unaltered in contrast to, e.g., covalently bound compounds.

  1. Untangleing the effects of chain rigidity on the structure and dynamics of strongly adsorbed polymer melts

    SciTech Connect

    Carrillo, Jan-Michael Y.; Cheng, Shiwang; Kumar, Rajeev; Goswami, Monojoy; Sokolov, Alexei P; Sumpter, Bobby G.

    2015-06-11

    Here, we present a detailed analysis of coarse-grained molecular dynamics simulations of semiflexible polymer melts in contact with a strongly adsorbing substrate. We have characterized the segments in the interfacial layer by counting the number of trains, loops, tails and unadsorbed segments. For more rigid chains, a tail and an adsorbed segment (a train) dominate while loops are more prevalent in more flexible chains. The tails exhibit a non-uniformly stretched conformation akin to the polydispersed pseudobrush envisioned by Guiselin. To probe the dynamics of the segments we computed the layer z-resolved intermediate coherent collective dynamics structure factor, S(q, t, z), mean-square displacement of segments, and the 2nd Legendre polynomial of the time-autocorrelation of unit bond vectors, 2[ni(t,z)•ni(0,z)]>. Our results show that segmental dynamics is slower for stiffer chains and there is a strong correlation between the structure and dynamics in the interfacial layer. There is no glassy layer, and the slowing down in dynamics of stiffer chains in the adsorbed region can be attributed to the densification and the more persistent layering of segments.

  2. Probing structure-induced optical behavior in a new class of self-activated luminescent 0D/1D CaWO₄ metal oxide – CdSe nanocrystal composite heterostructures

    DOE PAGES

    Han, Jinkyu; McBean, Coray; Wang, Lei; ...

    2015-01-30

    In this report, we synthesize and characterize the structural and optical properties of novel heterostructures composed of (i) semiconducting nanocrystalline CdSe quantum dot (QDs) coupled with (ii) both one and zero-dimensional (1D and 0D) motifs of self-activated luminescence CaWO₄ metal oxides. Specifically, ~4 nm CdSe QDs have been anchored onto (i) high-aspect ratio 1D nanowires, measuring ~230 nm in diameter and ~3 μm in length, as well as onto (ii) crystalline 0D nanoparticles (possessing an average diameter of ~ 80 nm) of CaWO₄ through the mediation of 3-mercaptopropionic acid (MPA) as a connecting linker. Composite formation was confirmed by complementarymore » electron microscopy and spectroscopy (i.e. IR and Raman) data. In terms of luminescent properties, our results show that our 1D and 0D heterostructures evince photoluminescence (PL) quenching and shortened PL lifetimes of CaWO₄ as compared with unbound CaWO₄. We propose that a photo-induced electron transfer process occurs from CaWO₄ to CdSe QDs, a scenario which has been confirmed by NEXAFS measurements and which highlights a decrease in the number of unoccupied orbitals in the conduction bands of CdSe QDs. By contrast, the PL signature and lifetimes of MPA-capped CdSe QDs within these heterostructures do not exhibit noticeable changes as compared with unbound MPA-capped CdSe QDs. The striking difference in optical behavior between CaWO₄ nanostructures and CdSe QDs within our heterostructures can be correlated with the relative positions of their conduction and valence energy band levels. In addition, the PL quenching behaviors for CaWO₄ within the heterostructure configuration were examined by systematically varying (i) the quantities and coverage densities of CdSe QDs as well as (ii) the intrinsic morphology (and by extension, the inherent crystallite size) of CaWO₄ itself.« less

  3. A novel method of preparing the monoform structure of catalytic antibody light chain.

    PubMed

    Hifumi, Emi; Matsumoto, Shingo; Nakashima, Hiroki; Itonaga, Shogo; Arakawa, Mitsue; Katayama, Yoshiki; Kato, Ryuichi; Uda, Taizo

    2016-02-01

    Along with the development of antibody drugs and catalytic antibodies, the structural diversity (heterogeneity) of antibodies has been given attention. For >20 yr, detailed studies on the subject have not been conducted, because the phenomenon presents many difficult and complex problems. Structural diversity provides some (or many) isoforms of an antibody distinguished by different charges, different molecular sizes, and modifications of amino acid residues. For practical use, the antibody and the subunits must have a defined structure. In recent work, we have found that the copper (Cu) ion plays a substantial role in solving the diversity problem. In the current study, we used several catalytic antibody light chains to examine the effect of the Cu ion. In all cases, the different electrical charges of the molecule converged to a single charge, giving 1 peak in cation-exchange chromatography, as well as a single spot in 2-dimensional gel electrophoresis. The Cu-binding site was investigated by using mutagenesis, ultraviolet-visible spectroscopy, atomic force microscope analysis, and molecular modeling, which suggested that histidine and cysteine residues close to the C-terminus are involved with the binding site. The constant region domain of the antibody light chain played an important role in the heterogeneity of the light chain. Our findings may be a significant tool for preparing a single defined, not multiple, isoform structure.

  4. Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations.

    PubMed

    Porebski, Przemyslaw Jerzy; Cymborowski, Marcin; Pasenkiewicz-Gierula, Marta; Minor, Wladek

    2016-02-01

    Improvements in crystallographic hardware and software have allowed automated structure-solution pipelines to approach a near-`one-click' experience for the initial determination of macromolecular structures. However, in many cases the resulting initial model requires a laborious, iterative process of refinement and validation. A new method has been developed for the automatic modeling of side-chain conformations that takes advantage of rotamer-prediction methods in a crystallographic context. The algorithm, which is based on deterministic dead-end elimination (DEE) theory, uses new dense conformer libraries and a hybrid energy function derived from experimental data and prior information about rotamer frequencies to find the optimal conformation of each side chain. In contrast to existing methods, which incorporate the electron-density term into protein-modeling frameworks, the proposed algorithm is designed to take advantage of the highly discriminatory nature of electron-density maps. This method has been implemented in the program Fitmunk, which uses extensive conformational sampling. This improves the accuracy of the modeling and makes it a versatile tool for crystallographic model building, refinement and validation. Fitmunk was extensively tested on over 115 new structures, as well as a subset of 1100 structures from the PDB. It is demonstrated that the ability of Fitmunk to model more than 95% of side chains accurately is beneficial for improving the quality of crystallographic protein models, especially at medium and low resolutions. Fitmunk can be used for model validation of existing structures and as a tool to assess whether side chains are modeled optimally or could be better fitted into electron density. Fitmunk is available as a web service at http://kniahini.med.virginia.edu/fitmunk/server/ or at http://fitmunk.bitbucket.org/.

  5. Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations

    PubMed Central

    Porebski, Przemyslaw Jerzy; Cymborowski, Marcin; Pasenkiewicz-Gierula, Marta; Minor, Wladek

    2016-01-01

    Improvements in crystallographic hardware and software have allowed automated structure-solution pipelines to approach a near-‘one-click’ experience for the initial determination of macromolecular structures. However, in many cases the resulting initial model requires a laborious, iterative process of refinement and validation. A new method has been developed for the automatic modeling of side-chain conformations that takes advantage of rotamer-prediction methods in a crystallographic context. The algorithm, which is based on deterministic dead-end elimination (DEE) theory, uses new dense conformer libraries and a hybrid energy function derived from experimental data and prior information about rotamer frequencies to find the optimal conformation of each side chain. In contrast to existing methods, which incorporate the electron-density term into protein-modeling frameworks, the proposed algorithm is designed to take advantage of the highly discriminatory nature of electron-density maps. This method has been implemented in the program Fitmunk, which uses extensive conformational sampling. This improves the accuracy of the modeling and makes it a versatile tool for crystallographic model building, refinement and validation. Fitmunk was extensively tested on over 115 new structures, as well as a subset of 1100 structures from the PDB. It is demonstrated that the ability of Fitmunk to model more than 95% of side chains accurately is beneficial for improving the quality of crystallographic protein models, especially at medium and low resolutions. Fitmunk can be used for model validation of existing structures and as a tool to assess whether side chains are modeled optimally or could be better fitted into electron density. Fitmunk is available as a web service at http://kniahini.med.virginia.edu/fitmunk/server/ or at http://fitmunk.bitbucket.org/. PMID:26894674

  6. Energetically unfavorable amide conformations for N6-acetyllysine side chains in refined protein structures.

    PubMed

    Genshaft, Alexander; Moser, Joe-Ann S; D'Antonio, Edward L; Bowman, Christine M; Christianson, David W

    2013-06-01

    The reversible acetylation of lysine to form N6-acetyllysine in the regulation of protein function is a hallmark of epigenetics. Acetylation of the positively charged amino group of the lysine side chain generates a neutral N-alkylacetamide moiety that serves as a molecular "switch" for the modulation of protein function and protein-protein interactions. We now report the analysis of 381 N6-acetyllysine side chain amide conformations as found in 79 protein crystal structures and 11 protein NMR structures deposited in the Protein Data Bank (PDB) of the Research Collaboratory for Structural Bioinformatics. We find that only 74.3% of N6-acetyllysine residues in protein crystal structures and 46.5% in protein NMR structures contain amide groups with energetically preferred trans or generously trans conformations. Surprisingly, 17.6% of N6-acetyllysine residues in protein crystal structures and 5.3% in protein NMR structures contain amide groups with energetically unfavorable cis or generously cis conformations. Even more surprisingly, 8.1% of N6-acetyllysine residues in protein crystal structures and 48.2% in NMR structures contain amide groups with energetically prohibitive twisted conformations that approach the transition state structure for cis-trans isomerization. In contrast, 109 unique N-alkylacetamide groups contained in 84 highly accurate small molecule crystal structures retrieved from the Cambridge Structural Database exclusively adopt energetically preferred trans conformations. Therefore, we conclude that cis and twisted N6-acetyllysine amides in protein structures deposited in the PDB are erroneously modeled due to their energetically unfavorable or prohibitive conformations.

  7. Energetic, Structural, and Antimicrobial Analyses of [beta]-Lactam Side Chain Recognition by [beta]-Lactamases

    SciTech Connect

    Caselli, E.; Powers, R.A.; Blaszczak, L.C.; Wu, C.Y.E.; Prati, F.; Shoichet, B.K.

    2010-03-05

    Penicillins and cephalosporins are among the most widely used and successful antibiotics. The emergence of resistance to these {beta}-lactams, most often through bacterial expression of {beta}-lactamases, threatens public health. To understand how {beta}-lactamases recognize their substrates, it would be helpful to know their binding energies. Unfortunately, these have been difficult to measure because {beta}-lactams form covalent adducts with {beta}-lactamases. This has complicated functional analyses and inhibitor design. To investigate the contribution to interaction energy of the key amide (R1) side chain of {beta}-lactam antibiotics, eight acylglycineboronic acids that bear the side chains of characteristic penicillins and cephalosporins, as well as four other analogs, were synthesized. These transition-state analogs form reversible adducts with serine {beta}-lactamases. Therefore, binding energies can be calculated directly from K{sub i} values. The K{sub i} values measured span four orders of magnitude against the Group I {beta}-lactamase AmpC and three orders of magnitude against the Group II {beta}-lactamase TEM-1. The acylglycineboronic acids have K{sub i} values as low as 20 nM against AmpC and as low as 390 nM against TEM-1. The inhibitors showed little activity against serine proteases, such as chymotrypsin. R1 side chains characteristic of {beta}-lactam inhibitors did not have better affinity for AmpC than did side chains characteristic of {beta}-lactam substrates. Two of the inhibitors reversed the resistance of pathogenic bacteria to {beta}-lactams in cell culture. Structures of two inhibitors in their complexes with AmpC were determined by X-ray crystallography to 1.90 {angstrom} and 1.75 {angstrom} resolution; these structures suggest interactions that are important to the affinity of the inhibitors. Acylglycineboronic acids allow us to begin to dissect interaction energies between {beta}-lactam side chains and {beta}-lactamases. Surprisingly

  8. Spin structure factors of Heisenberg spin chain in the presence of anisotropy and magnetic field

    NASA Astrophysics Data System (ADS)

    Rezania, H.

    2017-02-01

    We have theoretically studied the spin structure factors of spin chain in the presence of longitudinal field and transverse anisotropy. The possible effects of easy axis magnetization are investigated in terms of anisotropy in the Heisenberg interactions. This anisotropy is considered for exchange coupling constants perpendicular to magnetic field direction. The original spin model hamiltonian is mapped to a bosonic model via a hard core bosonic transformation where an infinite hard core repulsion is imposed to constrain one boson occupation per site. Using Green's function approach, the energy spectrum of quasiparticle excitation has been obtained. The spectrum of the bosonic gas has been implemented in order to obtain two particle propagator which corresponds to spin structure factor of original Heisenberg chain model Hamiltonian. The results show the position of peak in the longitudinal structure factor at fixed value for anisotropy moves to higher frequency with magnetic field. Also the intensity of dynamical structure factor decreases with magnetic field. A small dependence of longitudinal dynamical spin structure factor on the anisotropy is observed for fixed value of magnetic field. Our results show longitudinal static structure factor is found to be monotonically increasing with magnetic field due to increase of spins aligning along magnetic field. Furthermore the dispersion behaviors of static longitudinal and transverse structure factors for different magnetic fields and anisotropy parameters are addressed.

  9. The single chain limit of structural relaxation in a polyolefin blend

    NASA Astrophysics Data System (ADS)

    May, Andrew F.; Maranas, Janna K.

    2006-07-01

    The influence of composition on component dynamics and relevant static properties in a miscible polymer blend is investigated using molecular dynamics simulation. Emphasis is placed on dynamics in the single chain dilution limit, as this limit isolates the role of inherent component mobility in the polymer's dynamic behavior when placed in a blend. For our systems, a biased local concentration affecting dynamics must arise primarily from chain connectivity, which is quantified by the self-concentration, because concentration fluctuations are minimized due to restraints on chain lengths arising from simulation considerations. The polyolefins simulated [poly(ethylene-propylene) (PEP) and poly(ethylene-butene) (PEB)] have similar structures and glass transition temperatures, and all interactions are dispersive in nature. We find that the dependence of dynamics upon composition differs between the two materials. Specifically, PEB (slower component) is more influenced by the environment than PEP. This is linked to a smaller self-concentration for PEB than PEP. We examine the accuracy of the Lodge-McLeish model (which is based on chain connectivity acting over the Kuhn segment length) in predicting simulation results for effective concentration. The model predicts the simulation results with high accuracy when the model's single parameter, the self-concentration, is calculated from simulation data. However, when utilizing the theoretical prediction of the self-concentration the model is not quantitatively accurate. The ability of the model to link the simulated self-concentration with biased local compositions at the Kuhn segment length provides strong support for the claim that chain connectivity is the leading cause of distinct mobility in polymer blends. Additionally, the direct link between the willingness of a polymer to be influenced by the environment and the value of the self-concentration emphasizes the importance of the chain connectivity. Furthermore, these

  10. Cryo-EM reveals the steric zipper structure of a light chain-derived amyloid fibril

    PubMed Central

    Schmidt, Andreas; Annamalai, Karthikeyan; Schmidt, Matthias; Grigorieff, Nikolaus; Fändrich, Marcus

    2016-01-01

    Amyloid fibrils are proteinaceous aggregates associated with diseases in humans and animals. The fibrils are defined by intermolecular interactions between the fibril-forming polypeptide chains, but it has so far remained difficult to reveal the assembly of the peptide subunits in a full-scale fibril. Using electron cryomicroscopy (cryo-EM), we present a reconstruction of a fibril formed from the pathogenic core of an amyloidogenic immunoglobulin (Ig) light chain. The fibril density shows a lattice-like assembly of face-to-face packed peptide dimers that corresponds to the structure of steric zippers in peptide crystals. Interpretation of the density map with a molecular model enabled us to identify the intermolecular interactions between the peptides and rationalize the hierarchical structure of the fibril based on simple chemical principles. PMID:27185936

  11. Customer involvement in greening the supply chain: an interpretive structural modeling methodology

    NASA Astrophysics Data System (ADS)

    Kumar, Sanjay; Luthra, Sunil; Haleem, Abid

    2013-04-01

    The role of customers in green supply chain management needs to be identified and recognized as an important research area. This paper is an attempt to explore the involvement aspect of customers towards greening of the supply chain (SC). An empirical research approach has been used to collect primary data to rank different variables for effective customer involvement in green concept implementation in SC. An interpretive structural-based model has been presented, and variables have been classified using matrice d' impacts croises- multiplication appliqué a un classement analysis. Contextual relationships among variables have been established using experts' opinions. The research may help practicing managers to understand the interaction among variables affecting customer involvement. Further, this understanding may be helpful in framing the policies and strategies to green SC. Analyzing interaction among variables for effective customer involvement in greening SC to develop the structural model in the Indian perspective is an effort towards promoting environment consciousness.

  12. Characteristic Features of Molecular Structure and Packing of Organopolysilanes with Asymmetric Side Chains

    NASA Astrophysics Data System (ADS)

    Furukawa, Shoji; Ohta, Hidetaka

    2005-01-01

    The molecular structure and packing of poly(methyl ethyl silane), [(CH3)Si(C2H5)]n, and poly(methyl n-propyl silane), [(CH3)Si(C3H7)]n, have been examined by the X-ray diffraction method. For poly(methyl ethyl silane), several configurations are possible for the arrangement of the C2H5 group, whereas the C3H7 groups stretch along one equivalent direction for poly(methyl n-propyl silane). In both cases, the molecular structure and packing are mostly determined by the intramolecular steric hindrance and van der Waals interaction between side chains, which is the same as that of polysilanes with symmetric side chains.

  13. Crystal Structure of a Phosphorylated Light Chain Domain of Scallop Smooth-Muscle Myosin

    SciTech Connect

    Kumar, V.S.; Robinson, H.; O-Neall-Hennessey, E.; Reshetnikova, L.; Brown, J. H.; Szent-Gyorgyi, A. G.; Cohen, C.

    2011-11-02

    We have determined the crystal structure of a phosphorylated smooth-muscle myosin light chain domain (LCD). This reconstituted LCD is of a sea scallop catch muscle myosin with its phosphorylatable regulatory light chain (RLC SmoA). In the crystal structure, Arg{sup 16}, an arginine residue that is present in this isoform but not in vertebrate smooth-muscle RLC, stabilizes the phosphorylation site. This arginine interacts with the carbonyl group of the phosphorylation-site serine in the unphosphorylated LCD (determined previously), and with the phosphate group when the serine is phosphorylated. However, the overall conformation of the LCD is essentially unchanged upon phosphorylation. This result provides additional evidence that phosphorylation of the RLC is unlikely to act as an on-switch in regulation of scallop catch muscle myosin.

  14. Fiber Bragg gratings sensing network with a bus chain typology structure

    NASA Astrophysics Data System (ADS)

    Wen, Xiaoyan; Shuai, Huang; Zhu, Fangdong; Zhang, Dongsheng

    2016-06-01

    A fiber Bragg grating (FBG) sensing network with a bus chain typology structure based on time-division multiplexing (TDM) technology has been developed. Each FBG sensor was placed in an isolated branching circuit separated by an optical splitter. By doing this, multiple reflection and spectrum shadow, which are common in a traditional TDM network, were eliminated since incident light reflected by each sensor did not go through the other sensors. Interference among different FBGs was also avoided. The system was experimentally verified by constructing such a network with 17 FBGs involved. Wavelength and position interrogation were successfully realized. Temperature experiment was carried out on four of the FBGs and the sensitivity was 9.87, 9.92, 9.91, and 9.97 pm/°C, respectively. The durability, reliability, and measuring accuracy of the sensing network were effectively improved due to the bus chain typology structure.

  15. Single chain structure in thin polymer films: corrections to Flory's and Silberberg's hypotheses

    NASA Astrophysics Data System (ADS)

    Cavallo, A.; Müller, M.; Wittmer, J. P.; Johner, A.; Binder, K.

    2005-05-01

    Conformational properties of polymer melts confined between two hard structureless walls are investigated by Monte Carlo simulation of the bond fluctuation model. Parallel and perpendicular components of chain extension, bond-bond correlation function and structure factor are computed and compared with recent theoretical approaches attempting to go beyond Flory's and Silberberg's hypotheses. We demonstrate that for ultrathin films where the thickness, H, is smaller than the excluded volume screening length (blob size), ξ, the chain size parallel to the walls diverges logarithmically, R2/2Napb2+clog(N) with c~1/H. The corresponding bond-bond correlation function decreases like a power law, C(s) = d/sω with s being the curvilinear distance between bonds and ω = 1. Upon increasing the film thickness, H, we find—in contrast to Flory's hypothesis—the bulk exponent ω = 3/2 and, more importantly, a decreasing d(H) that gives direct evidence for an enhanced self-interaction of chain segments reflected at the walls. Systematic deviations from the Kratky plateau as a function of H are found for the single chain form factor parallel to the walls in agreement with the non-monotonic behaviour predicted by theory. This structure in the Kratky plateau might give rise to an erroneous estimation of the chain extension from scattering experiments. For large H the deviations are linear with the wavevector, q, but are very weak. In contrast, for ultrathin films, H<ξ, very strong corrections (albeit logarithmic in q) are found suggesting a possible experimental verification of our results.

  16. Analysis of the Rotational Structure in the High-Resolution Infrared Spectra of cis,cis- and trans,trans-1,4-DIFLUOROBUTADIENE-1-d_{1} and trans,trans-1,4-DIFLUOROBUTADIENE-1,4-d_{2}

    NASA Astrophysics Data System (ADS)

    Craig, Norman C.; Chen, Yihui; Lu, Yuhua; Neese, Christopher F.; Nemchick, Deacon J.; Blake, Thomas A.

    2013-06-01

    Samples of cis,cis- and trans,trans-1,4-difluorobutadiene-1-d_{1} (DFBD) and trans,trans-DFBD-1,4-d_{2} have been synthesized and investigated with high-resolution (0.0015 cm^{-1}) infrared spectroscopy. For the first two species the rotational structure in more than one band has been analyzed. For the 1,4-d_{2} species the spectrum of only one C-type band was available in an isotopic mixture. Ground state rotational constants are reported for all three molecules. It is proposed that quartic centrifugal distortion constants computed with a B3LYP/cc-pVTZ model can be used to assess the quality of observed rotational constants. The favorable comparison of predicted and observed ground state rotational constants for all four ^{13}C species of cis,trans-DFBD, which is MW active, demonstrates that the ground state rotational constants for the ^{13}C species of the cis,cis and trans,trans isomers can be successfully predicted with high accuracy. Rotational constants for a full set of isotopologues will be used to determine accurate semiexperimental equilibrium structures of the cis,cis and trans,trans species of DFBD. N. C. Craig, C. M. Oertel, D. C. Oertel, M. J. Tubergen, R. J. Lavrich, A. M Chaka J. Phys. Chem. A 106, 4230-4235 (2002).

  17. Ricin A-chain structural determinant for binding substrate analogues: a molecular dynamics simulation analysis.

    PubMed

    Olson, M A

    1997-01-01

    Ricin A-chain is a cytotoxic protein that attacks ribosomes by hydrolyzing a specific adenine base from a highly conserved, single-stranded rRNA hairpin containing the tetraloop sequence GAGA. Molecular-dynamics simulation methods are used to analyze the structural determinant for three substrate analogues bound to the ricin A-chain molecule. Simulations were applied to the binding of the dinucleotide adenyl-3',5'-guanosine employing the x-ray crystal structure of the ricin complex and a modeled CGAGAG hexanucleotide loop taken from the NMR solution structure of a 29-mer oligonucleotide hairpin. A third simulation model is also presented describing a conformational search of the docked 29-mer structure by using a simulated-annealing method. Analysis of the structural interaction energies for each model shows the overall binding dominated by nonspecific interactions, which are mediated by specific arginine contracts from the highly basic region on the protein surface. The tetraloop conformation of the 29-mer was found to make specific interactions with conserved protein residues, in a manner that favored the GAGA sequence. A comparison of the two docked loop conformations with the NMR structure revealed significant positional deviations, suggesting that ricin may use an induced fit mechanism to recognize and bind the rRNA substrate. The conserved Tyr-80 may play an important conformational entropic role in the binding and release of the target adenine in the active site.

  18. Synthesis and characterization of metal(II) fluconazole complexes: Chain-like structure and photoluminescence

    NASA Astrophysics Data System (ADS)

    Gong, Yun; Hu, Chang Wen; Xia, Zhi Ning

    2007-06-01

    Three coordination polymers (flu) 2CuBr 2·2H 2O ( 1), (flu) 2Zn(ClO 4) 2·2H 2O ( 2), (flu) 4Ni 2(H 2O) 4(Mo 8O 26) · 6H 2O ( 3), (flu = fluconazole) have been hydrothermally synthesized and characterized by elemental analysis, IR and single-crystal X-ray diffraction. Compounds 1- 3 exhibit similar one dimensional chain-like structures linked by double stranded fluconazole-bridge. In the self-assembly of compounds 1- 3, the introduction of anions with different sizes and geometrical configurations lead to the flexible C-C chain of fluconazole to be rotated for suitable position and angle to hold them. Similar inter-chain hydrogen bonding interactions are observed in compounds 1 and 2, whereas compound 3 exhibits a different three dimensional supramolecular architecture in which different chains are linked by [Mo 8O 26] 4- via hydrogen bonding interactions. Complex 1 is nonemissive at room temperature and compounds 2- 3 exhibit different photoluminescence properties.

  19. Molecular structure and rheological properties of short-side-chain heavily glycosylated porcine stomach mucin.

    PubMed

    Yakubov, Gleb E; Papagiannopoulos, Aristeidis; Rat, Elodie; Easton, Richard L; Waigh, Thomas A

    2007-11-01

    The current accepted model for high-molecular-weight gastric mucins of the MUC family is that they adopt a polydisperse coil conformation in bulk solutions. We develop this model using well-characterized highly purified porcine gastric mucin Orthana that is genetically close to the human MUC6 type. It has short side chains and low levels of sialic acid residues and includes minute amounts of cysteine residues that, if abundant, can be responsible for the self-polymerization of mucin. We have established that the mucin structure in bulk solutions corresponds to a daisy-chain random coil. Dynamic light scattering experiments probe the internal dynamics of globular subunits (individual daisies) at the approximately 9 nm length scale, whereas viscosity and light scattering measurements indicate that the size of the whole mucin chains is much larger, approximately 50 nm. The bulk viscosity (eta) scales with mucin concentration (c) in a manner similar to that found for short-side-chain synthetic comb polyelectrolytes and is characterized by a transition between semidilute (eta approximately c1/2) and entangled (eta approximately c3/2) regimes.

  20. Formation of undulated lamellar structure from ABC block terpolymer blends with different chain lengths

    NASA Astrophysics Data System (ADS)

    Matsushita, Yushu; Suzuki, Jiro; Izumi, Yuuki; Matsuoka, Kohei; Takahashi, Shuji; Aoyama, Yoshitaka; Mihira, Tomohiro; Takano, Atsushi

    2010-11-01

    The effect of molecular weight distribution of ABC linear terpolymers on the formation of periodic structures was investigated. Three poly(isoprene-b-styrene-b-2-vinylpridine) triblockterpolymers with molecular weights of 26k, 96k, and 150k were blended variously. Three-phase, four-layer lamellar structures were observed when polydispersity index (PDI) was low, but it has been found that simple lamellar structure with flat surface transforms into an undulated lamellar one, where two interfaces, i.e., I/S and S/P, are both undulated, and they are synchronizing each other if PDI exceeds the critical value. This new structure could be formed due to the periodic and "weak" localization of three chains along the domain interfaces, which produces periodic surfaces with nonconstant mean curvatures. With further increase of PDI, the blend macroscopically phase-separated into different microphase-separated structures.

  1. Medium-chain sugar amphiphiles: a new family of healthy vegetable oil structuring agents.

    PubMed

    Jadhav, Swapnil R; Hwang, Hyeondo; Huang, Qingrong; John, George

    2013-12-11

    Vegetable oils are frequently structured to enhance their organoleptic and mechanical properties. This is usually achieved by increasing the net amount of saturated and/or trans fatty acids in the oil. With the risk of coronary heart diseases associated with these fatty acids, the food industry is looking for better alternatives. In this context, the medium-chain dialkanoates of low-calorie sugars (sugar alcohol dioctanoates) are investigated as a healthy alternative structuring agent. Precursors of sugar amphiphiles, being FDA-approved GRAS materials, exhibited high cell viability at a concentration ~50 μg/mL. They readily formed nanoscale multilayered structures in an oil matrix to form a coherent network at low concentrations (1-3 wt %/v), which immobilized a wide range of oils (canola, soybean, and grapeseed oils). The structuring efficiency of sugar amphiphiles was computed in terms of mechanical, thermal, and structural properties and found to be a function of its type and concentration.

  2. Enzymic and structural studies on Drosophila alcohol dehydrogenase and other short-chain dehydrogenases/reductases.

    PubMed

    Smilda, T; Kamminga, A H; Reinders, P; Baron, W; van Hylckama Vlieg, J E; Beintema, J J

    2001-05-01

    Enzymic and structural studies on Drosophila alcohol dehydrogenases and other short-chain dehydrogenases/reductases (SDRs) are presented. Like alcohol dehydrogenases from other Drosophila species, the enzyme from D. simulans is more active on secondary than on primary alcohols, although ethanol is its only known physiological substrate. Several secondary alcohols were used to determine the kinetic parameters kcat and Km. The results of these experiments indicate that the substrate-binding region of the enzyme allows optimal binding of a short ethyl side-chain in a small binding pocket, and of a propyl or butyl side-chain in large binding pocket, with stereospecificity for R(-) alcohols. At a high concentration of R(-) alcohols substrate activation occurs. The kcat and Km values determined under these conditions are about two-fold, and two orders of magnitude, respectively, higher than those at low substrate concentrations. Sequence alignment of several SDRs of known, and unknown three-dimensional structures, indicate the presence of several conserved residues in addition to those involved in the catalyzed reactions. Structural roles of these conserved residues could be derived from observations made on superpositioned structures of several SDRs with known structures. Several residues are conserved in tetrameric SDRs, but not in dimeric ones. Two halohydrin-halide-lyases show significant homology with SDRs in the catalytic domains of these enzymes, but they do not have the structural features required for binding NAD+. Probably these lyases descend from an SDR, which has lost the capability to bind NAD+, but the enzyme reaction mechanisms may still be similar.

  3. Markov chain models of coupled intracellular calcium channels: Kronecker structured representations and benchmark stationary distribution calculations.

    PubMed

    Deremigio, Hilary; Kemper, Peter; Lamar, M Drew; Smith, Gregory D

    2008-01-01

    Mathematical models of calcium release sites derived from Markov chain models of intracellular calcium channels exhibit collective gating reminiscent of the experimentally observed phenomenon of stochastic calcium excitability (i.e., calcium puffs and sparks). We present a Kronecker structured representation for calcium release site models and perform benchmark stationary distribution calculations using numerical iterative solution techniques that leverage this structure. In this context we find multi-level methods and certain preconditioned projection methods superior to simple Gauss-Seidel type iterations. Response measures such as the number of channels in a particular state converge more quickly using these numerical iterative methods than occupation measures calculated via Monte Carlo simulation.

  4. A 1-D dusty plasma photonic crystal

    SciTech Connect

    Mitu, M. L.; Ticoş, C. M.; Toader, D.; Banu, N.; Scurtu, A.

    2013-09-21

    It is demonstrated numerically that a 1-D plasma crystal made of micron size cylindrical dust particles can, in principle, work as a photonic crystal for terahertz waves. The dust rods are parallel to each other and arranged in a linear string forming a periodic structure of dielectric-plasma regions. The dispersion equation is found by solving the waves equation with the boundary conditions at the dust-plasma interface and taking into account the dielectric permittivity of the dust material and plasma. The wavelength of the electromagnetic waves is in the range of a few hundred microns, close to the interparticle separation distance. The band gaps of the 1-D plasma crystal are numerically found for different types of dust materials, separation distances between the dust rods and rod diameters. The distance between levitated dust rods forming a string in rf plasma is shown experimentally to vary over a relatively wide range, from 650 μm to about 1350 μm, depending on the rf power fed into the discharge.

  5. Crystal structure and magnetic properties of linear chain potassium aquotetrafluoromanganate(III)

    NASA Astrophysics Data System (ADS)

    Palacio, Fernando; Andres, Mercedes; Esteban-Calderon, C.; Martinez-Ripoll, M.; Garcia-Blanco, S.

    1988-09-01

    The crystal structure and single-crystal ac magnetic susceptibilities of KMnF 4·H 2O are reported. The structure, which is isomorphous to that of RbMnF 4·H 2O, consists of chains of alternating trans-[ MnF 4F {2}/{2}] 2- and trans-[ MnF 2F {2}/{2}( H 2O ) 2] tetragonally elongated octahedra connected to each other by shared apical fluorine atoms. Crystal data: Space group {C2}/{c}, a = 13.907(1) Å, b = 6.2136(2) Å, c = 10.492(1)Å, β = 104.69(1)°, V = 877.0(2) Å 3, Dc = 2.85 g cm -3, Z = 8, R = 0.044. Magnetic susceptibility measurements show a broad maximum around 52 K indicative of lower dimensionality behavior. The data may be fit to a Heisenberg S = 2 linear chain model with {J}/{k B} = -6.5 K and g = 2.05. At 8.45 K a sharp peak in the susceptibility data parallel to the chains indicates weak ferromagnetic behavior.

  6. Beads on a string: structure of bound aggregates of globular particles and long polymer chains.

    PubMed

    Souslov, Anton; Curtis, Jennifer E; Goldbart, Paul M

    2015-11-07

    Macroscopic properties of suspensions, such as those composed of globular particles (e.g., colloidal or macromolecular), can be tuned by controlling the equilibrium aggregation of the particles. We examine how aggregation - and, hence, macroscopic properties - can be controlled in a system composed of both globular particles and long, flexible polymer chains that reversibly bind to one another. We base this on a minimal statistical mechanical model of a single aggregate in which the polymer chain is treated either as ideal or self-avoiding, and, in addition, the globular particles are taken to interact with one another via excluded volume repulsion. Furthermore, each of the globular particles is taken to have one single site to which at most one polymer segment may bind. Within the context of this model, we examine the statistics of the equilibrium size of an aggregate and, thence, the structure of dilute and semidilute suspensions of these aggregates. We apply the model to biologically relevant aggregates, specifically those composed of macromolecular proteoglycan globules and long hyaluronan polymer chains. These aggregates are especially relevant to the materials properties of cartilage and the structure-function properties of perineuronal nets in brain tissue, as well as the pericellular coats of mammalian cells.

  7. Biobased Fat Mimicking Molecular Structuring Agents for Medium-Chain Triglycerides (MCTs) and Other Edible Oils.

    PubMed

    Silverman, Julian R; John, George

    2015-12-09

    To develop sustainable value-added materials from biomass, novel small-molecule sugar ester gelators were synthesized using biocatalysis. The facile one-step regiospecific coupling of the pro-antioxidant raspberry ketone glucoside and unsaturated or saturated long- and medium-chain fatty acids provides a simple approach to tailor the structure and self-assembly of the amphiphilic product. These low molecular weight molecules demonstrated the ability to self-assemble in a variety of solvents and exhibited supergelation, with a minimum gelation concentration of 0.25 wt %, in numerous organic solvents, as well as in a range of natural edible oils, specifically a relatively unstudied group of liquids: natural medium-chain triglyceride oils, notably coconut oil. Spectroscopic analysis details the gelator structure as well as the intermolecular noncovalent interactions, which allow for gelation. X-ray diffraction studies indicate fatty acid chain packing of gelators is similar to that of natural fats, signifying the crystalline nature may lead to desirable textural properties and mouthfeel.

  8. Addimer chain structures: Metastable precursors to island formation on Ge Si(0 0 1)-(2 × n) alloyed surface

    NASA Astrophysics Data System (ADS)

    Solis, Kyle J.; Williams, Lance R.; Swartzentruber, B. S.; Han, Sang M.

    2007-01-01

    We have identified addimer chain structures as metastable precursors to compact epitaxial islands on the (2 × n) reconstructed SiGe wetting layer, using polarity-switching scanning tunneling microscopy (STM). These chain structures are comprised of 2-12 addimers residing in the troughs of neighboring substrate dimer rows. The chain structures extend along equivalent <1 3 0> directions across the substrate dimer rows in a zigzag fashion, giving rise to kinked and straight segments. We measure a kink-to-straight ratio of nearly 2:1. This ratio corresponds to a free energy difference of 17 ± 4 meV, favoring the formation of kinked segments. The chain structures convert to compact epitaxial islands at elevated temperatures (⩾90 °C). This conversion suggests that the chain structures are a precursor for compact island formation on the SiGe wetting layer. We digitally process filled- and empty-state STM images to distinguish chain structures from compact islands. By monitoring the populations of both species over time, the chain-to-island conversion rates are measured at substrate temperatures ranging from 90 to 150 °C. The activation energy for the conversion process is measured to be 0.7 ± 0.2 eV with a corresponding pre-exponential factor of 5 × 10 4±2 s -1.

  9. Detecting memory and structure in human navigation patterns using Markov chain models of varying order.

    PubMed

    Singer, Philipp; Helic, Denis; Taraghi, Behnam; Strohmaier, Markus

    2014-01-01

    One of the most frequently used models for understanding human navigation on the Web is the Markov chain model, where Web pages are represented as states and hyperlinks as probabilities of navigating from one page to another. Predominantly, human navigation on the Web has been thought to satisfy the memoryless Markov property stating that the next page a user visits only depends on her current page and not on previously visited ones. This idea has found its way in numerous applications such as Google's PageRank algorithm and others. Recently, new studies suggested that human navigation may better be modeled using higher order Markov chain models, i.e., the next page depends on a longer history of past clicks. Yet, this finding is preliminary and does not account for the higher complexity of higher order Markov chain models which is why the memoryless model is still widely used. In this work we thoroughly present a diverse array of advanced inference methods for determining the appropriate Markov chain order. We highlight strengths and weaknesses of each method and apply them for investigating memory and structure of human navigation on the Web. Our experiments reveal that the complexity of higher order models grows faster than their utility, and thus we confirm that the memoryless model represents a quite practical model for human navigation on a page level. However, when we expand our analysis to a topical level, where we abstract away from specific page transitions to transitions between topics, we find that the memoryless assumption is violated and specific regularities can be observed. We report results from experiments with two types of navigational datasets (goal-oriented vs. free form) and observe interesting structural differences that make a strong argument for more contextual studies of human navigation in future work.

  10. Effect of the chain length on the structure of ionic liquids: from spatial heterogeneity to ionic liquid crystals.

    PubMed

    Ji, Yumeng; Shi, Rui; Wang, Yanting; Saielli, Giacomo

    2013-01-31

    Ionic liquids with intermediate nonpolar cationic side-chain lengths are known to have nanoscale spatial heterogeneities with nonpolar tail domains separated by a continuous polar network. In this work, we use coarse-grained molecular dynamics simulations to show that, when the nonpolar cationic side chain is sufficiently long, due to the stronger van der Waals interactions between the side chains, the structure of ionic liquids goes through a transition from spatially heterogeneous to liquid crystalline-like. For XMIm(+)/NO(3)(-) ionic liquids, change occurs when the number of carbon groups on the cationic side chain varies from 14 to 16. In the liquid crystal-like phase, the cationic side chains tend to be parallel to each other, while the cationic head groups and anions, although being mostly layered perpendicularly to the direction along the side chains, still form a continuous polar network.

  11. 1D molecular ladder of the ionic complex of terbium-4-sebacoylbis(1-phenyl-3-methyl-5-pyrazolonate) and sodium dibenzo-18-crown-6: synthesis, crystal structure, and photophysical properties.

    PubMed

    Remya, P N; Biju, S; Reddy, M L P; Cowley, Alan H; Findlater, Michael

    2008-08-18

    On the basis of the novel heterocyclic beta-diketone, 4-sebacoylbis(1-phenyl-3-methyl-5-pyrazolone (H 2SbBP), three new lanthanide complexes Tb 2(SbBP) 3(H 2O) 2 ( 1), Gd 2(SbBP) 3(H 2O) 2 ( 2), and [Tb(SbBP) 2] [Na(DB18C6)H 2O] ( 3) have been synthesized and characterized by various spectroscopic techniques. The single-crystal X-ray diffraction analysis of 3 reveals that the complex crystallizes in the monoclinic space group C2/ c with a = 25.300(6) A, b = 19.204(7) A, c = 15.391(3) A, beta = 93.17(3) degrees , and V = 7466(4) A (3). The crystal structure of 3 is heterodinuclear and features a Tb (3+) center surrounded by two tetradentate bispyrazolone ligands in a somewhat distorted square-antiprismatic geometry. The Na (+) coordination environment is distorted hexagonal pyramidal and involves six oxygen atoms furnished by DB18C6 and one oxygen atom from a water molecule. The X-ray diffraction study of 3 also revealed an interesting 1D molecular ladder structure based on C-H/pi, intra- and intermolecular hydrogen-bonding interactions. The photophysical properties of 1 and 3 in solid state have been investigated, and the quantum yields and (5)D 4 lifetimes were found to be 4.82 +/- 0.01% and 18.13 +/- 0.82% and 1.11 +/- 0.01 and 2.82 +/- 0.02 ms, respectively.

  12. The crystal structure of 1-D-myo-inosityl 2-acetamido-2-deoxy-alpha-D-glucopyranoside deacetylase (MshB) from Mycobacterium tuberculosis reveals a zinc hydrolase with a lactate dehydrogenase fold.

    PubMed

    Maynes, Jason T; Garen, Craig; Cherney, Maia M; Newton, Gerald; Arad, Dorit; Av-Gay, Yossef; Fahey, Robert C; James, Michael N G

    2003-11-21

    Mycothiol (1-D-myo-inosityl 2-(N-acetyl-L-cysteinyl)amido-2-deoxy-alpha-D-glucopyranoside, MSH or AcCys-GlcN-inositol (Ins)) is the major reducing agent in actinomycetes, including Mycobacterium tuberculosis. The biosynthesis of MSH involves a deacetylase that removes the acetyl group from the precursor GlcNAc-Ins to yield GlcN-Ins. The deacetylase (MshB) corresponds to Rv1170 of M. tuberculosis with a molecular mass of 33,400 Da. MshB is a Zn2+ metalloprotein, and the deacetylase activity is completely dependent on the presence of a divalent metal cation. We have determined the x-ray crystallographic structure of MshB, which reveals a protein that folds in a manner resembling lactate dehydrogenase in the N-terminal domain and a C-terminal domain consisting of two beta-sheets and two alpha-helices. The zinc binding site is in the N-terminal domain occupying a position equivalent to that of the NAD+ co-factor of lactate dehydrogenase. The Zn2+ is 5 coordinate with 3 residues from MshB (His-13, Asp-16, His-147) and two water molecules. One water would be displaced upon binding of substrate (GlcNAc-Ins); the other is proposed as the nucleophilic water assisted by the general base carboxylate of Asp-15. In addition to the Zn2+ providing electrophilic assistance in the hydrolysis, His-144 imidazole could form a hydrogen bond to the oxyanion of the tetrahedral intermediate. The extensive sequence identity of MshB, the deacetylase, with mycothiol S-conjugate amidase, an amide hydrolase that mediates detoxification of mycothiol S-conjugate xenobiotics, has allowed us to construct a faithful model of the catalytic domain of mycothiol S-conjugate amidase based on the structure of MshB.

  13. A rational route to SCM materials based on a 1-D cobalt selenocyanato coordination polymer.

    PubMed

    Boeckmann, Jan; Näther, Christian

    2011-07-07

    Thermal annealing of a discrete complex with terminal SeCN anions and monodentate coligands enforces the formation of a 1D cobalt selenocyanato coordination polymer that shows slow relaxation of the magnetization. Therefore, this approach offers a rational route to 1D materials that might show single chain magnetic behaviour.

  14. Electronic Structure of Pure Selenium and Tellurium Chains and Selenium Rings and with Impurities

    NASA Astrophysics Data System (ADS)

    Maharjan, N. B.; Cho, Hwa-Suck; Scheicher, R. H.

    2005-03-01

    We have studied the electronic structures of pure chain-structured Selenium and Tellurium and with chalcogen impurities as well as ring-structured Selenium both pure and with Tellurium impurity atoms. The Hartree-Fock Cluster Theory procedure combined with many-body perturbation theory procedure has been used. The accuracy of the calculated electronic wave functions is tested by the investigation of ^77Se and ^125Te nuclear quadrupole interaction parameters. Good agreement is found with experiment for the pure systems. For the impurity systems, the agreement is reasonable but suggests the need for inclusion of more extensive relaxation around the impurity atoms. (*) Current Address: Dept. of Physics, Uppsala University, Sweden (**) Also: Dept. of Physics, University of Central Florida, Orlando, Florida

  15. Bacterial Social Networks: Structure and composition of Myxococcus xanthus outer membrane vesicle chains

    PubMed Central

    Remis, Jonathan P.; Wei, Doug; Gorur, Amita; Zemla, Marcin; Haraga, Jessica; Allen, Simon; Witkowska, H. Ewa; Costerton, J. William; Berleman, James E.; Auer, Manfred

    2014-01-01

    Summary The social soil bacterium, Myxococcus xanthus, displays a variety of complex and highly coordinated behaviors, including social motility, predatory rippling and fruiting body formation. Here we show that M. xanthus cells produce a network of outer membrane extensions in the form of vesicles and vesicle chains that interconnect cells. We observed peritrichous display of vesicles and vesicle chains and increased abundance in biofilms compared to planktonic cultures. By applying a range of imaging techniques, including 3D Focused Ion Beam Scanning Electron Microscopy (FIB/SEM), we determined these structures to range between 30-60 nm in width and up to 5 μm in length. Purified vesicle chains consist of typical M. xanthus lipids, fucose, mannose, N-acetylglucosamine (GlcNAc) and N-acetylgalactoseamine (GalNAc) carbohydrates and a small set of cargo protein. The protein content includes CglB and Tgl membrane proteins transferred in a contact-dependent manner. Most significantly, the 3D organization of cells within biofilms indicates that cells are connected via an extensive network of membrane extensions that may connect cells at the level of the periplasmic space. Such a network would allow the transfer of membrane proteins and other molecules between cells, and likely provides a mechanism for the coordination of social activities. PMID:23848955

  16. Immunological and structural characterization of a high affinity anti-fluorescein single-chain antibody.

    PubMed

    Bedzyk, W D; Weidner, K M; Denzin, L K; Johnson, L S; Hardman, K D; Pantoliano, M W; Asel, E D; Voss, E W

    1990-10-25

    Single-chain antibody of the (NH2) VL-linker-VH (COOH) design, was constructed based on prototype high affinity anti-fluorescein monoclonal antibody (mAb) 4-4-20. Purified single-chain antibody (SCA) 4-4-20/212 was studied relative to Ig mAb 4-4-20 in terms of ligand binding, kinetics, idiotypy, metatypy, and stability in denaturing agents. Ligand-binding data correlated with metatypic relatedness of the liganded site. Anti-metatypic reagents reacted preferentially with the liganded conformer of the 4-4-20 antibody active site and were unreactive with free ligand and the non-liganded (idiotypic) state. All results were consistent with the conclusion that SCA 4-4-20/212, with a 14-amino acid linker folded into a native conformational state that closely simulated the prototypical mAb. Furthermore, GndHCl unfolding and refolding studies demonstrated H and L chain variable domain intrinsic stability between SCA 4-4-20/212 and a 50 kDa antigen-binding fragment were nearly identical. This suggested CH1 and CL domain interactions may be more prevalent in V region molecular dynamics than structure.

  17. Lipidomic platform for structural identification of skin ceramides with α-hydroxyacyl chains.

    PubMed

    Wu, Zhexue; Shon, Jong Cheol; Lee, Doohyun; Park, Kab-Tae; Park, Chang Seo; Lee, Taeho; Lee, Hye Suk; Liu, Kwang-Hyeon

    2016-03-01

    Skin ceramides are sphingolipids consisting of sphingoid bases, which are linked to fatty acids via an amide bond. Typical fatty acid acyl chains are composed of α-hydroxy fatty acid (A), esterified ω-hydroxy fatty acid (EO), non-hydroxy fatty acid (N), and ω-hydroxy fatty acid (O). We recently established a lipidomic platform to identify skin ceramides with non-hydroxyacyl chains using tandem mass spectrometry. We expanded our study to establish a lipidomic platform to identify skin ceramides with α-hydroxyacyl chains. Tandem mass spectrometry analysis of A-type ceramides using chip-based direct infusion nanoelectrospray-mass spectrometry showed the characteristic fragmentation pattern of both acyl and sphingoid units, which can be applied for structural identification of ceramides. Based on the tandem mass spectrometry fragmentation patterns of A-type ceramides, comprehensive fragmentation schemes were proposed. Our results may be useful for identifying A-type ceramides in the stratum corneum of human skin.

  18. Bacterial social networks: structure and composition of Myxococcus xanthus outer membrane vesicle chains.

    PubMed

    Remis, Jonathan P; Wei, Dongguang; Gorur, Amita; Zemla, Marcin; Haraga, Jessica; Allen, Simon; Witkowska, H Ewa; Costerton, J William; Berleman, James E; Auer, Manfred

    2014-02-01

    The social soil bacterium, Myxococcus xanthus, displays a variety of complex and highly coordinated behaviours, including social motility, predatory rippling and fruiting body formation. Here we show that M. xanthus cells produce a network of outer membrane extensions in the form of outer membrane vesicle chains and membrane tubes that interconnect cells. We observed peritrichous display of vesicles and vesicle chains, and increased abundance in biofilms compared with planktonic cultures. By applying a range of imaging techniques, including three-dimensional (3D) focused ion beam scanning electron microscopy, we determined these structures to range between 30 and 60 nm in width and up to 5 μm in length. Purified vesicle chains consist of typical M. xanthus lipids, fucose, mannose, N-acetylglucosamine and N-acetylgalactoseamine carbohydrates and a small set of cargo protein. The protein content includes CglB and Tgl outer membrane proteins known to be transferable between cells in a contact-dependent manner. Most significantly, the 3D organization of cells within biofilms indicates that cells are connected via an extensive network of membrane extensions that may connect cells at the level of the periplasmic space. Such a network would allow the transfer of membrane proteins and other molecules between cells, and therefore could provide a mechanism for the coordination of social activities.

  19. Effect of A Long Chain Carboxylate Acid on Sodium Dodecyl Sulfate Micelle Structure: A SANS Study

    NASA Astrophysics Data System (ADS)

    Patriati, Arum; Giri Rachman Putra, Edy; Seok Seong, Baek

    2010-01-01

    The effect of a different hydrocarbon chain length of carboxylate acid, i.e. dodecanoic acid, CH3(CH)10COOH or lauric acid and hexadecanoic acid, CH3(CH2)14COOH or palmitic acid as a co-surfactant in the 0.3 M sodium dedecyl sulfate, SDS micellar solution has been studied using small angle neutron scattering (SANS). The present of lauric acid has induced the SDS structural micelles. The ellipsoid micelles structures changed significantly in length (major axis) from 22.6 Å to 37.1 Å at a fixed minor axis of 16.7 Å in the present of 0.005 M to 0.1 M lauric acid. Nevertheless, this effect did not occur in the present of palmitic acid with the same concentration range. The present of palmitic acid molecules performed insignificant effect on the SDS micelles growth where the major axis of the micelle was elongated from 22.9 Å to 25.3 Å only. It showed that the appropriate hydrocarbon chain length between surfactant and co-surfactant molecules emerged as one of the determining factors in forming a mixed micelles structure.

  20. Pressure dependence of structural and dynamical properties in melt sulfur: Evidence for two successive chain breakages

    NASA Astrophysics Data System (ADS)

    Zhao, G.; Mu, H. F.

    2014-11-01

    Using ab initio molecular dynamics simulations, the pressure dependence of structural and dynamical properties in melt sulfur along 1085 K isotherm was studied with pressure range from 4.18 to 15.8 GPa. It was found that the atomic chains in melt sulfur abruptly break twice with increasing pressure. The electric density of state near EF and the diffusion coefficient both show abrupt increase along with these two times of breakages. These changes would strongly influence the physical properties such as conductivity and viscosity. However, the density discontinuity along the isotherm, indication of a first-order phase transition, was not found.

  1. Crystal structures and thermodynamics/kinetics of Zn(II) coordination polymers with helical chains

    NASA Astrophysics Data System (ADS)

    He, Tian; Yue, Ke-Fen; Zhao, Yi-xing; Chen, San-Ping; Zhou, Chun-sheng; Yan, Ni

    2016-07-01

    Solvothermal reactions of Zn(II) acetates and four V-shaped carboxylates ligands in the presence of 1,4-Bis(2-methyl-imidazol-1-yl)butane afforded four interesting Zn(II) coordination polymers with helical chains, namely, {[Zn(bib)(atibdc)]·2H2O}n (1), {[Zn(bib)(atbip)]·H2O}n (2), [Zn(bib)(2,2‧-tda)]}n (3) and {[Zn(bib)(5-tbipa)]·EtOH}n (4), (H2atibdc=5-amino-2,4,6-triiodoisophthalic acid, H2atbip=5-amino-2,4,6-tribromoisophthalic acid, 2,2‧-H2tad=2,2‧-thiodiacetic acid, 5-H2tbipa=5-tert-butyl-isophthalic acid). 1 reveals a 3D chiral framework with three kinds of helical chains along a, b and c axis. 2 shows a 2D step-type chiral framework with right-handed helical chains. 3 displays a wavelike 2D layer network possessing alternate left- and right-handed helical chains. 4 presents a four-connected 3D framework with zigzag and meso-helical chains. The different spacers and substituent group of carboxylic acid ligands may lead to the diverse network structures of 1-4. The fluorescent properties of complexes 1-4 were studied. In addition, the thermal decompositions properties of 1-4 were investigated by simultaneous TG/DTG-DSC technique. The apparent activation energy E and the pre-exponential factor (A) of skeleton collapse for the complexes 1-4 are calculated by the integral Kissinger's method and Ozawa-Doyle's method. The activation energy E (E1=209.658 kJ·mol-1, E2=250.037 kJ mol-1, E3=225.300 kJ mol-1, E4=186.529 kJ·mol-1) demonstrates that the reaction rate of the melting decomposition is slow. The thermodynamic parameters (ΔH‡, ΔG‡ and ΔS‡) at the peak temperatures of the DTG curves were also calculated. ΔG‡>0 indicates that the skeleton collapse is not spontaneous. ΔHd>0 suggests that the skeleton collapse is endothermic, corresponding to the intense endothermic peak of the DSC curve. The structural stability could be illustrated from the point of thermodynamics and kinetics.

  2. Clathrin light chain B: gene structure and neuron-specific splicing.

    PubMed Central

    Stamm, S; Casper, D; Dinsmore, J; Kaufmann, C A; Brosius, J; Helfman, D M

    1992-01-01

    The clathrin light chains are components of clathrin coated vesicles, structural constituents involved in endocytosis and membrane recycling. The clathrin light chain B (LCB) gene encodes two isoforms, termed LCB2 and LCB3, via an alternative RNA splicing mechanism. We have determined the structure of the rat clathrin light chain B gene. The gene consists of six exons that extend over 11.9 kb. The first four exons and the last exon are common to the LCB2 and LCB3 isoforms. The fifth exon, termed EN, is included in the mRNA in brain, giving rise to the brain specific form LCB2 but is excluded in other tissues, generating the LCB3 isoform. Primary rat neuronal cell cultures express predominantly the brain specific LCB2 isoform, whereas primary rat cultures of glia express only the LCB3 isoform, suggesting that expression of the brain-specific LCB2 form is limited to neurons. Further evidence for neuronal localization of the LCB2 form is provided using a teratocarcinoma cell line, P19, which can be induced by retinoic acid to express a neuronal phenotype, concomitant with the induction of the LCB2 form. In order to determine the sequences involved in alternative splice site selection, we constructed a minigene containing the alternative spliced exon EN and its flanking intron and exon sequences. This minigene reflects the splicing pattern of the endogenous gene upon transfection in HeLa cell and primary neuronal cell cultures, indicating that this region of the LCB gene contains all the necessary information for neuron-specific splicing. Images PMID:1408826

  3. Straight-Chain Alkyl Isocyanides Open the Distal Histidine Gate in Crystal Structures of Myoglobin†

    PubMed Central

    Smith, Rober D.; Blouin, George C.; Johnson, Kenneth A.; Phillips, George N.; Olson, John S.

    2014-01-01

    Crystal structures of methyl, ethyl, propyl and butyl isocyanide bound to sperm whale myoglobin (Mb) reveal two major conformations. In the in conformer, His(E7) is in a “closed” position, forcing the ligand alkyl chain to point inward. In the out conformer, His(E7) is in an “open” position, allowing the ligand side chain to point outward. A progressive increase in the population of the out conformer is observed with increasing ligand length in P21 crystals of native Mb at pH 7.0. This switch from in to out with increasing ligand size also occurs in solution as measured by the decrease in the relative intensity of the low (~2075 cm 1) versus high frequency (~2125 cm 1) isocyano bands. In contrast, all four isocyanides in P6 crystals of wild type recombinant Mb occupy the in conformation. However, mutating either His64 to Ala, creating a “hole” to solvent, or Phe46 to Val, freeing rotation of His64, causes bound butyl isocyanide to point completely outward in P6 crystals. Thus, the unfavorable hindrance caused with crowding a large alkyl side chain into the distal pocket appears to be roughly equal to that for pushing open the His(E7) gate and is easily affected by crystal packing. This structural conclusion supports the “side path” kinetic mechanism for O2 release, in which the dissociated ligand first moves toward the protein interior and then encounters steric resistance, which is roughly equal to that for escaping to solvent through the His(E7) channel. PMID:20481504

  4. Insights into Medium-chain Acyl-CoA Dehydrogenase Structure by Molecular Dynamics Simulations.

    PubMed

    Bonito, Cátia A; Leandro, Paula; Ventura, Fátima V; Guedes, Rita C

    2016-08-01

    The medium-chain acyl-CoA dehydrogenase (MCAD) is a mitochondrial enzyme that catalyzes the first step of mitochondrial fatty acid β-oxidation (mFAO) pathway. Its deficiency is the most common genetic disorder of mFAO. Many of the MCAD disease-causing variants, including the most common p.K304E variant, show loss of function due to protein misfolding. Herein, we used molecular dynamics simulations to provide insights into the structural stability and dynamic behavior of MCAD wild-type (MCADwt) and validate a structure that would allow reliable new studies on its variants. Our results revealed that in both proteins the flavin adenine dinucleotide (FAD) has an important structural role on the tetramer stability and also in maintaining the volume of the enzyme catalytic pockets. We confirmed that the presence of substrate changes the dynamics of the catalytic pockets and increases FAD affinity. A comparison between the porcine MCADwt (pMCADwt) and human MCADwt (hMCADwt) structures revealed that both proteins are essentially similar and that the reversion of the double mutant E376G/T255E of hMCAD enzyme does not affect the structure of the protein neither its behavior in simulation. Our validated hMCADwt structure is crucial for complementing and accelerating the experimental studies aiming for the discovery and development of potential stabilizers of MCAD variants as candidates for the treatment of MCAD deficiency (MCADD).

  5. Crystal Structure of Botulinum Neurotoxin Type G Light Chain - Serotype Divergence in Substrate Recognition†,‡

    PubMed Central

    Arndt, Joseph W.; Yu, Wayne; Bi, Fay; Stevens, Raymond C.

    2008-01-01

    The seven serotypes (A–G) of botulinum neurotoxins (BoNTs) block neurotransmitter release through their specific proteolysis of one of the three proteins of the soluble N-ethylmaleimide-sensitive-factor attachment protein receptor (SNARE) complex. BoNTs have stringent substrate specificities that are unique for metalloprotease in that they require exceptionally long substrates (1). In order to understand the molecular reasons for the unique specificities of the BoNTs, we determined the crystal structure of the catalytic light chain (LC) of Clostridium botulinum neurotoxin type G (BoNT/G-LC) at 2.35 Å resolution. The structure of BoNT/G-LC reveals a C-terminal β-sheet that is critical for LC oligomerization and is unlike that seen in the other LC structures. Its structural comparison with thermolysin and the available pool of LC structures reveals important serotype differences that are likely to be involved in substrate recognition of the P1’ residue. In addition, structural and sequence analysis have identified a potential exosite of BoNT/G-LC that recognizes a SNARE recognition motif of VAMP. PMID:16008342

  6. Crystal structure of botulinum neurotoxin type G light chain: serotype divergence in substrate recognition.

    PubMed

    Arndt, Joseph W; Yu, Wayne; Bi, Fay; Stevens, Raymond C

    2005-07-19

    The seven serotypes (A-G) of botulinum neurotoxins (BoNTs) block neurotransmitter release through their specific proteolysis of one of the three proteins of the soluble N-ethylmaleimide-sensitive-factor attachment protein receptor (SNARE) complex. BoNTs have stringent substrate specificities that are unique for metalloprotease in that they require exceptionally long substrates (1). To understand the molecular reasons for the unique specificities of the BoNTs, we determined the crystal structure of the catalytic light chain (LC) of Clostridium botulinum neurotoxin type G (BoNT/G-LC) at 2.35 A resolution. The structure of BoNT/G-LC reveals a C-terminal beta-sheet that is critical for LC oligomerization and is unlike that seen in the other LC structures. Its structural comparison with thermolysin and the available pool of LC structures reveals important serotype differences that are likely to be involved in substrate recognition of the P1' residue. In addition, structural and sequence analyses have identified a potential exosite of BoNT/G-LC that recognizes a SNARE recognition motif of VAMP.

  7. A one-dimensional chain structure based on unusual tetranuclear manganese(II) clusters.

    PubMed

    Che, Guang Bo; Wang, Jian; Liu, Chun Bo; Li, Xiu Ying; Liu, Bo

    2008-11-01

    The title coordination polymer, poly[bis(mu(4)-biphenyl-2,2'-dicarboxylato)(dipyrido[3,2-a:2',3'-c]phenazine)manganese(II)], [Mn(2)(C(14)H(8)O(4))(2)(C(18)H(10)N(4))](n), was obtained through the reaction of MnCl(2).4H(2)O, biphenyl-2,2'-dicarboxylic acid (H(2)dpdc) and dipyrido[3,2-a:2',3'-c]phenazine (L) under hydrothermal conditions. The asymmetric unit contains two crystallographically unique Mn(II) ions, one unique L ligand and two unique dpdc ligands. One Mn ion is six-coordinated by four O atoms from three different dpdc ligands and two N atoms from one L ligand, adopting a distorted octahedral coordination geometry. The distortions from ideal octahedral geometry are largely due to the presence of chelating ligands and the resulting acute N-Mn-N and O-Mn-O angles. The second Mn ion is coordinated in a distorted trigonal bipyramidal fashion by five O atoms from four distinct dpdc ligands. Four Mn(II) ions are bridged by the carboxylate groups of the dpdc ligands to form an unusual tetranuclear Mn(II) cluster. Clusters are further connected by the aromatic backbone of the dicarboxylate ligands, forming a one-dimensional chain structure along the b axis. The title compound is the first example of a chain structure based on a tetranuclear Mn(II) cluster.

  8. Primary structure and chain conformation of fucoidan extracted from sea cucumber Holothuria tubulosa.

    PubMed

    Chang, Yaoguang; Hu, Yanfang; Yu, Long; McClements, David Julian; Xu, Xiaoqi; Liu, Guanchen; Xue, Changhu

    2016-01-20

    Knowledge of the structure of polysaccharides is essential for understanding and controlling their functional properties. In this study, fucoidan was extracted from Holothuria tubulosa, a species of sea cucumber that has recently become commercially important. The primary structure of the H. tubulosa fucoidan was clarified using a combination of enzymatic degradation, methylation analysis, and NMR, and its chain conformation was further elucidated by utilizing high performance size exclusion chromatography combined with multiple angle laser light scattering and viscometry. The fucoidan was composed of a tetrafucose repeating unit [ → 3-α-L-Fucp2(OSO3(-))-1 → 3-α-L-Fucp2,4(OSO3(-))-1 → 3-α-L-Fucp-1 → 3-α-L-Fucp2(OSO3(-))-1 → ]. Its sulfate content was determined to be 31.2 ± 1.6% and the weight-average molecular mass was 1567.6 ± 34.1 kDa. The molecule adapted a random coil conformation in 0.15M NaCl solution (pH 7.4) at 25 °C, with a root-mean-square radius of 63.9 ± 1.8 nm and a hydrodynamic radius of 44.5 ± 4.5 nm. This is the first report on the chain conformation of sea cucumber fucoidan.

  9. Structure and function of outer dynein arm intermediate and light chain complex

    PubMed Central

    Oda, Toshiyuki; Abe, Tatsuki; Yanagisawa, Haruaki; Kikkawa, Masahide

    2016-01-01

    The outer dynein arm (ODA) is a molecular complex that drives the beating motion of cilia/flagella. Chlamydomonas ODA is composed of three heavy chains (HCs), two ICs, and 11 light chains (LCs). Although the three-dimensional (3D) structure of the whole ODA complex has been investigated, the 3D configurations of the ICs and LCs are largely unknown. Here we identified the 3D positions of the two ICs and three LCs using cryo–electron tomography and structural labeling. We found that these ICs and LCs were all localized at the root of the outer-inner dynein (OID) linker, designated the ODA-Beak complex. Of interest, the coiled-coil domain of IC2 extended from the ODA-Beak to the outer surface of ODA. Furthermore, we investigated the molecular mechanisms of how the OID linker transmits signals to the ODA-Beak, by manipulating the interaction within the OID linker using a chemically induced dimerization system. We showed that the cross-linking of the OID linker strongly suppresses flagellar motility in vivo. These results suggest that the ICs and LCs of the ODA form the ODA-Beak, which may be involved in mechanosignaling from the OID linker to the HCs. PMID:26864626

  10. Sulfation effect on levan polysaccharide chains structure with molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Coskunkan, Binnaz; Turgut, Deniz; Rende, Deniz; Malta, Seyda; Baysal, Nihat; Ozisik, Rahmi; Toksoy-Oner, Ebru

    Diversity in conformations and structural heterogeneity make polysaccharides the most challenging biopolymer type for experimental and theoretical characterization studies. Levan is a biopolymer chain that consists of fructose rings with β(2-6) linkages. It is a glycan that has great potential as a functional biopolymer in foods, feeds, cosmetics, pharmaceutical and chemical industries. Sulfated polysaccharides are group of macromolecules with sulfated groups in their hydroxyl parts with a range of important biological properties. Sulfate groups and their positions have a major effect on anticoagulant activity. It is reported that sulfate modified levan has anticoagulant activity such as heparin. In the current study, the effect of sulfation on the structure and dynamics of unmodified and sulfate modified levan are investigated via fully atomistic Molecular Dynamics simulations in aqueous media and varying salt concentrations at 310 K. This material is based upon work supported by the National Science Foundation under Grant No. CMMI-1538730.

  11. Crystal structure of a supercharged variant of the human enteropeptidase light chain.

    PubMed

    Simeonov, Peter; Zahn, Michael; Sträter, Norbert; Zuchner, Thole

    2012-07-01

    The highly specific serine protease human enteropeptidase light chain cleaves the Asp4Lys recognition sequence and represents an interesting enzyme for biotechnological applications. The human enzyme shows 10 times faster kinetics compared to other animal sources but low solubility under low salt conditions, which hampers protein production and crystallization. Therefore, a supercharged variant (N6D/G21D/G22D/N142D/K210E/C112S) with increased solubility was used for crystallization. The structure (resolution, 1.9 Å) displays a typical α/β trypsin-like serine protease-fold. The mutations introduced for protein supercharging generate larger clusters of negative potential on both sites of the active cleft but do not affect the structural integrity of the protein.

  12. Crystal structure of Sr2CdPt2 containing linear platinum chains

    PubMed Central

    Nawawi, Effendi; Gulo, Fakhili; Köhler, Jürgen

    2016-01-01

    The ternary inter­metallic title phase, distrontium cadmium diplatinum, was prepared from stoichiometric amounts of the elements at 1123 K for one day. The crystal structure adopts the ortho­rhom­bic Ca2GaCu2 structure type in space group Immm. Its main features are characterized by linear (Pt—Pt⋯Pt—Pt)n chains that are aligned along [010] and condensed through cadmium atoms forming Cd-centred Pt2Cd2/2 rectangles to build up sheets parallel to (001). These sheets are connected to each other via alternating (001) sheets of strontium atoms along [001]. The strontium sheets consists of corrugated Sr4 units that are condensed to each other through edge-sharing parallel to [100]. PMID:26958374

  13. Crystalline structures of polymeric hydrocarbon with 3,4-fold helical chains.

    PubMed

    Lian, Chao-Sheng; Li, Han-Dong; Wang, Jian-Tao

    2015-01-12

    Molecular hydrocarbons are well-known to polymerize under pressure to form covalently bonded frameworks. Here we predict by ab initio calculations two distinct three-dimensional hydrocarbon crystalline structures composed of 3-fold and 4-fold helical CH chains in rhombohedral (R3) and tetragonal (I4₁/a) symmetry, respectively. Both structures with 1:1 stoichiometry are found to be energetically more favorable than solid acetylene and cubane, and even more stable than benzene II solid at high pressure. The calculations on vibrational, electronic, and optical properties reveal that the new chiral hydrocarbons are dynamically stable with large bulk moduli around 200 GPa, and exhibit a transparent insulating behavior with indirect band gaps of 5.9 ~ 6.7 eV and anisotropic adsorption spectra. Such forms of hydrocarbon, once synthesized, would have wide applications in mechanical, optoelectronic, and biological materials.

  14. Crystal structures and thermodynamics/kinetics of Zn(II) coordination polymers with helical chains

    SciTech Connect

    He, Tian; Yue, Ke-Fen; Zhao, Yi-xing; Chen, San-Ping; Zhou, Chun-sheng; Yan, Ni

    2016-07-15

    Solvothermal reactions of Zn(II) acetates and four V-shaped carboxylates ligands in the presence of 1,4-Bis(2-methyl-imidazol-1-yl)butane afforded four interesting Zn(II) coordination polymers with helical chains, namely, {[Zn(bib)(atibdc)]·2H_2O}{sub n} (1), {[Zn(bib)(atbip)]·H_2O}{sub n} (2), {[Zn(bib)(2,2′-tda)]}{sub n} (3) and {[Zn(bib)(5-tbipa)]·EtOH}{sub n} (4), (H{sub 2}atibdc=5-amino-2,4,6-triiodoisophthalic acid, H{sub 2}atbip=5-amino-2,4,6-tribromoisophthalic acid, 2,2′-H{sub 2}tad=2,2′-thiodiacetic acid, 5-H{sub 2}tbipa=5-tert-butyl-isophthalic acid). 1 reveals a 3D chiral framework with three kinds of helical chains along a, b and c axis. 2 shows a 2D step-type chiral framework with right-handed helical chains. 3 displays a wavelike 2D layer network possessing alternate left- and right-handed helical chains. 4 presents a four-connected 3D framework with zigzag and meso-helical chains. The different spacers and substituent group of carboxylic acid ligands may lead to the diverse network structures of 1–4. The fluorescent properties of complexes 1−4 were studied. In addition, the thermal decompositions properties of 1–4 were investigated by simultaneous TG/DTG–DSC technique. The apparent activation energy E and the pre-exponential factor (A) of skeleton collapse for the complexes 1–4 are calculated by the integral Kissinger's method and Ozawa–Doyle's method. The activation energy E (E{sub 1}=209.658 kJ·mol{sup −1}, E{sub 2}=250.037 kJ mol{sup −1}, E{sub 3}=225.300 kJ mol{sup −1}, E{sub 4}=186.529 kJ·mol{sup −1}) demonstrates that the reaction rate of the melting decomposition is slow. The thermodynamic parameters (ΔH{sup ‡}, ΔG{sup ‡} and ΔS{sup ‡}) at the peak temperatures of the DTG curves were also calculated. ΔG{sup ‡}>0 indicates that the skeleton collapse is not spontaneous. ΔH{sub d}>0 suggests that the skeleton collapse is endothermic, corresponding to the intense endothermic peak of the DSC curve. The

  15. New hybrid lead iodides: From one-dimensional chain to two-dimensional layered perovskite structure

    SciTech Connect

    Xiong, Kecai; Liu, Wei; Teat, Simon J.; An, Litao; Wang, Hao; Emge, Thomas J.; Li, Jing

    2015-10-15

    Two new hybrid lead halides (H{sub 2}BDA)[PbI{sub 4}] (1) (H{sub 2}BDA=1,4-butanediammonium dication) and (HNPEIM)[PbI{sub 3}] (2) (HNPEIM=N-​phenyl-ethanimidamidine cation) have been synthesized and structurally characterized. X-ray diffraction analyses reveal that compound 1 features a two-dimensional corner-sharing perovskite layer whereas compound 2 contains one-dimensional edge-sharing double chains. The N-​phenyl-ethanimidamidine cation within compound 2 was generated in-situ under solvothermal conditions. The optical absorption spectra collected at room temperature suggest that both compounds are semiconductors having direct band gaps, with estimated values of 2.64 and 2.73 eV for 1 and 2, respectively. Results from the density functional theory (DFT) calculations are consistent with the experimental data. Density of states (DOS) analysis reveals that in both compounds 1 and 2, the energy states in the valence band maximum region are iodine 5p atomic orbitals with a small contribution from lead 6s, while in the region of conduction band minimum, the major contributions are from the inorganic (Pb 6p atomic orbitals) and organic components (C and N 2p atomic orbitals) in compound 1 and 2, respectively. - Graphical abstract: Two new hybrid lead halides built on one-dimensional edge-sharing double chains and two-dimensional corner-sharing perovskite layers are synthesized and their structural and electronic properties are analyzed. - Highlights: • Two new hybrid lead iodides are designed, synthesized, and characterized. • They are closely related to, but different from, perovskite structures. • The electronic properties of both compounds are analyzed by DFT calculations.

  16. Scaffolding, ladders, chains, and rare ferrimagnetism in intermetallic borides: electronic structure calculations and magnetic ordering.

    PubMed

    Brgoch, Jakoah; Goerens, Christian; Fokwa, Boniface P T; Miller, Gordon J

    2011-05-04

    The electronic structures of "Ti(9-n)Fe(2+n)Ru(18)B(8)" (n=0, 0.5, 1, 2, 3), in connection to the recently synthesized Ti(9-n)Fe(2+n)Ru(18)B(8) (n=1, 2), have been investigated and analyzed using LSDA tight-binding calculations to elucidate the distribution of Fe and Ti, to determine the maximum Fe content, and to explore possible magnetic structures to interpret experimental magnetization results. Through a combination of calculations on specific models and using the rigid band approximation, which is validated by the DOS curves for "Ti(9-n)Fe(2+n)Ru(18)B(8)" (n=0, 0.5, 1, 2, 3), mixing of Fe and Ti is anticipated at both the 2b- and 4h-chain sites. The model "Ti(8.5)Fe(2.5)Ru(18)B(8)" (n=0.5) revealed that both Brewer-type Ti-Ru interactions as well as ligand field splitting of the Fe 3d orbitals regulated the observed valence electron counts between 220 and 228 electrons/formula unit. Finally, models of magnetic structures were created using "Ti(6)Fe(5)Ru(18)B(8)" (n=3). A rigid band analysis of the LSDA DOS curves concluded preferred ferromagnetic ordering at low Fe content (n≤0.75) and ferrimagnetic ordering at higher Fe content (n>0.75). Ferrimagnetism arises from antiferromagnetic exchange coupling in the scaffold of Fe1-ladder and 4h-chain sites.

  17. Crystal Structures of the Tetratricopeptide Repeat Domains of Kinesin Light Chains: Insight into Cargo Recognition Mechanisms

    SciTech Connect

    Zhu, Haizhong; Lee, Han Youl; Tong, Yufeng; Hong, Bum-Soo; Kim, Kyung-Phil; Shen, Yang; Lim, Kyung Jik; Mackenzie, Farrell; Tempel, Wolfram; Park, Hee-Won

    2012-10-23

    Kinesin-1 transports various cargos along the axon by interacting with the cargos through its light chain subunit. Kinesin light chains (KLC) utilize its tetratricopeptide repeat (TPR) domain to interact with over 10 different cargos. Despite a high sequence identity between their TPR domains (87%), KLC1 and KLC2 isoforms exhibit differential binding properties towards some cargos. We determined the structures of human KLC1 and KLC2 tetratricopeptide repeat (TPR) domains using X-ray crystallography and investigated the different mechanisms by which KLCs interact with their cargos. Using isothermal titration calorimetry, we attributed the specific interaction between KLC1 and JNK-interacting protein 1 (JIP1) cargo to residue N343 in the fourth TRP repeat. Structurally, the N343 residue is adjacent to other asparagines and lysines, creating a positively charged polar patch within the groove of the TPR domain. Whereas, KLC2 with the corresponding residue S328 did not interact with JIP1. Based on these finding, we propose that N343 of KLC1 can form 'a carboxylate clamp' with its neighboring asparagine to interact with JIP1, similar to that of HSP70/HSP90 organizing protein-1's (HOP1) interaction with heat shock proteins. For the binding of cargos shared by KLC1 and KLC2, we propose a different site located within the groove but not involving N343. We further propose a third binding site on KLC1 which involves a stretch of polar residues along the inter-TPR loops that may form a network of hydrogen bonds to JIP3 and JIP4. Together, these results provide structural insights into possible mechanisms of interaction between KLC TPR domains and various cargo proteins.

  18. Glutamine and Asparagine Side Chain Hyperconjugation-Induced Structurally Sensitive Vibrations.

    PubMed

    Punihaole, David; Hong, Zhenmin; Jakubek, Ryan S; Dahlburg, Elizabeth M; Geib, Steven; Asher, Sanford A

    2015-10-15

    We identified vibrational spectral marker bands that sensitively report on the side chain structures of glutamine (Gln) and asparagine (Asn). Density functional theory (DFT) calculations indicate that the Amide III(P) (AmIII(P)) vibrations of Gln and Asn depend cosinusoidally on their side chain OCCC dihedral angles (the χ3 and χ2 angles of Gln and Asn, respectively). We use UV resonance Raman (UVRR) and visible Raman spectroscopy to experimentally correlate the AmIII(P) Raman band frequency to the primary amide OCCC dihedral angle. The AmIII(P) structural sensitivity derives from the Gln (Asn) Cβ-Cγ (Cα-Cβ) stretching component of the vibration. The Cβ-Cγ (Cα-Cβ) bond length inversely correlates with the AmIII(P) band frequency. As the Cβ-Cγ (Cα-Cβ) bond length decreases, its stretching force constant increases, which results in an upshift in the AmIII(P) frequency. The Cβ-Cγ (Cα-Cβ) bond length dependence on the χ3 (χ2) dihedral angle results from hyperconjugation between the Cδ═Oϵ (Cγ═Oδ) π* and Cβ-Cγ (Cα-Cβ) σ orbitals. Using a Protein Data Bank library, we show that the χ3 and χ2 dihedral angles of Gln and Asn depend on the peptide backbone Ramachandran angles. We demonstrate that the inhomogeneously broadened AmIII(P) band line shapes can be used to calculate the χ3 and χ2 angle distributions of peptides. The spectral correlations determined in this study enable important new insights into protein structure in solution, and in Gln- and Asn-rich amyloid-like fibrils and prions.

  19. Proton–proton Overhauser NMR spectroscopy with polypeptide chains in large structures

    PubMed Central

    Horst, Reto; Wider, Gerhard; Fiaux, Jocelyne; Bertelsen, Eric B.; Horwich, Arthur L.; Wüthrich, Kurt

    2006-01-01

    The use of 1H–1H nuclear Overhauser effects (NOE) for structural studies of uniformly deuterated polypeptide chains in large structures is investigated by model calculations and NMR experiments. Detailed analysis of the evolution of the magnetization during 1H–1H NOE experiments under slow-motion conditions shows that the maximal 1H–1H NOE transfer is independent of the overall rotational correlation time, even in the presence of chemical exchange with the bulk water, provided that the mixing time is adjusted for the size of the structure studied. 1H–1H NOE buildup measurements were performed for the 472-kDa complex of the 72-kDa cochaperonin GroES with a 400-kDa single-ring variant of the chaperonin GroEL (SR1). These experiments demonstrate that multidimensional NOESY experiments with cross-correlated relaxation-enhanced polarization transfer and transverse relaxation-optimized spectroscopy elements can be applied to structures of molecular masses up to several hundred kilodaltabs, which opens new possibilities for studying functional interactions in large maromolecular assemblies in solution. PMID:17032756

  20. Chemistry of the rock-forming silicates: Multiple-chain, sheet, and framework structures

    NASA Astrophysics Data System (ADS)

    Papike, J. J.

    1988-08-01

    The crystal chemistry of 16 groups of multiple-chain, sheet, and framework silicates is reviewed. Crystal structure drawings are presented to illustrate crystal chemical features necessary to interpret chemical data for each mineral group. The 16 silicate groups considered in this review are the amphibole; nonclassical, ordered pyriboles; mica; pyrophyllite-talc; chlorite; greenalite; minnesotaite; stilpnomelane; prehnite; silica polymorphs; feldspar; nepheline-kalsilite; leucite-analcite; sodalite group; cancrinite group; and scapolite. Electron microprobe analyses should be augmented by independent determinations of Fe2+/Fe3+ and H2O for many of the silicate groups discussed and by determinations of CO32-, SO42-, S2-, and Li in some of the others. However, microprobe data augmented as suggested will still be ambiguous for some of the silicate groups considered here because the structures are not completely determined or are variable, with disparate domains and/or structural modulations, e.g., pyriboles, greenalite, minnesotaite, and stilpnomelane. Nevertheless, the most rigorous way to interpret silicate mineral chemical data is based on the crystal structures involved.

  1. Spectral characteristics of heterocyclic compounds with a chain structure, cooled in an ultrasonic jet

    NASA Astrophysics Data System (ADS)

    Povedailo, V. A.; Yakovlev, D. L.

    2006-11-01

    We have recorded the fluorescence excitation spectra of three heterocyclic compounds with a chain structure [BPO (2-phenyl-5-(4-diphenylyl)oxazole), POPOP (1,4-di[2-(5-phenyloxazolyl)]benzene, and TOPOT (1,4-di[2-(5-n-tolyloxazolyl)]benzene] and the fluorescence spectra of POPOP, under conditions where the molecules were cooled in an ultrasonic helium jet. A line structure is observed in the spectra of POPOP and TOPOT; for the BPO molecules, whose configuration changes considerably during electronic excitation, vibrational structure is apparent only in the low-frequency region of the excitation spectrum, and a diffuse spectrum is recorded starting from ν 0 0 + 200 cm-1. For all the compounds, in the spectra we recorded vibrations with frequencies up to 100 cm-1, arising due to the flexibility of the molecular structure. The rotational contours of the lines for the electronic and vibronic transitions of the POPOP molecules (Trot = 10.5 K) and TOPOT molecules (Trot = 15 K) are structureless and bell-shaped. The degree of polarization of the fluorescence Pfl for the jet-cooled POPOP molecules for excitation of vibrations along the absorption band up to 2000 cm-1 above ν 0 0 is practically constant (˜8.4%) and matches Pfl for high-temperature vapors.

  2. Selenium dimers and linear chains in one-dimensional cancrinite nanochannels: Structure, dynamics, and optical properties

    NASA Astrophysics Data System (ADS)

    Poborchii, Vladimir V.; Lindner, Gottlieb-Georg; Sato, Mitsuo

    2002-02-01

    Cancrinite crystals possessing parallel nanochannels are attractive for incorporation of guest materials and preparation of one-dimensional structures. In this work, we study variety of cancrinite crystals synthesized with Se inside their channels. Single crystal x-ray diffraction, polarized Raman, optical absorption, and luminescence spectra are investigated. It is shown that Se is stabilized in the form of Se22- and Se2- dimers located in the center of the channel and oriented along the channel. Different absolute and relative concentrations of Se22- and Se2- are obtained for different samples. The Se22- dimers at high concentration show tendency to organize linear chains. At low temperatures, quite strong interdimer bonding for both Se22- and Se2- is observed. Another important low-temperature effect is appearance of additional Raman bands, which are attributed to the vibrations of linear Se22- chains distorted by the incommensurate potential of cancrinite. Strong near-infrared polarized luminescence is observed for all samples. Photoionization of dimers is shown to be important step in the mechanism of the luminescence.

  3. Structural identification of skin ceramides containing ω-hydroxy acyl chains using mass spectrometry.

    PubMed

    Wu, Zhexue; Shon, Jong Cheol; Kim, Jong Yei; Cho, Yunhi; Liu, Kwang-Hyeon

    2016-10-01

    The stratum corneum (SC) acts as a barrier that protects organisms against the environment and from transepidermal water loss. It consists of corneocytes embedded in a matrix of lipid metabolites (ceramides, cholesterol, and free fatty acids). Of these lipids, ceramides are sphingolipids consisting of sphingoid bases, linked to fatty acyl chains. Typical fatty acid acyl chains are composed of α-hydroxy fatty acids (A), esterified ω-hydroxy fatty acids (EO), non-hydroxy fatty acids (N), and ω-hydroxy fatty acids (O). Of these, O-type ceramides are ester-linked via their ω-hydroxyl group to proteins in the cornified envelope and can be released and extracted following mild alkaline hydrolysis. Tandem mass spectrometry (MS/MS) analysis of O-type ceramides using chip-based direct infusion nanoelectrospray-ion trap mass spectrometry generated the characteristic fragmentation pattern of both acyl and sphingoid units, suggesting that this method could be applied to the structural identification of O-type ceramides. Based on the MS/MS fragmentation patterns of O-type ceramides, comprehensive fragmentation schemes are proposed. In addition, we have also developed a method for identifying and profiling O-type ceramides in the mouse and guinea pig SC. This information may be used to identify O-type ceramides in the SC of animal skin.

  4. Understanding influential factors on implementing green supply chain management practices: An interpretive structural modelling analysis.

    PubMed

    Agi, Maher A N; Nishant, Rohit

    2017-03-01

    In this study, we establish a set of 19 influential factors on the implementation of Green Supply Chain Management (GSCM) practices and analyse the interaction between these factors and their effect on the implementation of GSCM practices using the Interpretive Structural Modelling (ISM) method and the "Matrice d'Impacts Croisés Multiplication Appliquée à un Classement" (MICMAC) analysis on data compiled from interviews with supply chain (SC) executives based in the Gulf countries (Middle East region). The study reveals a strong influence and driving power of the nature of the relationships between SC partners on the implementation of GSCM practices. We especially found that dependence, trust, and durability of the relationship with SC partners have a very high influence. In addition, the size of the company, the top management commitment, the implementation of quality management and the employees training and education exert a critical influence on the implementation of GSCM practices. Contextual elements such as the industry sector and region and their effect on the prominence of specific factors are also highlighted through our study. Finally, implications for research and practice are discussed.

  5. Nonlinear electrical conductivity in a 1D granular medium

    NASA Astrophysics Data System (ADS)

    Falcon, E.; Castaing, B.; Creyssels, M.

    2004-04-01

    We report on observations of the electrical transport within a chain of metallic beads (slightly oxidized) under an applied stress. A transition from an insulating to a conductive state is observed as the applied current is increased. The voltage-current ( U- I) characteristics are nonlinear and hysteretic, and saturate to a low voltage per contact (0.4 V). Our 1D experiment allows us to understand phenomena (such as the “Branly effect”) related to this conduction transition by focusing on the nature of the contacts instead of the structure of the granular network. We show that this transition comes from an electro-thermal coupling in the vicinity of the microcontacts between each bead - the current flowing through these contact points generates their local heating which leads to an increase of their contact areas, and thus enhances their conduction. This current-induced temperature rise (up to 1050 ^{circ}C) results in the microsoldering of the contact points (even for voltages as low as 0.4 V). Based on this self-regulated temperature mechanism, an analytical expression for the nonlinear U- I back trajectory is derived, and is found to be in very good agreement with the experiments. In addition, we can determine the microcontact temperature with no adjustable parameters. Finally, the stress dependence of the resistance is found to be strongly non-hertzian due to the presence of the surface films. This dependence cannot be usually distinguished from the one due to the disorder of the granular contact network in 2D or 3D experiments.

  6. Photoconductivity Relaxation Mechanisms of InGaAs/GaAs Quantum Dot Chain Structures

    NASA Astrophysics Data System (ADS)

    Kondratenko, Serhiy V.; Iliash, Sviatoslav A.; Vakulenko, Oleg V.; Mazur, Yuriy I.; Benamara, Mourad; Marega, Euclydes; Salamo, Gregory J.

    2017-03-01

    An experimental study of the photoconductivity time decay in InGaAs/GaAs quantum dot chain structures is reported. Different photoconductivity relaxations resulting from spectrally selecting photoexcitation of InGaAs QWR or QDs as well as GaAs spacers were measured. The photoconductivity relaxation after excitation of 650 nm follows a stretched exponent with decay constant dependent on morphology of InGaAs epitaxial layers. Kinetics with 980 nm excitation are successfully described by equation that takes into account the linear recombination involving Shockley-Read centers in the GaAs spacers and bimolecular recombination via quantum-size states of InGaAs QWRs or QDs.

  7. Spin Frustration in an Organic Radical Ion Salt Based on a Kagome-Coupled Chain Structure.

    PubMed

    Postulka, Lars; Winter, Stephen M; Mihailov, Adam G; Mailman, Aaron; Assoud, Abdeljalil; Robertson, Craig M; Wolf, Bernd; Lang, Michael; Oakley, Richard T

    2016-08-31

    Electro-oxidation of the quinoidal bisdithiazole BT in dichloroethane in the presence of [Bu4N][GaBr4] affords the 1:1 radical ion salt [BT][GaBr4], crystals of which belong to the trigonal space group P3. The packing pattern of the radical cations provides a rare example of an organic kagome basket structure, with S = 1/2 radical ion chains located at the triangular corners of a trihexagonal lattice. Magnetic measurements over a wide temperature range from 30 mK to 300 K suggest strongly frustrated AFM interactions on the scale of J/kb ∼ 30 K, but reveal no anomalies that would be associated with magnetic order. These observations are discussed in terms of the symmetry allowed magnetic interactions within and between the frustrated layers.

  8. EMODEL_1D v. 1.0

    SciTech Connect

    Aldridge, David F.

    2016-07-06

    Program EMODEL_1D is an electromagnetic earth model construction utility designed to generate a three-dimensional (3D) uniformly-gridded representation of one-dimensional (1D) layered earth model. Each layer is characterized by the isotropic EM properties electric permittivity ?, magnetic permeability ?, and current conductivity ?. Moreover, individual layers of the model may possess a linear increase/decrease of any or all of these properties with depth.

  9. Nonlocal order parameters for the 1D Hubbard model.

    PubMed

    Montorsi, Arianna; Roncaglia, Marco

    2012-12-07

    We characterize the Mott-insulator and Luther-Emery phases of the 1D Hubbard model through correlators that measure the parity of spin and charge strings along the chain. These nonlocal quantities order in the corresponding gapped phases and vanish at the critical point U(c)=0, thus configuring as hidden order parameters. The Mott insulator consists of bound doublon-holon pairs, which in the Luther-Emery phase turn into electron pairs with opposite spins, both unbinding at U(c). The behavior of the parity correlators is captured by an effective free spinless fermion model.

  10. Nonlocal Order Parameters for the 1D Hubbard Model

    NASA Astrophysics Data System (ADS)

    Montorsi, Arianna; Roncaglia, Marco

    2012-12-01

    We characterize the Mott-insulator and Luther-Emery phases of the 1D Hubbard model through correlators that measure the parity of spin and charge strings along the chain. These nonlocal quantities order in the corresponding gapped phases and vanish at the critical point Uc=0, thus configuring as hidden order parameters. The Mott insulator consists of bound doublon-holon pairs, which in the Luther-Emery phase turn into electron pairs with opposite spins, both unbinding at Uc. The behavior of the parity correlators is captured by an effective free spinless fermion model.

  11. PHAISTOS: a framework for Markov chain Monte Carlo simulation and inference of protein structure.

    PubMed

    Boomsma, Wouter; Frellsen, Jes; Harder, Tim; Bottaro, Sandro; Johansson, Kristoffer E; Tian, Pengfei; Stovgaard, Kasper; Andreetta, Christian; Olsson, Simon; Valentin, Jan B; Antonov, Lubomir D; Christensen, Anders S; Borg, Mikael; Jensen, Jan H; Lindorff-Larsen, Kresten; Ferkinghoff-Borg, Jesper; Hamelryck, Thomas

    2013-07-15

    We present a new software framework for Markov chain Monte Carlo sampling for simulation, prediction, and inference of protein structure. The software package contains implementations of recent advances in Monte Carlo methodology, such as efficient local updates and sampling from probabilistic models of local protein structure. These models form a probabilistic alternative to the widely used fragment and rotamer libraries. Combined with an easily extendible software architecture, this makes PHAISTOS well suited for Bayesian inference of protein structure from sequence and/or experimental data. Currently, two force-fields are available within the framework: PROFASI and OPLS-AA/L, the latter including the generalized Born surface area solvent model. A flexible command-line and configuration-file interface allows users quickly to set up simulations with the desired configuration. PHAISTOS is released under the GNU General Public License v3.0. Source code and documentation are freely available from http://phaistos.sourceforge.net. The software is implemented in C++ and has been tested on Linux and OSX platforms.

  12. Structure-preserving model reduction of large-scale logistics networks. Applications for supply chains

    NASA Astrophysics Data System (ADS)

    Scholz-Reiter, B.; Wirth, F.; Dashkovskiy, S.; Makuschewitz, T.; Schönlein, M.; Kosmykov, M.

    2011-12-01

    We investigate the problem of model reduction with a view to large-scale logistics networks, specifically supply chains. Such networks are modeled by means of graphs, which describe the structure of material flow. An aim of the proposed model reduction procedure is to preserve important features within the network. As a new methodology we introduce the LogRank as a measure for the importance of locations, which is based on the structure of the flows within the network. We argue that these properties reflect relative importance of locations. Based on the LogRank we identify subgraphs of the network that can be neglected or aggregated. The effect of this is discussed for a few motifs. Using this approach we present a meta algorithm for structure-preserving model reduction that can be adapted to different mathematical modeling frameworks. The capabilities of the approach are demonstrated with a test case, where a logistics network is modeled as a Jackson network, i.e., a particular type of queueing network.

  13. Effects of molecular structure on microscopic heat transport in chain polymer liquids

    SciTech Connect

    Matsubara, Hiroki Kikugawa, Gota; Ohara, Taku; Bessho, Takeshi; Yamashita, Seiji

    2015-04-28

    In this paper, we discuss the molecular mechanism of the heat conduction in a liquid, based on nonequilibrium molecular dynamics simulations of a systematic series of linear- and branched alkane liquids, as a continuation of our previous study on linear alkane [T. Ohara et al., J. Chem. Phys. 135, 034507 (2011)]. The thermal conductivities for these alkanes in a saturated liquid state at the same reduced temperature (0.7T{sub c}) obtained from the simulations are compared in relation to the structural difference of the liquids. In order to connect the thermal energy transport characteristics with molecular structures, we introduce the new concept of the interatomic path of heat transfer (atomistic heat path, AHP), which is defined for each type of inter- and intramolecular interaction. It is found that the efficiency of intermolecular AHP is sensitive to the structure of the first neighbor shell, whereas that of intramolecular AHP is similar for different alkane species. The dependence of thermal conductivity on different lengths of the main and side chain can be understood from the natures of these inter- and intramolecular AHPs.

  14. Self-assembled decanuclear Na(I)2Mn(II)4Mn(III)4 complexes: from discrete clusters to 1-D and 2-D structures, with the Mn(II)4Mn(III)4 unit displaying a large spin ground state and probable SMM behaviour.

    PubMed

    Langley, Stuart K; Chilton, Nicholas F; Moubaraki, Boujemaa; Murray, Keith S

    2011-12-07

    The synthesis, magnetic characterization and X-ray crystal structures are reported for five new manganese compounds, [Mn(III)(teaH(2))(sal)]·(1/2)H(2)O (1), [Na(I)(2)Mn(II)(4)Mn(III)(4)(teaH)(6)(sal)(4)(N(3))(2)(MeOH)(4)]·6MeOH (2), [Na(I)(2)Mn(II)(4)Mn(III)(4)(teaH)(6)(sal)(4)(N(3))(2)(MeOH)(2)](n)·7MeOH (3), [Na(I)(2)Mn(II)(4)Mn(III)(4)(teaH)(6)(sal)(4)(N(3))(2)(MeOH)(2)](n)·2MeOH·Et(2)O (4) and [K(I)(2)Mn(II)(4)Mn(III)(4)(teaH)(6)(sal)(4)(N(3))(2)(H(2)O)(2)](n)·5MeOH (5). Complex 1 is a mononuclear compound, formed via the reaction of Mn(NO(3))(2)·4H(2)O, triethanolamine (teaH(3)) and salicylic acid (salH(2)) in a basic methanolic solution. Compound 2 is a mixed-valent hetero-metallic cluster made up of a Mn(8)Na(2) decanuclear core and is formed via the reaction of sodium azide (NaN(3)) with 1. Compounds 3-5 are isolated as 1- or 2-D coordination polymers, each containing the decanuclear Mn(8)M(2) (M = Na(+) or K(+)) core building block as the repeating unit. Compound 3 is isolated when 1 is reacted with NaN(3) over a very short reaction time and forms a 1-D coordination polymer. Each unit displays inter-cluster bridges via the O-atoms of teaH(2-) ligands bonding to the sodium ions of an adjacent cluster. Increasing the reaction time appears to drive the formation of 4 which forms 2-D polymeric sheets and is a packing polymorph of 3. The addition of KMnO(4) and NaN(3) to 1 resulted in compound 5, which also forms a 1-D coordination polymer of the decanuclear core unit. The 1-D chains are now linked via inter-cluster potassium and salicylate bridges. Solid state DC susceptibility measurements were performed on compounds 1-5. The data for 1 are as expected for an S = 2 Mn(III) ion, with the isothermal M vs. H data being fitted by matrix diagonalization methods to give values of g and the axial (D) and rhombic (E) zero field splitting parameters of 2.02, -2.70 cm(-1) and 0.36 cm(-1) respectively. The data for 2-5, each with an identical Mn(II)(4)Mn(III)(4

  15. Structural Origins of Nitroxide Side Chain Dynamics on Membrane Protein [alpha]-Helical Sites

    SciTech Connect

    Kroncke, Brett M.; Horanyi, Peter S.; Columbus, Linda

    2010-12-07

    Understanding the structure and dynamics of membrane proteins in their native, hydrophobic environment is important to understanding how these proteins function. EPR spectroscopy in combination with site-directed spin labeling (SDSL) can measure dynamics and structure of membrane proteins in their native lipid environment; however, until now the dynamics measured have been qualitative due to limited knowledge of the nitroxide spin label's intramolecular motion in the hydrophobic environment. Although several studies have elucidated the structural origins of EPR line shapes of water-soluble proteins, EPR spectra of nitroxide spin-labeled proteins in detergents or lipids have characteristic differences from their water-soluble counterparts, suggesting significant differences in the underlying molecular motion of the spin label between the two environments. To elucidate these differences, membrane-exposed {alpha}-helical sites of the leucine transporter, LeuT, from Aquifex aeolicus, were investigated using X-ray crystallography, mutational analysis, nitroxide side chain derivatives, and spectral simulations in order to obtain a motional model of the nitroxide. For each crystal structure, the nitroxide ring of a disulfide-linked spin label side chain (R1) is resolved and makes contacts with hydrophobic residues on the protein surface. The spin label at site I204 on LeuT makes a nontraditional hydrogen bond with the ortho-hydrogen on its nearest neighbor F208, whereas the spin label at site F177 makes multiple van der Waals contacts with a hydrophobic pocket formed with an adjacent helix. These results coupled with the spectral effect of mutating the i {+-} 3, 4 residues suggest that the spin label has a greater affinity for its local protein environment in the low dielectric than on a water-soluble protein surface. The simulations of the EPR spectra presented here suggest the spin label oscillates about the terminal bond nearest the ring while maintaining weak contact

  16. Human lambda light-chain constant region gene CMor lambda: the primary structure of lambda VI Bence Jones protein Mor.

    PubMed Central

    Frangione, B; Moloshok, T; Prelli, F; Solomon, A

    1985-01-01

    Serologic, structural, and genetic analyses have shown that the constant (C) region of human kappa light chains is encoded by a single gene, whereas that of lambda chains is encoded by multiple genes. We have determined the complete C region amino acid sequence of two monoclonal lambda VI light chains, Bence Jones proteins Sut and Mor. The C region of lambda chains Sut and Mor consists of 105 residues, as is characteristic for human lambda light chains, of which 102 are identical in sequence. Protein Sut has the C region sequence associated with the C lambda isotype Mcg-, Kern-, Oz+ and represents a product of the C lambda 3 (Kern-, Oz+) gene. Protein Mor has a C region sequence associated with Mcg-, Kern-, and Oz- proteins but differs from protein Sut by the presence of three amino acid interchanges at positions 168, 176, and 194. These substitutions distinguish protein Mor from lambda chains encoded by the C lambda 1 (Mcg+), C lambda 2 (Kern-, Oz-), and C lambda 3 (Kern-, Oz+) genes and provide further evidence for polymorphism of the human C lambda genome. The gene encoding the C region sequence of lambda chain Mor is designated CMor lambda. PMID:3923477

  17. Systematic investigation of zinc aminoalkylphosphonates: influence of the alkyl chain lengths on the structure formation.

    PubMed

    Schmidt, Corinna; Stock, Norbert

    2012-03-05

    With the high-throughput (HT) methodology, the bifunctional aminoalkylphosphonic acids (AAPA) linker molecules 2-aminoethyl- (AEPA), 3-aminopropyl- (APPA), and 4-aminobutylphosphonic acid (ABPA) [HO(3)P-C(n)H(2n)-NH(2) (n = 2-4)] and zinc nitrate were used to synthesize new metal phosphonates in order to investigate the influence of the alkyl chain length on the structure formation. The systematic investigations led to one known (ZnO(3)PC(2)H(4)NH(2)) and six new compounds: one using AEPA, three using APPA, and two using ABPA. The crystal structures of five compounds were determined by single crystal X-ray diffraction, using X-ray powder diffraction (XRPD) data as well as structure modeling employing force field methods. For compound 1, Zn(O(3)P-C(2)H(4)-NH(3))(NO(3))(H(2)O) (monoclinic, Cc, a = 4.799(1) Å, b = 29.342(6) Å, c = 5.631(1) Å, β = 91.59(3)°, V = 792.7(3) Å(3), Z = 4), and compound 2, Zn(2)(OH)(O(3)P-C(3)H(6)-NH(3))(NO(3)) (monoclinic, P2/c, a = 12.158(2) Å, b = 5.0315(10) Å, c = 13.952(3) Å, β = 113.23(3)°, V = 784.3(3) Å(3), Z = 2), the structures were determined using single crystal X-ray diffraction data. The crystal structures of [Zn(O(3)P-C(3)H(6)-NH(2))]·H(2)O (3) (monoclinic, P2(1)/c, a = 9.094(2) Å, b = 5.0118(7) Å, c = 16.067(4) Å, β = 90.38(2)°, V = 732.3(2) Å(3), Z = 4) and Zn(O(3)P-C(4)H(8)-NH(2)) (5) (monoclinic, P2(1)/c, a = 8.570(7) Å, b = 8.378(4) Å, c = 9.902(6) Å, β = 90.94(5)°, V = 710.9(8) Å(3), Z = 4) were determined using XRPD data. The structural model for compound 6, Zn(O(3)P-C(4)H(8)-NH(3))(NO(3))(H(2)O), was established using lattice parameters from XRPD data and following crystal structure modeling employing force field methods. The structures depend strongly on the alkyl chain length n. For n = 2 and 4 isoreticular compounds are observed, while n = 3 leads to new structures. Larger amounts of all compounds were obtained employing scale-up syntheses in a conventional oven as well as in a microwave

  18. Single‐Layered Hybrid Materials Based on 1D Associated Metalorganic Nanoribbons for Controlled Release of Pheromones

    PubMed Central

    Moreno, José María; Navarro, Ismael; Díaz, Urbano; Primo, Jaime

    2016-01-01

    Abstract A new family of stable layered organic–inorganic materials has been prepared, in one‐step solvothermal process. They are based on an ordered nickel cluster‐type nanoribbons separated from each other by specific alkyl (heptyl‐ or dodecyl‐) arylic mono‐carboxylate moieties acting as molecular spacers, perpendicular to the 1D inorganic chains. These organic spacers contain hydrocarbon tails with different length which control the separation level between inorganic 1D sub‐units, inhibiting the 3D growth of conventional DUT‐8‐type metal–organic frameworks (MOFs). The lamellar nature of the materials formed was studied and confirmed by different characterization techniques, showing the structural location of individual organic and inorganic building units. They have been successfully used as a long‐lasting biodegradable and water‐proof materials for controlled release of chemicals, such as pheromones for sustainable treatment of insect plagues. PMID:27444798

  19. Chain-like structure elements in Ni40Ta60 metallic glasses observed by scanning tunneling microscopy.

    PubMed

    Pawlak, Rémy; Marot, Laurent; Sadeghi, Ali; Kawai, Shigeki; Glatzel, Thilo; Reimann, Peter; Goedecker, Stefan; Güntherodt, Hans-Joachim; Meyer, Ernst

    2015-08-13

    The structure of metallic glasses is a long-standing question because the lack of long-range order makes diffraction based techniques difficult to be applied. Here, we used scanning tunneling microscopy with large tunneling resistance of 6 GΩ at low temperature in order to minimize forces between probe and sample and reduce thermal fluctuations of metastable structures. Under these extremely gentle conditions, atomic structures of Ni40Ta60 metallic glasses are revealed with unprecedented lateral resolution. In agreement with previous models and experiments, icosahedral-like clusters are observed. The clusters show a high degree of mobility, which explains the need of low temperatures for stable imaging. In addition to icosahedrons, chain-like structures are resolved and comparative density functional theory (DFT) calculations confirm that these structures are meta-stable. The co-existence of icosahedral and chain-like structures might be an key ingredient for the understanding of the mechanical properties of metallic glasses.

  20. Chain-like structure elements in Ni40Ta60 metallic glasses observed by scanning tunneling microscopy

    NASA Astrophysics Data System (ADS)

    Pawlak, Rémy; Marot, Laurent; Sadeghi, Ali; Kawai, Shigeki; Glatzel, Thilo; Reimann, Peter; Goedecker, Stefan; Güntherodt, Hans-Joachim; Meyer, Ernst

    2015-08-01

    The structure of metallic glasses is a long-standing question because the lack of long-range order makes diffraction based techniques difficult to be applied. Here, we used scanning tunneling microscopy with large tunneling resistance of 6 GΩ at low temperature in order to minimize forces between probe and sample and reduce thermal fluctuations of metastable structures. Under these extremely gentle conditions, atomic structures of Ni40Ta60 metallic glasses are revealed with unprecedented lateral resolution. In agreement with previous models and experiments, icosahedral-like clusters are observed. The clusters show a high degree of mobility, which explains the need of low temperatures for stable imaging. In addition to icosahedrons, chain-like structures are resolved and comparative density functional theory (DFT) calculations confirm that these structures are meta-stable. The co-existence of icosahedral and chain-like structures might be an key ingredient for the understanding of the mechanical properties of metallic glasses.

  1. Perylene diimides with different side chains are selective in inducing different G-quadruplex DNA structures and in inhibiting telomerase.

    PubMed

    Rossetti, Luigi; Franceschin, Marco; Bianco, Armandodoriano; Ortaggi, Giancarlo; Savino, Maria

    2002-09-16

    Four N,N'-disubstituted perylene diimides, having different side chains, have been studied for their ability in inducing G-quadruplex DNA structures. We found that electrostatic interactions between ligands side chains and DNA grooves play a main role not only in the amount of G-quadruplex formed, but also in selecting its topology. Moreover, such compounds show also a different ability to inhibit telomerase. The correlation of these findings suggests the intriguing possibility that different G-quadruplex structures could differently inhibit the enzyme.

  2. Residual structure and dynamics in DMSO-d6 denatured dynein light chain protein.

    PubMed

    Chakraborty, Swagata; Mohan, P M Krishna; Hosur, Ramakrishna V

    2012-01-01

    Structural and motional features in the denatured state of a protein dictate the early folding events starting from that state and these features vary depending upon the nature of the denaturant used. Here, we have attempted to decipher the early events in the folding of Dynein Light Chain protein (DLC8), starting from DMSO-d6 denatured state. Multinuclear NMR experiments were used to obtain the full spectral assignment. The HSQC spectrum shows the presence of two sets of peaks for the residues Met 1, Ser 2, Arg 4, Ala 11, Met 17, Thr 26, Lys 44, Tyr 50, Asn 51, Trp 54, His 55, Val 58, Gly 59, Ser 64, Tyr 65, His 68, Phe 86, Lys 87 indicating the presence of slow conformational transition in the heterogeneous ensemble. Analysis of residual structural propensities with secondary (13)C chemical shifts, (3)J(H(N)(-)H(α)) coupling constants and (1)H-(1)H NOE revealed the presence of local preferences which encompass both native and non-native like structures. The spectral density calculations, as obtained from measured R(1), R(2) and (1)H-(15)N steady state NOE values provide insights into the backbone dynamics on the milli to picosecond timescale. The segment Ser 14 - His 55 exhibits slow motions on the milli- to microsecond timescale arising from conformational exchange. The presence of native like structural preference, as well as conformational exchange classifies the above segment as the nucleation site of folding. Based on the observations, we propose here, the probable hierarchy of folding of DLC8 on dilution of denaturant: the two helices are formed first followed by the formation of β2 and β5.

  3. Mycobacterium tuberculosis utilizes a unique heterotetrameric structure for dehydrogenation of the cholesterol side chain

    PubMed Central

    Thomas, Suzanne T.; Sampson, Nicole S.

    2013-01-01

    Compounding evidence supports the important role in pathogenesis that the metabolism of cholesterol by Mycobacterium tuberculosis (M. tuberculosis) plays. Elucidating the pathway by which cholesterol is catabolized is necessary to understand the molecular mechanism by which this pathway contributes to infection. Based on early metabolite identification studies in multiple actinomycetes, it has been proposed that cholesterol side chain metabolism requires one or more acyl-CoA dehydrogenases (ACADs). There are 35 genes annotated as encoding ACADs in the M. tuberculosis genome. Here we characterize a heteromeric ACAD encoded by Rv3544c and Rv3543c, formerly named fadE28 and fadE29, respectively. We now refer to genes Rv3544c and Rv3543c as chsE1 and chsE2 in recognition of their validated activity in cholesterol side chain dehydrogenation. Analytical ultracentrifugation and LC/UV experiments establish that ChsE1-ChsE2 forms an α2β2 heterotetramer, a new architecture for an ACAD. Our bioinformatic analysis and mutagenesis studies reveal that heterotetrameric ChsE1-ChsE2 has only two active sites. E241 in ChsE2 is required for catalysis of dehydrogenation by ChsE1-ChsE2. Steady state kinetic analysis establishes the enzyme is specific for an intact steroid ring system compared to hexahydroindanone substrates with specificity constants (kcat/KM) of 2.5 × 105 ± 0.5 s-1 M-1 vs 9.8 × 102 ± s-1 M-1 respectively, at pH 8.5. The characterization of a unique ACAD quaternary structure involved in sterol metabolism that is encoded by two distinct cistronic ACAD genes opens the way to identification of additional sterol metabolizing ACADs in M. tuberculosis and other actinomycetes through bioinformatic analysis. PMID:23560677

  4. Mycobacterium tuberculosis utilizes a unique heterotetrameric structure for dehydrogenation of the cholesterol side chain.

    PubMed

    Thomas, Suzanne T; Sampson, Nicole S

    2013-04-30

    Compounding evidence supports the important role in pathogenesis that the metabolism of cholesterol by Mycobacterium tuberculosis plays. Elucidating the pathway by which cholesterol is catabolized is necessary to understand the molecular mechanism by which this pathway contributes to infection. On the basis of early metabolite identification studies in multiple actinomycetes, it has been proposed that cholesterol side chain metabolism requires one or more acyl-CoA dehydrogenases (ACADs). There are 35 genes annotated as encoding ACADs in the M. tuberculosis genome. Here we characterize a heteromeric ACAD encoded by Rv3544c and Rv3543c, formerly named fadE28 and fadE29, respectively. We now refer to genes Rv3544c and Rv3543c as chsE1 and chsE2, respectively, in recognition of their validated activity in cholesterol side chain dehydrogenation. Analytical ultracentrifugation and liquid chromatography-ultraviolet experiments establish that ChsE1-ChsE2 forms an α(2)β(2) heterotetramer, a new architecture for an ACAD. Our bioinformatic analysis and mutagenesis studies reveal that heterotetrameric ChsE1-ChsE2 has only two active sites. E241 in ChsE2 is required for catalysis of dehydrogenation by ChsE1-ChsE2. Steady state kinetic analysis establishes the enzyme is specific for an intact steroid ring system versus hexahydroindanone substrates with specificity constants (k(cat)/K(M)) of (2.5 ± 0.5) × 10(5) s(-1) M(-1) versus 9.8 × 10(2) s(-1) M(-1), respectively, at pH 8.5. The characterization of a unique ACAD quaternary structure involved in sterol metabolism that is encoded by two distinct cistronic ACAD genes opens the way to identification of additional sterol-metabolizing ACADs in M. tuberculosis and other actinomycetes through bioinformatic analysis.

  5. Structure-activity relationship of synthetic branched-chain distearoylglycerol (distearin) as protein kinase C activators

    SciTech Connect

    Zhou, Qingzhong; Raynor, R.L.; Wood, M.G. Jr.; Menger, F.M.; Kuo, J.F. )

    1988-09-20

    Several representative branched-chain analogues of distearin (DS) were synthesized and tested for their abilities to activate protein kinase C (PKC) and to compete for the binding of ({sup 3}H)phorbol 12,13-dibutyrate (PDBu) to the enzyme. Substitutions of stearoyl moieties at sn-1 and sn-2 with 8-methylstearate decreased activities on these parameters, relative to those of the parental diacylglycerol DS, a weak PKC activator. Substitutions with 8-butyl, 4-butyl, or 8-phenyl derivatives, on the other hand, increased activities of the resulting analogues to levels comparable to those seen for diolein (DO), a diacylglycerol prototype shown to be a potent PKC activator. Kinetic analysis indicated that 8-methyldistearin (8-MeDS) acted by decreasing, whereas 8-butyldistearin (8-BuDS) and 8-phenyldistearin (8-PhDS) acted by increasing, the affinities of PKC for phosphatidylserine (PS, a phospholipid cofactor) and Ca{sup 2+} compared to the values seen in the absence or presence of DS. The stimulatory effect of 8-BuDS and 8-PhDS on PKC, as DO, was additive to that of 1,2-(8-butyl)distearoylphosphatidylcholine (1,2(8-Bu)DSPC) and, moreover, they abolished the marked inhibition of the enzyme activity caused by high concentrations of 1,2(8-Bu)DSPC. The present findings demonstrated a structure-activity relationship of the branched-chain DS analogues in the regulation of PKC, perhaps related to their abilities to specifically modify interactions of PKC with PS and/or Ca{sup 2+} critically involved in enzyme activation/inactivation.

  6. A lipidomic platform establishment for structural identification of skin ceramides with non-hydroxyacyl chains.

    PubMed

    Shin, Jung-Hoon; Shon, Jong Cheol; Lee, Kyohoon; Kim, Sunki; Park, Chang Seo; Choi, Eung Ho; Lee, Choong Hwan; Lee, Hye Suk; Liu, Kwang-Hyeon

    2014-03-01

    The stratum corneum (SC) is the outermost layer of skin that functions as a barrier and protects against environmental influences and transepidermal water loss. Its unique morphology consists of keratin-enriched corneocytes embedded in a distinctive mixture of lipids containing mainly ceramides, free fatty acids, and cholesterol. Ceramides are sphingolipids consisting of sphingoid bases, which are linked to fatty acids by an amide bond. Typical sphingoid bases in the skin are composed of dihydrosphingosine (dS), sphingosine (S), phytosphingosine (P), and 6-hydroxysphingosine (H), and the fatty acid acyl chains are composed of non-hydroxy fatty acid (N), α-hydroxy fatty acid (A), ω-hydroxy fatty acid (O), and esterified ω-hydroxy fatty acid (E). The 16 ceramide classes include several combinations of sphingoid bases and fatty acid acyl chains. Among them, N-type ceramides are the most abundant in the SC. Mass spectrometry (MS)/MS analysis of N-type ceramides using chip-based direct infusion nanoelectrospray-ion trap mass spectrometry generated the characteristic fragmentation pattern of both acyl and sphingoid units, which could be applied to structural identification of ceramides. Based on the MS/MS fragmentation patterns of N-type ceramides, comprehensive fragmentation schemes were proposed. In addition, mass fragmentation patterns, which are specific to the sphingoid backbone of N-type ceramides, were found in higher m/z regions of tandem mass spectra. These characteristic and general fragmentation patterns were used to identify N-type ceramides in human SC. Based on established MS/MS fragmentation patterns of N-type ceramides, 52 ceramides (including different classes of NS, NdS, NP, and NH) were identified in human SC. The MS/MS fragmentation patterns of N-type ceramides were characterized by interpreting their product ion scan mass spectra. This information may be used to identify N-type ceramides in the SC of human, rat, and mouse skin.

  7. Complex magnetic structure of clusters and chains of Ni and Fe on Pt(111)

    PubMed Central

    Bezerra-Neto, Manoel M.; Ribeiro, Marcelo S.; Sanyal, Biplab; Bergman, Anders; Muniz, Roberto B.; Eriksson, Olle; Klautau, Angela B.

    2013-01-01

    We present an approach to control the magnetic structure of adatoms adsorbed on a substrate having a high magnetic susceptibility. Using finite Ni-Pt and Fe-Pt nanowires and nanostructures on Pt(111) surfaces, our ab initio results show that it is possible to tune the exchange interaction and magnetic configuration of magnetic adatoms (Fe or Ni) by introducing different numbers of Pt atoms to link them, or by including edge effects. The exchange interaction between Ni (or Fe) adatoms on Pt(111) can be considerably increased by introducing Pt chains to link them. The magnetic ordering can be regulated allowing for ferromagnetic or antiferromagnetic configurations. Noncollinear magnetic alignments can also be stabilized by changing the number of Pt-mediated atoms. An Fe-Pt triangularly-shaped nanostructure adsorbed on Pt(111) shows the most complex magnetic structure of the systems considered here: a spin-spiral type of magnetic order that changes its propagation direction at the triangle vertices. PMID:24165828

  8. A molecular ruler for chain elongation catalyzed by octaprenyl pyrophosphate synthase and its structure-based engineering to produce unprecedented long chain trans-prenyl products.

    PubMed

    Guo, Rey-Ting; Kuo, Chih-Jung; Ko, Tzu-Ping; Chou, Chia-Cheng; Liang, Po-Huang; Wang, Andrew H-J

    2004-06-22

    Octaprenyl pyrophosphate synthase (OPPs) catalyzes consecutive condensation reactions of farnesyl pyrophosphate (FPP) with five molecules of isopentenyl pyrophosphate (IPP) to generate C(40) octaprenyl pyrophosphate (OPP) which constitutes the side chain of menaquinone. We have previously reported the X-ray structure of OPPs from Thermotoga maritima, which is composed entirely of alpha-helices joined by connecting loops and is arranged with nine core helices around a large central cavity [Guo, R. T., Kuo, C. J., Ko, T. P., Chou, C. C., Shr, R. L., Liang, P. H., and Wang, A. H.-J. (2004) J. Biol. Chem. 279, 4903-4912]. A76 and S77 are located on top of the active site close to where FPP is bound. A76Y and A76Y/S77F OPPs mutants produce C(20), indicating that the substituted larger residues interfere with the substrate chain elongation. Surprisingly, the A76Y/S77F mutant synthesizes a larger amount of C(20) than the A76Y mutant. In the crystal structure of the A76Y/S77F mutant, F77 is pushed away by Y76, thereby creating more space between those two large amino acids to accommodate the C(20) product. A large F132 residue at the bottom of the tunnel-shaped active site serves as the "floor" and determines the final product chain length. The substitution of F132 with a small Ala, thereby removing the blockade, led to the synthesis of a C(50) product larger than that produced by the wild-type enzyme. On the basis of the structure, we have sequentially mutated the large amino acids, including F132, L128, I123, and D62, to Ala underneath the tunnel. The products of the F132A/L128A/I123A/D62A mutant reach C(95), beyond the largest chain length generated by all known trans-prenyltransferases. Further modifications of the enzyme reaction conditions, including new IPP derivatives, may allow the preparation of high-molecular weight polyprenyl products resembling the rubber molecule.

  9. Two distinct myosin light chain structures are induced by specific variations within the bound IQ motifs—functional implications

    PubMed Central

    Terrak, Mohammed; Wu, Guanming; Stafford, Walter F.; Lu, Renne C.; Dominguez, Roberto

    2003-01-01

    IQ motifs are widespread in nature. Mlc1p is a calmodulin-like myosin light chain that binds to IQ motifs of a class V myosin, Myo2p, and an IQGAP-related protein, Iqg1p, playing a role in polarized growth and cytokinesis in Saccharomyces cerevisiae. The crystal structures of Mlc1p bound to IQ2 and IQ4 of Myo2p differ dramatically. When bound to IQ2, Mlc1p adopts a compact conformation in which both the N- and C-lobes interact with the IQ motif. However, in the complex with IQ4, the N-lobe no longer interacts with the IQ motif, resulting in an extended conformation of Mlc1p. The two light chain structures relate to two distinct subfamilies of IQ motifs, one of which does not interact with the N-lobes of calmodulin-like light chains. The correlation between light chain structure and IQ sequence is demonstrated further by sedimentation velocity analysis of complexes of Mlc1p with IQ motifs from Myo2p and Iqg1p. The resulting ‘free’ N-lobes of myosin light chains in the extended conformation could mediate the formation of ternary complexes during protein localization and/or partner recruitment. PMID:12554638

  10. Transformation of a 4-membered ring zinc phosphate SBU to a sodalite-related 3-dimensional structure through a linear chain structure.

    PubMed

    Dan, Meenakshi; Udayakumar, D; Rao, C N R

    2003-09-07

    A zero-dimensional zinc phosphate, comprising a 4-membered ring, is shown to spontaneously transform at room temperature, to a linear chain structure consisting of corner-shared 4-membered rings, the latter transforming to a 3-dimensional sodalite-related structure under mild conditions.

  11. Field induced changes in the ring/chain equilibrium of hydrogen bonded structures: 5-methyl-3-heptanol

    NASA Astrophysics Data System (ADS)

    Young-Gonzales, Amanda R.; Richert, Ranko

    2016-08-01

    Using non-linear dielectric techniques, we have measured the dynamics of 5-methyl-3-heptanol at a temperature at which the Kirkwood correlation factor gK indicates the coexistence of ring- and chain-like hydrogen-bonded structures. Steady state permittivity spectra recorded in the presence of a high dc bias electric field (17 MV/m) reveal that both the amplitude and the time constant are increased by about 10% relative to the low field limit. This change is attributed to the field driven conversion from ring-like to the more polar chain-like structures, and a direct observation of its time dependence shows that the ring/chain structural transition occurs on a time scale that closely matches that of the dielectric Debye peak. This lends strong support to the picture that places fluctuations of the end-to-end vector of hydrogen bonded structures at the origin of the Debye process, equivalent to fluctuations of the net dipole moment or gK. Recognizing that changes in the ring/chain equilibrium constant also impact the spectral separation between Debye and α-process may explain the difference in their temperature dependence whenever gK is sensitive to temperature, i.e., when the structural motifs of hydrogen bonding change considerably.

  12. Potent neutralizing anti-CD1d antibody reduces lung cytokine release in primate asthma model

    PubMed Central

    Nambiar, Jonathan; Clarke, Adam W; Shim, Doris; Mabon, David; Tian, Chen; Windloch, Karolina; Buhmann, Chris; Corazon, Beau; Lindgren, Matilda; Pollard, Matthew; Domagala, Teresa; Poulton, Lynn; Doyle, Anthony G

    2015-01-01

    CD1d is a receptor on antigen-presenting cells involved in triggering cell populations, particularly natural killer T (NKT) cells, to release high levels of cytokines. NKT cells are implicated in asthma pathology and blockade of the CD1d/NKT cell pathway may have therapeutic potential. We developed a potent anti-human CD1d antibody (NIB.2) that possesses high affinity for human and cynomolgus macaque CD1d (KD ∼100 pM) and strong neutralizing activity in human primary cell-based assays (IC50 typically <100 pM). By epitope mapping experiments, we showed that NIB.2 binds to CD1d in close proximity to the interface of CD1d and the Type 1 NKT cell receptor β-chain. Together with data showing that NIB.2 inhibited stimulation via CD1d loaded with different glycolipids, this supports a mechanism whereby NIB.2 inhibits NKT cell activation by inhibiting Type 1 NKT cell receptor β-chain interactions with CD1d, independent of the lipid antigen in the CD1d antigen-binding cleft. The strong in vitro potency of NIB.2 was reflected in vivo in an Ascaris suum cynomolgus macaque asthma model. Compared with vehicle control, NIB.2 treatment significantly reduced bronchoalveolar lavage (BAL) levels of Ascaris-induced cytokines IL-5, IL-8 and IL-1 receptor antagonist, and significantly reduced baseline levels of GM-CSF, IL-6, IL-15, IL-12/23p40, MIP-1α, MIP-1β, and VEGF. At a cellular population level NIB.2 also reduced numbers of BAL lymphocytes and macrophages, and blood eosinophils and basophils. We demonstrate that anti-CD1d antibody blockade of the CD1d/NKT pathway modulates inflammatory parameters in vivo in a primate inflammation model, with therapeutic potential for diseases where the local cytokine milieu is critical. PMID:25751125

  13. Potent neutralizing anti-CD1d antibody reduces lung cytokine release in primate asthma model.

    PubMed

    Nambiar, Jonathan; Clarke, Adam W; Shim, Doris; Mabon, David; Tian, Chen; Windloch, Karolina; Buhmann, Chris; Corazon, Beau; Lindgren, Matilda; Pollard, Matthew; Domagala, Teresa; Poulton, Lynn; Doyle, Anthony G

    2015-01-01

    CD1d is a receptor on antigen-presenting cells involved in triggering cell populations, particularly natural killer T (NKT) cells, to release high levels of cytokines. NKT cells are implicated in asthma pathology and blockade of the CD1d/NKT cell pathway may have therapeutic potential. We developed a potent anti-human CD1d antibody (NIB.2) that possesses high affinity for human and cynomolgus macaque CD1d (KD ∼100 pM) and strong neutralizing activity in human primary cell-based assays (IC50 typically <100 pM). By epitope mapping experiments, we showed that NIB.2 binds to CD1d in close proximity to the interface of CD1d and the Type 1 NKT cell receptor β-chain. Together with data showing that NIB.2 inhibited stimulation via CD1d loaded with different glycolipids, this supports a mechanism whereby NIB.2 inhibits NKT cell activation by inhibiting Type 1 NKT cell receptor β-chain interactions with CD1d, independent of the lipid antigen in the CD1d antigen-binding cleft. The strong in vitro potency of NIB.2 was reflected in vivo in an Ascaris suum cynomolgus macaque asthma model. Compared with vehicle control, NIB.2 treatment significantly reduced bronchoalveolar lavage (BAL) levels of Ascaris-induced cytokines IL-5, IL-8 and IL-1 receptor antagonist, and significantly reduced baseline levels of GM-CSF, IL-6, IL-15, IL-12/23p40, MIP-1α, MIP-1β, and VEGF. At a cellular population level NIB.2 also reduced numbers of BAL lymphocytes and macrophages, and blood eosinophils and basophils. We demonstrate that anti-CD1d antibody blockade of the CD1d/NKT pathway modulates inflammatory parameters in vivo in a primate inflammation model, with therapeutic potential for diseases where the local cytokine milieu is critical.

  14. Upstream Design and 1D-CAE

    NASA Astrophysics Data System (ADS)

    Sawada, Hiroyuki

    Recently, engineering design environment of Japan is changing variously. Manufacturing companies are being challenged to design and bring out products that meet the diverse demands of customers and are competitive against those produced by rising countries(1). In order to keep and strengthen the competitiveness of Japanese companies, it is necessary to create new added values as well as conventional ones. It is well known that design at the early stages has a great influence on the final design solution. Therefore, design support tools for the upstream design is necessary for creating new added values. We have established a research society for 1D-CAE (1 Dimensional Computer Aided Engineering)(2), which is a general term for idea, methodology and tools applicable for the upstream design support, and discuss the concept and definition of 1D-CAE. This paper reports our discussion about 1D-CAE.

  15. A series of novel 1D coordination polymers constructed from metal?quinolone complex fragments linked by aromatic dicarboxylate ligands

    NASA Astrophysics Data System (ADS)

    He, Jiang-Hong; Xiao, Dong-Rong; Yan, Shi-Wei; Sun, Dian-Zhen; Chen, Hai-Yan; Wang, Xin; Yang, Juan; Ye, Zhong-Li; Yuan, Ruo; Wang, En-Bo

    2012-08-01

    Self-assembly of quinolones with metal salts in the presence of aromatic dicarboxylate ligands affords a series of novel 1D metal-quinolone complexes, namely [Mn(Hppa)(oba)]·3H2O (1), [Co(Hppa)(oba)]·3.25H2O (2), [Zn(Hppa)(sdba)]·1.5H2O (3), [Mn(Hcf)(bpda)(H2O)]·2H2O (4), [Mn(Hppa)2(bpdc)] (5) and [Mn(Hlome)2(bpdc)]·4H2O (6) (Hppa = Pipemidic acid, Hcf = ciprofloxacin, Hlome = lomefloxacin). The structures of compounds 1-3 consist of novel polymeric chains spanning two different directions, which display an intriguing 1D → 3D inclined polycatenation of supramolecular ladders. Compound 4 exhibits a chain compound formed from the interconnection of [Mn2(Hcf)2(μ-CO2)2] dimers with bpda ligands. Compounds 5 and 6 are similar chain compounds constructed from [Mn(Hppa)2] (or [Mn(Hlome)2]) fragments linked by bpdc ligands. The magnetic properties of 4 have been studied, which indicate the existence of antiferromagnetic interactions. Furthermore, the luminescent properties of compound 3 are discussed.

  16. Helical Floquet Channels in 1D Lattices

    NASA Astrophysics Data System (ADS)

    Budich, Jan Carl; Hu, Ying; Zoller, Peter

    2017-03-01

    We show how dispersionless channels exhibiting perfect spin-momentum locking can arise in a 1D lattice model. While such spectra are forbidden by fermion doubling in static 1D systems, here we demonstrate their appearance in the stroboscopic dynamics of a periodically driven system. Remarkably, this phenomenon does not rely on any adiabatic assumptions, in contrast to the well known Thouless pump and related models of adiabatic spin pumps. The proposed setup is shown to be experimentally feasible with state-of-the-art techniques used to control ultracold alkaline earth atoms in optical lattices.

  17. Structural Characterization of the Partially Folded Intermediates of An Immunoglobulin Light Chain Leading to Amyloid Fibrillation And Amorphous Aggregation

    SciTech Connect

    Qin, Z.; Hu, D.; Zhu, M.; Fink, A.L.; /UC, Santa Cruz

    2007-07-12

    Immunoglobulin light chain deposition diseases involve various types of extracellular deposition of light chain variable domains, including amyloid fibrils and amorphous deposits. The decreased thermodynamic stability of the light chain is believed to be the major factor leading to fibrillation. However, the differences in the nature of the deposits among the light chain deposition diseases raise the question of whether the mechanisms leading to fibrillar or amorphous aggregation is different. In this study, we generated two partially folded intermediates of the light chain variable domain SMA in the presence of guanidine hydrochloride (GuHCl) and characterized their conformations. The more unfolded intermediate formed fibrils most rapidly, while the more native-like intermediate predominantly led to amorphous deposits. The results also show that the monomeric, rather than the dimeric state, was critical for fibrillation. The data also indicate that fibril elongation involves addition of a partially unfolded intermediate, rather than the native state. We postulate that a more highly unfolded intermediate is more suited to undergo the topological rearrangements necessary to form amyloid fibrils than a more structured one and that this also correlates with increased destabilization. In the case of light chain aggregation, it appears that more native-like intermediate conformations are more prone to form amorphous deposits.

  18. Development of steady-state electrical-heating fluorescence-sensing (SEF) technique for thermal characterization of one dimensional (1D) structures by employing graphene quantum dots (GQDs) as temperature sensors

    NASA Astrophysics Data System (ADS)

    Wan, Xiang; Li, Changzheng; Yue, Yanan; Xie, Danmei; Xue, Meixin; Hu, Niansu

    2016-11-01

    A fluorescence signal has been demonstrated as an effective implement for micro/nanoscale temperature measurement which can be realized by either direct fluorescence excitation from materials or by employing nanoparticles as sensors. In this work, a steady-state electrical-heating fluorescence-sensing (SEF) technique is developed for the thermal characterization of one-dimensional (1D) materials. In this method, the sample is suspended between two electrodes and applied with steady-state Joule heating. The temperature response of the sample is monitored by collecting a simultaneous fluorescence signal from the sample itself or nanoparticles uniformly attached on it. According to the 1D heat conduction model, a linear temperature dependence of heating powers is obtained, thus the thermal conductivity of the sample can be readily determined. In this work, a standard platinum wire is selected to measure its thermal conductivity to validate this technique. Graphene quantum dots (GQDs) are employed as the fluorescence agent for temperature sensing. Parallel measurement by using the transient electro-thermal (TET) technique demonstrates that a small dose of GQDs has negligible influence on the intrinsic thermal property of platinum wire. This SEF technique can be applied in two ways: for samples with a fluorescence excitation capability, this method can be implemented directly; for others with weak or no fluorescence excitation, a very small portion of nanoparticles with excellent fluorescence excitation can be used for temperature probing and thermophysical property measurement.

  19. Lattice and off-lattice side chain models of protein folding: Linear time structure prediction better than 86% of optimal

    SciTech Connect

    Hart, W.E.; Istrail, S.

    1996-08-09

    This paper considers the protein structure prediction problem for lattice and off-lattice protein folding models that explicitly represent side chains. Lattice models of proteins have proven extremely useful tools for reasoning about protein folding in unrestricted continuous space through analogy. This paper provides the first illustration of how rigorous algorithmic analyses of lattice models can lead to rigorous algorithmic analyses of off-lattice models. The authors consider two side chain models: a lattice model that generalizes the HP model (Dill 85) to explicitly represent side chains on the cubic lattice, and a new off-lattice model, the HP Tangent Spheres Side Chain model (HP-TSSC), that generalizes this model further by representing the backbone and side chains of proteins with tangent spheres. They describe algorithms for both of these models with mathematically guaranteed error bounds. In particular, the authors describe a linear time performance guaranteed approximation algorithm for the HP side chain model that constructs conformations whose energy is better than 865 of optimal in a face centered cubic lattice, and they demonstrate how this provides a 70% performance guarantee for the HP-TSSC model. This is the first algorithm in the literature for off-lattice protein structure prediction that has a rigorous performance guarantee. The analysis of the HP-TSSC model builds off of the work of Dancik and Hannenhalli who have developed a 16/30 approximation algorithm for the HP model on the hexagonal close packed lattice. Further, the analysis provides a mathematical methodology for transferring performance guarantees on lattices to off-lattice models. These results partially answer the open question of Karplus et al. concerning the complexity of protein folding models that include side chains.

  20. Structural transformation between long and short-chain form of liquid sulfur from ab initio molecular dynamics

    SciTech Connect

    Plašienka, Dušan Martoňák, Roman; Cifra, Peter

    2015-04-21

    We present results of ab initio molecular dynamics study of the structural transformation occurring in hot liquid sulfur under high pressure, which corresponds to the recently observed chain-breakage phenomenon and to the electronic transition reported earlier. The transformation is temperature-induced and separates two distinct polymeric forms of liquid sulfur: high-temperature form composed of short chain-like fragments with open endings and low-temperature form with very long chains. We offer a structural description of the two liquid forms in terms of chain lengths, cross-linking, and chain geometry and investigate several physical properties. We conclude that the transformation is accompanied by changes in energy (but not density) as well as in diffusion coefficient and electronic properties—semiconductor-metal transition. We also describe the analogy of the investigated process to similar phenomena that take place in two other chalcogens selenium and tellurium. Finally, we remark that the behavior of heated liquid sulfur at ambient pressure might indicate a possible existence of a critical point in the low-pressure region of sulfur phase diagram.

  1. Effect of short-chain fatty acids on colonic function and structure.

    PubMed

    Friedel, D; Levine, G M

    1992-01-01

    Short-chain fatty acids (SCFA), fermentation products of fiber, are believed to play a role in intestinal adaptation. Although the administration of fiber or the infusion of SCFA has been shown to cause colonic growth, studies have been done primarily in enterally fed animals. In addition, the effects of SCFA on absorptive function have not been determined. Adult male rats were maintained on total parenteral nutrition (TPN) and, in addition, received either 150 mmol/L of saline or 150 mmol/L of SCFA mixture (60:25:15, acetate:propionate:butyrate) into the proximal colon. One week later, the in vivo absorption of water, electrolytes, and 20 mmol/L of butyrate was measured. After the rats were killed, parameters of colonic mass were determined. SCFA infusion into the colon had no significant effect on absorptive function. However, significantly greater mucosal height (p less than .01) and mucosal DNA (p less than .05), were observed. Although SCFA has a modest effect on colonic structure, they do not influence absorptive function in TPN rats.

  2. Changes in nuclear structure along the Mn isotopic chain studied via charge radii

    NASA Astrophysics Data System (ADS)

    Heylen, H.; Babcock, C.; Beerwerth, R.; Billowes, J.; Bissell, M. L.; Blaum, K.; Bonnard, J.; Campbell, P.; Cheal, B.; Day Goodacre, T.; Fedorov, D.; Fritzsche, S.; Garcia Ruiz, R. F.; Geithner, W.; Geppert, Ch.; Gins, W.; Grob, L. K.; Kowalska, M.; Kreim, K.; Lenzi, S. M.; Moore, I. D.; Maass, B.; Malbrunot-Ettenauer, S.; Marsh, B.; Neugart, R.; Neyens, G.; Nörtershäuser, W.; Otsuka, T.; Papuga, J.; Rossel, R.; Rothe, S.; Sánchez, R.; Tsunoda, Y.; Wraith, C.; Xie, L.; Yang, X. F.; Yordanov, D. T.

    2016-11-01

    The hyperfine spectra of 51,53 -64Mn were measured in two experimental runs using collinear laser spectroscopy at ISOLDE, CERN. Laser spectroscopy was performed on the atomic 3 d54 s25/2 6S →3 d54 s 4 p 3/2 6P and ionic 3 d54 s 5S2→3 d54 p 5P3 transitions, yielding two sets of isotope shifts. The mass and field shift factors for both transitions have been calculated in the multiconfiguration Dirac-Fock framework and were combined with a King plot analysis in order to obtain a consistent set of mean-square charge radii which, together with earlier work on neutron-deficient Mn, allow the study of nuclear structure changes from N =25 across N =28 up to N =39 . A clear development of deformation is observed towards N =40 , confirming the conclusions of the nuclear moments studies. From a Monte Carlo shell-model study of the shape in the Mn isotopic chain, it is suggested that the observed development of deformation is not only due to an increase in static prolate deformation but also due to shape fluctuations and triaxiality. The changes in mean-square charge radii are well reproduced using the Duflo-Zuker formula except in the case of large deformation.

  3. Long-chain omega-3 fatty acids improve brain function and structure in older adults.

    PubMed

    Witte, A Veronica; Kerti, Lucia; Hermannstädter, Henrike M; Fiebach, Jochen B; Schreiber, Stephan J; Schuchardt, Jan Philipp; Hahn, Andreas; Flöel, Agnes

    2014-11-01

    Higher intake of seafish or oil rich in long-chain omega-3 polyunsaturated fatty acids (LC-n3-FA) may be beneficial for the aging brain. We tested in a prospective interventional design whether high levels of supplementary LC-n3-FA would improve cognition, and addressed potential mechanisms underlying the effects. Sixty-five healthy subjects (50-75 years, 30 females) successfully completed 26 weeks of either fish oil (2.2 g/day LC-n3-FA) or placebo intake. Before and after the intervention period, cognitive performance, structural neuroimaging, vascular markers, and blood parameters were assayed. We found a significant increase in executive functions after LC-n3-FA compared with placebo (P = 0.023). In parallel, LC-n3-FA exerted beneficial effects on white matter microstructural integrity and gray matter volume in frontal, temporal, parietal, and limbic areas primarily of the left hemisphere, and on carotid intima media thickness and diastolic blood pressure. Improvements in executive functions correlated positively with changes in omega-3-index and peripheral brain-derived neurotrophic factor, and negatively with changes in peripheral fasting insulin. This double-blind randomized interventional study provides first-time evidence that LC-n3-FA exert positive effects on brain functions in healthy older adults, and elucidates underlying mechanisms. Our findings suggest novel strategies to maintain cognitive functions into old age.

  4. Ricin A-chain substrate specificity in RNA, DNA, and hybrid stem-loop structures.

    PubMed

    Amukele, Tim K; Schramm, Vern L

    2004-05-04

    Ricin toxin A-chain (RTA) is the catalytic subunit of ricin, a heterodimeric toxin from castor beans. Its ribosomal inactivating activity arises from depurination of a single adenine from position A(4324) in a GAGA tetraloop from 28S ribosomal RNA. Minimal substrate requirements are the GAGA tetraloop and stem of two or more base pairs. Depurination activity also occurs on stem-loop DNA with the same sequence, but with the k(cat) reduced 200-fold. Systematic variation of RNA 5'-G(1)C(2)G(3)C(4)[G(5)A(6)G(7)A(8)]G(9)C(10)G(11)C(12)-3' 12mers via replacement of each nucleotide in the tetraloop with a deoxynucleotide showed a 16-fold increase in k(cat) for A(6) --> dA(6) but reduced k(cat) up to 300-fold for the other sites. Methylation of individual 2'-hydroxyls in a similar experiment reduced k(cat) by as much as 3 x 10(-3)-fold. In stem-loop DNA, replacement of d[G(5)A(6)G(7)A(8)] with individual ribonucleotides resulted in small kinetic changes, except for the dA(6) --> A(6) replacement for which k(cat) decreased 6-fold. Insertion of d[G(5)A(6)G(7)A(8)] into an RNA stem-loop or G(5)A(6)G(7)A(8) into a DNA stem-loop reduced k(cat) by 30- and 5-fold, respectively. Multiple substitutions of deoxyribonucleotides into RNA stem-loops in one case (dG(5),dG(7)) decreased k(cat)/K(m) by 10(5)-fold, while a second change (dG(5),dA(8)) decreased k(cat) by 100-fold. Mapping these interactions on the structure of GAGA stem-loop RNA suggests that all the loop 2'-hydroxyl groups play a significant role in the action of ricin A-chain. Improved binding of RNA-DNA stem-loop hybrids provides a scaffold for inhibitor design. Replacing the adenosine of the RTA depurination site with deoxyadenosine in a small RNA stem-loop increased k(cat) 20-fold to 1660 min(-1), a value similar to RTA's k(cat) on intact ribosomes.

  5. TCTEX1D2 mutations underlie Jeune asphyxiating thoracic dystrophy with impaired retrograde intraflagellar transport

    PubMed Central

    Schmidts, Miriam; Hou, Yuqing; Cortés, Claudio R.; Mans, Dorus A.; Huber, Celine; Boldt, Karsten; Patel, Mitali; van Reeuwijk, Jeroen; Plaza, Jean-Marc; van Beersum, Sylvia E. C.; Yap, Zhi Min; Letteboer, Stef J. F.; Taylor, S. Paige; Herridge, Warren; Johnson, Colin A.; Scambler, Peter J.; Ueffing, Marius; Kayserili, Hulya; Krakow, Deborah; King, Stephen M.; Beales, Philip L.; Al-Gazali, Lihadh; Wicking, Carol; Cormier-Daire, Valerie; Roepman, Ronald; Mitchison, Hannah M.; Witman, George B.; Al-Turki, Saeed; Anderson, Carl; Anney, Richard; Antony, Dinu; Asimit, Jennifer; Ayub, Mohammad; Barrett, Jeff; Barroso, Inês; Bentham, Jamie; Bhattacharya, Shoumo; Blackwood, Douglas; Bobrow, Martin; Bochukova, Elena; Bolton, Patrick; Boustred, Chris; Breen, Gerome; Brion, Marie-Jo; Brown, Andrew; Calissano, Mattia; Carss, Keren; Chatterjee, Krishna; Chen, Lu; Cirak, Sebhattin; Clapham, Peter; Clement, Gail; Coates, Guy; Collier, David; Cosgrove, Catherine; Cox, Tony; Craddock, Nick; Crooks, Lucy; Curran, Sarah; Daly, Allan; Danecek, Petr; Smith, George Davey; Day-Williams, Aaron; Day, Ian; Durbin, Richard; Edkins, Sarah; Ellis, Peter; Evans, David; Farooqi, I. Sadaf; Fatemifar, Ghazaleh; Fitzpatrick, David; Flicek, Paul; Floyd, Jamie; Foley, A. Reghan; Franklin, Chris; Futema, Marta; Gallagher, Louise; Gaunt, Tom; Geschwind, Daniel; Greenwood, Celia; Grozeva, Detelina; Guo, Xiaosen; Gurling, Hugh; Hart, Deborah; Hendricks, Audrey; Holmans, Peter; Huang, Jie; Humphries, Steve E.; Hurles, Matt; Hysi, Pirro; Jackson, David; Jamshidi, Yalda; Jewell, David; Chris, Joyce; Kaye, Jane; Keane, Thomas; Kemp, John; Kennedy, Karen; Kent, Alastair; Kolb-Kokocinski, Anja; Lachance, Genevieve; Langford, Cordelia; Lee, Irene; Li, Rui; Li, Yingrui; Ryan, Liu; Lönnqvist, Jouko; Lopes, Margarida; MacArthur, Daniel G.; Massimo, Mangino; Marchini, Jonathan; Maslen, John; McCarthy, Shane; McGuffin, Peter; McIntosh, Andrew; McKechanie, Andrew; McQuillin, Andrew; Memari, Yasin; Metrustry, Sarah; Min, Josine; Moayyeri, Alireza; Morris, James; Muddyman, Dawn; Muntoni, Francesco; Northstone, Kate; O'Donovan, Michael; O'Rahilly, Stephen; Onoufriadis, Alexandros; Oualkacha, Karim; Owen, Michael; Palotie, Aarno; Panoutsopoulou, Kalliope; Parker, Victoria; Parr, Jeremy; Paternoster, Lavinia; Paunio, Tiina; Payne, Felicity; Perry, John; Pietilainen, Olli; Plagnol, Vincent; Quail, Michael A.; Quaye, Lydia; Raymond, Lucy; Rehnström, Karola; Brent Richards, J.; Ring, Sue; Ritchie, Graham R S; Savage, David B.; Schoenmakers, Nadia; Semple, Robert K.; Serra, Eva; Shihab, Hashem; Shin, So-Youn; Skuse, David; Small, Kerrin; Smee, Carol; Soler, Artigas María; Soranzo, Nicole; Southam, Lorraine; Spector, Tim; St Pourcain, Beate; St. Clair, David; Stalker, Jim; Surdulescu, Gabriela; Suvisaari, Jaana; Tachmazidou, Ioanna; Tian, Jing; Timpson, Nic; Tobin, Martin; Valdes, Ana; van Kogelenberg, Margriet; Vijayarangakannan, Parthiban; Wain, Louise; Walter, Klaudia; Wang, Jun; Ward, Kirsten; Wheeler, Ellie; Whittall, Ros; Williams, Hywel; Williamson, Kathy; Wilson, Scott G.; Wong, Kim; Whyte, Tamieka; ChangJiang, Xu; Zeggini, Eleftheria; Zhang, Feng; Zheng, Hou-Feng

    2015-01-01

    The analysis of individuals with ciliary chondrodysplasias can shed light on sensitive mechanisms controlling ciliogenesis and cell signalling that are essential to embryonic development and survival. Here we identify TCTEX1D2 mutations causing Jeune asphyxiating thoracic dystrophy with partially penetrant inheritance. Loss of TCTEX1D2 impairs retrograde intraflagellar transport (IFT) in humans and the protist Chlamydomonas, accompanied by destabilization of the retrograde IFT dynein motor. We thus define TCTEX1D2 as an integral component of the evolutionarily conserved retrograde IFT machinery. In complex with several IFT dynein light chains, it is required for correct vertebrate skeletal formation but may be functionally redundant under certain conditions. PMID:26044572

  6. Clathrin heavy chain, light chain interactions.

    PubMed Central

    Winkler, F K; Stanley, K K

    1983-01-01

    Purified pig brain clathrin can be reversibly dissociated and separated into heavy chain trimers and light chains in the presence of non-denaturing concentrations of the chaotrope thiocyanate. The isolated heavy chain trimers reassemble into regular polygonal cage structures in the absence of light chains. The light chain fraction can be further resolved into its two components L alpha and L beta which give different one-dimensional peptide maps. Radiolabelled light chains bind with high affinity (KD < 10(-10) M) to heavy chain trimers, to heavy chain cages and to a 110,000 mol. wt. tryptic fragment of the heavy chain. Both light chains compete with each other and with light chains from other sources for the same binding sites on heavy chains and c.d. spectroscopy shows that the two pig brain light chains possess very similar structures. We conclude that light chains from different sources, despite some heterogeneity, have a highly conserved, high affinity binding site on the heavy chain but are not essential for the formation of regular cage structures. Images Fig. 1. Fig. 2. Fig. 3. Fig. 4. Fig. 8. PMID:10872336

  7. Calibration of a 1D/1D urban flood model using 1D/2D model results in the absence of field data.

    PubMed

    Leandro, J; Djordjević, S; Chen, A S; Savić, D A; Stanić, M

    2011-01-01

    Recently increased flood events have been prompting researchers to improve existing coupled flood-models such as one-dimensional (1D)/1D and 1D/two-dimensional (2D) models. While 1D/1D models simulate sewer and surface networks using a one-dimensional approach, 1D/2D models represent the surface network by a two-dimensional surface grid. However their application raises two issues to urban flood modellers: (1) stormwater systems planning/emergency or risk analysis demands for fast models, and the 1D/2D computational time is prohibitive, (2) and the recognized lack of field data (e.g. Hunter et al. (2008)) causes difficulties for the calibration/validation of 1D/1D models. In this paper we propose to overcome these issues by calibrating a 1D/1D model with the results of a 1D/2D model. The flood-inundation results show that: (1) 1D/2D results can be used to calibrate faster 1D/1D models, (2) the 1D/1D model is able to map the 1D/2D flood maximum extent well, and the flooding limits satisfactorily in each time-step, (3) the 1D/1D model major differences are the instantaneous flow propagation and overestimation of the flood-depths within surface-ponds, (4) the agreement in the volume surcharged by both models is a necessary condition for the 1D surface-network validation and (5) the agreement of the manholes discharge shapes measures the fitness of the calibrated 1D surface-network.

  8. Design and synthesis of new 1D and 2D R-isophthalic acid-based coordination polymers (R = hydrogen or bromine).

    PubMed

    Zhang, Ren; Gong, Qihan; Emge, Thomas J; Banerjee, Debasis; Li, Jing

    2013-01-01

    Three new R-isophthalic acid-based (R = H or Br) coordination polymers have been designed and synthesized. By changing the N-containing ligand in the system, we are able to tune the dimensionality of coordination polymers from one-dimension (1D) to two-dimensions (2D) with the same basic building unit. Also, different metal ions can be incorporated into the same structures. Compound 1 [Cu(bipa)(py)2]·0.5(H2O) (H2bipa = 5-bromoisophthalic acid; py = pyridine) and compound 2 [Co(bipa)(py)2] are 1D chain structures. Compound 3 [Cu8(ipa)8(bpe)8]·2(bpe)·4(H2O) (bpe=1,2-bis(4-pyridyl)ethane) is a 2D layered structure.

  9. Structural insight into SUMO chain recognition and manipulation by the ubiquitin ligase RNF4

    PubMed Central

    Xu, Yingqi; Plechanovová, Anna; Simpson, Peter; Marchant, Jan; Leidecker, Orsolya; Kraatz, Sebastian; Hay, Ronald T.; Matthews, Steve J.

    2014-01-01

    The small ubiquitin-like modifier (SUMO) can form polymeric chains that are important signals in cellular processes such as meiosis, genome maintenance and stress response. The SUMO-targeted ubiquitin ligase RNF4 engages with SUMO chains on linked substrates and catalyses their ubiquitination, which targets substrates for proteasomal degradation. Here we use a segmental labelling approach combined with solution nuclear magnetic resonance (NMR) spectroscopy and biochemical characterization to reveal how RNF4 manipulates the conformation of the SUMO chain, thereby facilitating optimal delivery of the distal SUMO domain for ubiquitin transfer. PMID:24969970

  10. The Effect of Chain Structures on the Crystallization Behavior and Membrane Formation of Poly(Vinylidene Fluoride) Copolymers

    PubMed Central

    Ma, Wenzhong; Yuan, Haoge; Wang, Xiaolin

    2014-01-01

    The crystallization behaviors of two copolymers of PVDF were studied, and the effect of copolymerized chains on the crystallization behavior was investigated. The results indicated that both copolymers had a lowered crystallization temperature and crystallinity. The crystallization rate was improved by the copolymer with symmetrical units in PVDF chains, but hindered by asymmetrical units, compared with the neat PVDF. The symmetrical units in PVDF chains favored the β-crystals with fiber-like structures. According to the solubility parameter rule, methyl salicylate (MS) can be chosen as a diluent for PVDF copolymers. Both diluted systems had liquid-liquid (L-L) regions in the phase diagrams, which was due to the lowered crystallization temperature. PMID:24957175

  11. Structural and solubility parameter correlations of gelation abilities for dihydroxylated derivatives of long-chain, naturally occurring fatty acids.

    PubMed

    Zhang, Mohan; Selvakumar, Sermadurai; Zhang, Xinran; Sibi, Mukund P; Weiss, Richard G

    2015-06-01

    Creating structure-property correlations at different distance scales is one of the important challenges to the rational design of molecular gelators. Here, a series of dihydroxylated derivatives of long-chain fatty acids, derived from three naturally occurring molecules-oleic, erucic and ricinoleic acids-are investigated as gelators of a wide variety of liquids. Conclusions about what constitutes a more (or less!) efficient gelator are based upon analyses of a variety of thermal, structural, molecular modeling, and rheological results. Correlations between the manner of molecular packing in the neat solid or gel states of the gelators and Hansen solubility data from the liquids leads to the conclusion that diol stereochemistry, the number of carbon atoms separating the two hydroxyl groups, and the length of the alkanoic chains are the most important structural parameters controlling efficiency of gel formation for these gelators. Some of the diol gelators are as efficient or even more efficient than the well-known, excellent gelator, (R)-12-hydroxystearic acid; others are much worse. The ability to form extensive intermolecular H-bonding networks along the alkyl chains appears to play a key role in promoting fiber growth and, thus, gelation. In toto, the results demonstrate how the efficiency of gelation can be modulated by very small structural changes and also suggest how other structural modifications may be exploited to create efficient gelators.

  12. Perturbation theory for multicomponent fluids based on structural properties of hard-sphere chain mixtures

    SciTech Connect

    Hlushak, Stepan

    2015-09-28

    An analytical expression for the Laplace transform of the radial distribution function of a mixture of hard-sphere chains of arbitrary segment size and chain length is used to rigorously formulate the first-order Barker-Henderson perturbation theory for the contribution of the segment-segment dispersive interactions into thermodynamics of the Lennard-Jones chain mixtures. Based on this approximation, a simple variant of the statistical associating fluid theory is proposed and used to predict properties of several mixtures of chains of different lengths and segment sizes. The theory treats the dispersive interactions more rigorously than the conventional theories and provides means for more accurate description of dispersive interactions in the mixtures of highly asymmetric components.

  13. Resolution-optimized NMR measurement of (1)D(CH), (1)D(CC) and (2)D(CH) residual dipolar couplings in nucleic acid bases.

    PubMed

    Boisbouvier, Jérôme; Bryce, David L; O'neil-Cabello, Erin; Nikonowicz, Edward P; Bax, Ad

    2004-11-01

    New methods are described for accurate measurement of multiple residual dipolar couplings in nucleic acid bases. The methods use TROSY-type pulse sequences for optimizing resolution and sensitivity, and rely on the E.COSY principle to measure the relatively small two-bond (2)D(CH) couplings at high precision. Measurements are demonstrated for a 24-nt stem-loop RNA sequence, uniformly enriched in (13)C, and aligned in Pf1. The recently described pseudo-3D method is used to provide homonuclear (1)H-(1)H decoupling, which minimizes cross-correlation effects and optimizes resolution. Up to seven (1)H-(13)C and (13)C-(13)C couplings are measured for pyrimidines (U and C), including (1)D(C5H5), (1)D(C6H6), (2)D(C5H6), (2)D(C6H5), (1)D(C5C4), (1)D(C5C6), and (2)D(C4H5). For adenine, four base couplings ((1)D(C2H2), (1)D(C8H8), (1)D(C4C5), and (1)D(C5C6)) are readily measured whereas for guanine only three couplings are accessible at high relative accuracy ((1)D(C8H8), (1)D(C4C5), and (1)D(C5C6)). Only three dipolar couplings are linearly independent in planar structures such as nucleic acid bases, permitting cross validation of the data and evaluation of their accuracies. For the vast majority of dipolar couplings, the error is found to be less than +/-3% of their possible range, indicating that the measurement accuracy is not limiting when using these couplings as restraints in structure calculations. Reported isotropic values of the one- and two-bond J couplings cluster very tightly for each type of nucleotide.

  14. Structural and functional aspects of the myosin essential light chain in cardiac muscle contraction

    SciTech Connect

    Muthu, Priya; Wang, Li; Yuan, Chen-Ching; Kazmierczak, Katarzyna; Huang, Wenrui; Hernandez, Olga M.; Kawai, Masataka; Irving, Thomas C.; Szczesna-Cordary, Danuta

    2012-04-02

    The myosin essential light chain (ELC) is a structural component of the actomyosin cross-bridge, but its function is poorly understood, especially the role of the cardiac specific N-terminal extension in modulating actomyosin interaction. Here, we generated transgenic (Tg) mice expressing the A57G (alanine to glycine) mutation in the cardiac ELC known to cause familial hypertrophic cardiomyopathy (FHC). The function of the ELC N-terminal extension was investigated with the Tg-{Delta}43 mouse model, whose myocardium expresses a truncated ELC. Low-angle X-ray diffraction studies on papillary muscle fibers in rigor revealed a decreased interfilament spacing ({approx} 1.5 nm) and no alterations in cross-bridge mass distribution in Tg-A57G mice compared to Tg-WT, expressing the full-length nonmutated ELC. The truncation mutation showed a 1.3-fold increase in I{sub 1,1}/I{sub 1,0}, indicating a shift of cross-bridge mass from the thick filament backbone toward the thin filaments. Mechanical studies demonstrated increased stiffness in Tg-A57G muscle fibers compared to Tg-WT or Tg-{Delta}43. The equilibrium constant for the cross-bridge force generation step was smallest in Tg-{Delta}43. These results support an important role for the N-terminal ELC extension in prepositioning the cross-bridge for optimal force production. Subtle changes in the ELC sequence were sufficient to alter cross-bridge properties and lead to pathological phenotypes.

  15. Secondary Structures in Phe-Containing Isolated Dipeptide Chains: Laser Spectroscopy vs Quantum Chemistry.

    PubMed

    Loquais, Yohan; Gloaguen, Eric; Habka, Sana; Vaquero-Vara, Vanesa; Brenner, Valérie; Tardivel, Benjamin; Mons, Michel

    2015-06-11

    The intrinsic conformational landscape of two phenylalanine-containing protein chain models (-Gly-Phe- and -Ala-Phe- sequences) has been investigated theoretically and experimentally in the gas phase. The near UV spectroscopy (first ππ* transition of the Phe ring) is obtained experimentally under jet conditions where the conformational features can be resolved. Single-conformation IR spectroscopy in the NH stretch region is then obtained by IR/UV double resonance in the ground state, leading to resolved vibrational spectra that are assigned in terms of conformation and H-bonding content from comparison with quantum chemistry calculations. For the main conformer, whose UV spectrum exhibits a significant Franck-Condon activity in low frequency modes involving peptide backbone motions relative to the Phe chromophore, excited state IR spectroscopy has also been recorded in a UV/IR/UV experiment. The NH stretch spectral changes observed in such a ππ* labeling experiment enable us to determine those NH bonds that are coupled to the phenyl ring; they are compared to CC2 excited state calculations to quantify the geometry change upon ππ* excitation. The complete and consistent series of data obtained enable us to propose an unambiguous assignment for the gallery of conformers observed and to demonstrate that, in these two sequences, three conceptually important local structural motifs of proteins (β-strands, 27 ribbons, and β-turns) are represented. The satisfactory agreement between the experimental conformational distribution and the predicted landscape anticipated from the DFT-D approach demonstrates the capabilities of a theoretical method that accounts for dispersive interactions. It also shows that the flaws, inherent to a resonant two-photon ionization detection scheme, often evoked for aromatic chromophores, do not seem to be significant in the case of Phe.

  16. Encapsulated discrete octameric water cluster, 1D water tape, and 3D water aggregate network in diverse MOFs based on bisimidazolium ligands

    NASA Astrophysics Data System (ADS)

    Shi, Ruo-Bing; Pi, Min; Jiang, Shuang-Shuang; Wang, Yuan-Yuan; Jin, Chuan-Ming

    2014-08-01

    Four new metal-organic frameworks, [Zn(2-mBIM)2(SO3CF3)2·(H2O)4] (1), [Zn(BMIE)(1,4-BDC)]·(H2O)3 (2), [Cd(BIM)2(OH)(H2O)2(PF6)]·(H2O)4 (3), and [Cd(PA-BIM)2 (ClO4)2]·11.33H2O (4) (2-mBIM = bis(2-methylimidazol-1-yl)methane, BMIE = 1,2-bis[1-(2-methylimidazole)-diethoxy]ethane, BIM = bis(imidazol-1-yl)methane, and PA-BIM = 1,1-bis [(2-phenylazo)imidazol-1-yl]methane) have been prepared and structurally characterized. Complex 1 exhibits an infinite 1D cationic beaded-chain structure, which encapsulated discrete octameric water clusters that are comprised of a chair-like hexameric water cluster with two extra water molecules dangling on two diagonal vertices of the chair. Complex 2 forms a 1D infinite zigzag metal-organic chain structure with a 1D T4(0)A(4) water tape. Complexes 3 show a 2D grid-like sheet structure with the 1D water tape T4(0)A(0)2(0) motif. Complex 4 is a porous 3D MOF with tetrahedron-coordinated Cd(II) centers and trans-conformation PA-BIM ligands. These holes are occupied by a fascinating three-dimensional water clathrate network, which consists of cage-shaped structural tetradecameric water cluster (H2O)14 units and six independent bridged water molecules. The results suggest that the bisimidazolium ligands and anions play crucial roles in the formation of the different host structures and different guest water aggregations. Additionally, the thermal stabilities and photoluminescence spectra of the complexes have been discussed.

  17. Plasmonic Excitations of 1D Metal-Dielectric Interfaces in 2D Systems: 1D Surface Plasmon Polaritons

    NASA Astrophysics Data System (ADS)

    Mason, Daniel R.; Menabde, Sergey G.; Yu, Sunkyu; Park, Namkyoo

    2014-04-01

    Surface plasmon-polariton (SPP) excitations of metal-dielectric interfaces are a fundamental light-matter interaction which has attracted interest as a route to spatial confinement of light far beyond that offered by conventional dielectric optical devices. Conventionally, SPPs have been studied in noble-metal structures, where the SPPs are intrinsically bound to a 2D metal-dielectric interface. Meanwhile, recent advances in the growth of hybrid 2D crystals, which comprise laterally connected domains of distinct atomically thin materials, provide the first realistic platform on which a 2D metal-dielectric system with a truly 1D metal-dielectric interface can be achieved. Here we show for the first time that 1D metal-dielectric interfaces support a fundamental 1D plasmonic mode (1DSPP) which exhibits cutoff behavior that provides dramatically improved light confinement in 2D systems. The 1DSPP constitutes a new basic category of plasmon as the missing 1D member of the plasmon family: 3D bulk plasmon, 2DSPP, 1DSPP, and 0D localized SP.

  18. Linear rheology and structure of molecular bottlebrushes with short side chains

    SciTech Connect

    López-Barrón, Carlos R. Brant, Patrick; Crowther, Donna J.; Eberle, Aaron P. R.

    2015-05-15

    We investigate the microstructure and linear viscoelasticity of model molecular bottlebrushes (BBs) using rheological and small-angle X-ray and neutron scattering measurements. Our polymers have short atactic polypropylene (aPP) side chains of molecular weight ranging from 119 g/mol to 259 g/mol and narrow molecular weight distribution (M{sub w}/M{sub n} 1.02–1.05). The side chain molecular weights are a small fraction of the entanglement molecular weight of the corresponding linear polymer (M{sub e,aPP}= 7.05 kg/mol), and as such, they are unentangled. The morphology of the aPP BBs is characterized as semiflexible thick chains with small side chain interdigitation. Their dynamic master curves, obtained by time-temperature superposition, reveal two sequential relaxation processes corresponding to the segmental relaxation and the relaxation of the BB backbone. Due to the short length of the side chains, their fast relaxation could not be distinguished from the glassy relaxation. The fractional free volume is an increasing function of the side chain length (N{sub SC}). Therefore, the glassy behavior of these polymers as well as their molecular friction and dynamic properties are influenced by their N{sub SC} values. The apparent flow activation energies are a decreasing function of N{sub SC}, and their values explain the differences in zero-shear viscosity measured at different temperatures.

  19. Centrosome Positioning in 1D Cell Migration

    NASA Astrophysics Data System (ADS)

    Adlerz, Katrina; Aranda-Espinoza, Helim

    During cell migration, the positioning of the centrosome and nucleus define a cell's polarity. For a cell migrating on a two-dimensional substrate the centrosome is positioned in front of the nucleus. Under one-dimensional confinement, however, the centrosome is positioned behind the nucleus in 60% of cells. It is known that the centrosome is positioned by CDC42 and dynein for cells moving on a 2D substrate in a wound-healing assay. It is currently unknown, however, if this is also true for cells moving under 1D confinement, where the centrosome position is often reversed. Therefore, centrosome positioning was studied in cells migrating under 1D confinement, which mimics cells migrating through 3D matrices. 3 to 5 μm fibronectin lines were stamped onto a glass substrate and cells with fluorescently labeled nuclei and centrosomes migrated on the lines. Our results show that when a cell changes directions the centrosome position is maintained. That is, when the centrosome is between the nucleus and the cell's trailing edge and the cell changes direction, the centrosome will be translocated across the nucleus to the back of the cell again. A dynein inhibitor did have an influence on centrosome positioning in 1D migration and change of directions.

  20. A new copper borophosphate with novel polymeric chains and its structural correlation with raw materials in molten hydrated flux synthesis

    SciTech Connect

    Duan, Ruijing; Liu, Wei Cao, Lixin; Su, Ge; Xu, Hongmei; Zhao, Chenggong

    2014-02-15

    A novel copper borophosphate, Cu{sub 3}[B{sub 2}P{sub 3}O{sub 12}(OH){sub 3}] has been prepared by the molten hydrated flux method. Its crystal structure was determined by the single-crystal X-ray diffraction (monoclinic, Cc, a=6.1895 Å, b=13.6209 Å, c=11.9373 Å, β=97.62°, V=997.5 Å{sup 3}, Z=4). The three-dimensional framework of the titled compound, is composed by two kinds of polymeric chains and isolated PO{sub 4} tetrahedral. One novel 4-membered tetrahedral rings has been observed in borophosphates. Magnetic measurements indicate that the title compound exits antiferromagnetic interactions. Due to the special reaction medium created by the molten hydrated flux method, a possible structural correlation between the final solids and the raw materials has been noted. - Graphical abstract: The 3D structure consists of a framework composed of CuO{sub x} polyhedra, BO{sub 4} and PO{sub 4} tetrahedra. A intersection angle between the metal chains and borophosphate chains can be noted. Display Omitted - Highlights: • A novel copper borophosphate has been prepared by the molten hydrated flux method. • One novel 4-membered tetrahedral ring has been observed firstly in borophosphates. • A possible structural correlation between the final solids and the raw materials has been noted.

  1. Influence of the side chain and substrate on polythiophene thin film surface, bulk, and buried interfacial structures.

    PubMed

    Xiao, Minyu; Jasensky, Joshua; Zhang, Xiaoxian; Li, Yaoxin; Pichan, Cayla; Lu, Xiaolin; Chen, Zhan

    2016-08-10

    The molecular structures of organic semiconducting thin films mediate the performance of various devices composed of such materials. To fully understand how the structures of organic semiconductors alter on substrates due to different polymer side chains and different interfacial interactions, thin films of two kinds of polythiophene derivatives with different side-chains, poly(3-hexylthiophene) (P3HT) and poly(3-potassium-6-hexanoate thiophene) (P3KHT), were deposited and compared on various surfaces. A combination of analytical tools was applied in this research: contact angle goniometry and X-ray photoelectron spectroscopy (XPS) were used to characterize substrate dielectric surfaces with varied hydrophobicity for polymer film deposition; X-ray diffraction and UV-vis spectroscopy were used to examine the polythiophene film bulk structure; sum frequency generation (SFG) vibrational spectroscopy was utilized to probe the molecular structures of polymer film surfaces in air and buried solid/solid interfaces. Both side-chain hydrophobicity and substrate hydrophobicity were found to mediate the crystallinity of the polythiophene film, as well as the orientation of the thiophene ring within the polymer backbone at the buried polymer/substrate interface and the polymer thin film surface in air. For the same type of polythiophene film deposited on different substrates, a more hydrophobic substrate surface induced thiophene ring alignment with the surface normal at both the buried interface and on the surface in air. For different films (P3HT vs. P3KHT) deposited on the same dielectric substrate, a more hydrophobic polythiophene side chain caused the thiophene ring to align more towards the surface at the buried polymer/substrate interface and on the surface in air. We believe that the polythiophene surface, bulk, and buried interfacial molecular structures all influence the hole mobility within the polythiophene film. Successful characterization of an organic conducting

  2. The stability of 1-D soliton in transverse direction

    NASA Astrophysics Data System (ADS)

    Verma, Deepa; Bera, Ratan Kumar; Das, Amita; Kaw, Predhiman

    2016-12-01

    The complete characterization of the exact 1-D solitary wave solutions (both stationary and propagating) for light plasma coupled system have been studied extensively in the parameter space of light frequency and the group speed [Poornakala et al., Phys. Plasmas 9(5), 1820 (2002)]. It has been shown in 1-D that solutions with single light wave peak and paired structures are stable and hence long lived. However, solutions having multiple peaks of light wave are unstable due to Raman scattering instability [Saxena et al., Phys. Plasmas 14, 072307 (2007)]. Here, we have shown with the help of 2-D fluid simulation that single peak and paired solutions too get destabilized by the transverse filamentation instability. The numerical growth rates obtained from simulations is seen to compare well with the analytical values. It is also shown that multiple peaks solitons first undergo the regular 1-D forward Raman scattering instability. Subsequently, they undergo a distinct second phase of destabilization through transverse filamentation instability. This is evident from the structure as well as the plot of the perturbed energy which shows a second phase of growth after saturating initially. The growth rate of the filamentation instability being comparatively slower than the forward Raman instability this phase comes quite late and is clearly distinguishable.

  3. Applying Alkyl-Chain Surface Functionalizations in Mesoporous Inorganic Structures: Their Impact on Gas Flow and Selectivity Depending on Temperature.

    PubMed

    Besser, Benjamin; Ahmed, Atiq; Baune, Michael; Kroll, Stephen; Thöming, Jorg; Rezwan, Kurosch

    2016-10-12

    Porous inorganic capillary membranes are prepared to serve as model structures for the experimental investigation of the gas transport in functionalized mesopores. The porous structures possess a mean pore diameter of 23 nm which is slightly reduced to 20 nm after immobilizing C16-alkyl chains on the surface. Gas permeation measurements are performed at temperatures ranging from 0 to 80 °C using Ar, N2, and CO2. Nonfunctionalized structures feature a gas transport according to Knudsen diffusion with regard to gas flow and selectivity. After C16-functionalization, the gas flow is reduced by a factor of 10, and the ideal selectivities deviate from the Knudsen theory. CO2 adsorption measurements show a decrease in total amount of adsorbed gas and isosteric heat of adsorption. It is hypothesized that the immobilized C16-chains sterically influence the gas transport behavior without a contribution from adsorption effects. The reduced gas flow derives from an additional surface resistance caused by the C16-chains spacially limiting the adsorption and desorption directions for gas molecules propagating through the structure, resulting in longer diffusion paths. In agreement, the gas flow is found to correlate with the molecular diameter of the gas species (CO2 < Ar < N2) increasing the resistance for larger molecules. This affects the ideal selectivities with the relation [Formula: see text]. The influence on selectivity increases with increasing temperature which leads to the conclusion that the temperature induced movement of the C16-chains is responsible for the stronger interaction between gas molecules and surface functional groups.

  4. Structural, electrochemical characterization and SOD mimic activities of 1D chain or 3D network encouraged by unique μ2-bridging by adipate ion in mixed ligand complexes containing α-diimine as auxiliary ligand

    NASA Astrophysics Data System (ADS)

    Siddiqi, Zafar A.; Sharma, Prashant K.; Shahid, M.; Kumar, Sarvendra; Anjuli; Siddique, Armeen

    The present ternary complexes [Cu(ada)(phen)(H2O)]·2H2O (1), [Co2(ada)2(phen)2(H2O)2] (2) and [{Cu(ada)3(bipy)}n·3nH2O] (3) (H2ada = adipic acid, phen = 1,10-phenanthroline and bipy = 2,2'-bipyridine) obtained under varying experimental conditions were characterized by spectral, electrochemical and thermal studies. The bonding modes and the spatial arrangements of the carboxylate dianion around the metal ions have been investigated employing FTIR, EPR and X-ray crystallographic studies. Present data revealed a six coordinate distorted octahedral geometry for 2 with a = 8.068, b = 9.788, c = 11.788 Å, α = 70.464, β = 75.109, γ = 72.063° and a five coordinate square pyramidal geometry for 3 with a = 9.509, b = 9.912, c = 12.656 Å, α = 70.486, β = 73.604, γ = 75.162°. The superoxide dismutase (SOD) mimic activities of the complexes are in the order 1 > 3 > 2.

  5. Automotive Lithium-ion Cell Manufacturing: Regional Cost Structures and Supply Chain Considerations

    SciTech Connect

    Chung, Donald; Elgqvist, Emma; Santhanagopalan, Shriram

    2016-04-01

    Manufacturing capacity for lithium-ion batteries (LIBs) — which power many consumer electronics and are increasingly used to power electric vehicles — is heavily concentrated in East Asia. To illuminate the factors that drive regional competitiveness in automotive LIB cell production, this study models cell manufacturing cost and minimum sustainable price, and examines development of LIB supply chains and current LIB market conditions. The study shows that factors driving the cost competitiveness of LIB manufacturing locations are mostly built—supply chain developments and competition, access to materials, and production expertise. Some regional costs — including cost of capital, labor, and materials — are significant and should be considered.

  6. Extended-Range Ultrarefractive 1D Photonic Crystal Prisms

    NASA Technical Reports Server (NTRS)

    Ting, David Z.

    2007-01-01

    A proposal has been made to exploit the special wavelength-dispersive characteristics of devices of the type described in One-Dimensional Photonic Crystal Superprisms (NPO-30232) NASA Tech Briefs, Vol. 29, No. 4 (April 2005), page 10a. A photonic crystal is an optical component that has a periodic structure comprising two dielectric materials with high dielectric contrast (e.g., a semiconductor and air), with geometrical feature sizes comparable to or smaller than light wavelengths of interest. Experimental superprisms have been realized as photonic crystals having three-dimensional (3D) structures comprising regions of amorphous Si alternating with regions of SiO2, fabricated in a complex process that included sputtering. A photonic crystal of the type to be exploited according to the present proposal is said to be one-dimensional (1D) because its contrasting dielectric materials would be stacked in parallel planar layers; in other words, there would be spatial periodicity in one dimension only. The processes of designing and fabricating 1D photonic crystal superprisms would be simpler and, hence, would cost less than do those for 3D photonic crystal superprisms. As in 3D structures, 1D photonic crystals may be used in applications such as wavelength-division multiplexing. In the extended-range configuration, it is also suitable for spectrometry applications. As an engineered structure or artificially engineered material, a photonic crystal can exhibit optical properties not commonly found in natural substances. Prior research had revealed several classes of photonic crystal structures for which the propagation of electromagnetic radiation is forbidden in certain frequency ranges, denoted photonic bandgaps. It had also been found that in narrow frequency bands just outside the photonic bandgaps, the angular wavelength dispersion of electromagnetic waves propagating in photonic crystal superprisms is much stronger than is the angular wavelength dispersion obtained

  7. The primary structure of rat brain (cytoplasmic) dynein heavy chain, a cytoplasmic motor enzyme.

    PubMed Central

    Zhang, Z; Tanaka, Y; Nonaka, S; Aizawa, H; Kawasaki, H; Nakata, T; Hirokawa, N

    1993-01-01

    Overlapping cDNA clones encoding the heavy chain of rat brain cytoplasmic dynein have been isolated. The isolated cDNA clones contain an open reading frame of 13,932 bp encoding 4644 aa (M(r), 532,213). The deduced protein sequence of the heavy chain of rat brain dynein shows significant similarity to sea urchin flagellar beta-dynein (27.0% identical) and to Dictyostelium cytoplasmic dynein (53.5% identical) throughout the entire sequence. The heavy chain of rat brain (cytoplasmic) dynein contains four putative nucleotide-binding consensus sequences [GX4GK(T/S)] in the central one-third region that are highly similar to those of sea urchin and Dictyostelium dyneins. The N-terminal one-third of the heavy chain of rat brain (cytoplasmic) dynein shows high similarity (43.8% identical) to that of Dictyostelium cytoplasmic dynein but poor similarity (19.4% identical) to that of sea urchin flagellar dynein. These results suggested that the C-terminal two-thirds of the dynein molecule is conserved and plays an essential role in microtubule-dependent motility activity, whereas the N-terminal regions are different between cytoplasmic and flagellar dyneins. Images Fig. 1 PMID:7690137

  8. Effect of cholesterol on structural and mechanical properties of membranes depends on lipid chain saturation

    SciTech Connect

    Pan Jianjun; Tristram-Nagle, Stephanie; Nagle, John F.

    2009-08-15

    The effects of cholesterol on membrane bending modulus K{sub C}, membrane thickness D{sub HH}, the partial and apparent areas of cholesterol and lipid, and the order parameter S{sub xray} are shown to depend upon the number of saturated hydrocarbon chains in the lipid molecules. Particularly striking is the result that up to 40% cholesterol does not increase the bending modulus K{sub C} of membranes composed of phosphatidylcholine lipids with two cis monounsaturated chains, although it does have the expected stiffening effect on membranes composed of lipids with two saturated chains. The B fluctuational modulus in the smectic liquid crystal theory is obtained and used to discuss the interactions between bilayers. Our K{sub C} results motivate a theory of elastic moduli in the high cholesterol limit and they challenge the relevance of universality concepts. Although most of our results were obtained at 30 deg. C, additional data at other temperatures to allow consideration of a reduced temperature variable do not support universality for the effect of cholesterol on all lipid bilayers. If the concept of universality is to be valid, different numbers of saturated chains must be considered to create different universality classes. The above experimental results were obtained from analysis of x-ray scattering in the low angle and wide angle regions.

  9. Modeling the structure and operation of drug supply chains: The case of cocaine and heroin in Italy and Slovenia.

    PubMed

    Caulkins, Jonathan P; Disley, Emma; Tzvetkova, Marina; Pardal, Mafalda; Shah, Hemali; Zhang, Xiaoke

    2016-05-01

    Multiple layers of dealers connect international drug traffickers to users. The fundamental activity of these dealers is buying from higher-level dealers and re-selling in smaller quantities at the next lower market level. Each instance of this can be viewed as completing a drug dealing "cycle". This paper introduces an approach for combining isolated accounts of such cycles into a coherent model of the structure, span, and profitability of the various layers of the domestic supply chain for illegal drugs. The approach is illustrated by synthesizing data from interviews with 116 incarcerated dealers to elucidate the structure and operation of distribution networks for cocaine and heroin in Italy and Slovenia. Inmates' descriptions of cycles in the Italian cocaine market suggest fairly orderly networks, with reasonably well-defined market levels. The Italian heroin market appears to have more "level-jumpers" who skip a market level by making a larger number of sales per cycle, with each sale being of a considerably smaller weight. Slovenian data are sparser, but broadly consistent. Incorporating prices allows calculation of how much of the revenue from retail sales is retained by dealers at each market level. In the Italian cocaine market, both retail sellers and the international supply chain outside of Italy each appear to receive about 30-40% of what users spend, with the remaining 30% going to higher-level dealers operating in Italy (roughly 10% to those at the multi-kilo level and 20% to lower level wholesale dealers). Factoring in cycle frequencies permits rough estimation of the number of organizations at each market level per billion euros in retail sales, and of annual net revenues for organizations at each level. These analyses provide an approach to gaining insight into the structure and operation of the supply chain for illegal drugs. They also illustrate the value of two new graphical tools for describing illicit drug supply chains and hint at possible

  10. Complete backbone and DENQ side chain NMR assignments in proteins from a single experiment: implications to structure-function studies.

    PubMed

    Reddy, Jithender G; Hosur, Ramakrishna V

    2014-03-01

    Resonance assignment is the first and the most crucial step in all nuclear magnetic resonance (NMR) investigations on structure-function relationships in biological macromolecules. Often, the assignment exercise has to be repeated several times when specific interactions with ligands, substrates etc., have to be elucidated for understanding the functional mechanisms. While the protein backbone serves to provide a scaffold, the side chains interact directly with the ligands. Such investigations will be greatly facilitated, if there are rapid methods for obtaining exhaustive information with minimum of NMR experimentation. In this context, we present here a pulse sequence which exploits the recently introduced technique of parallel detection of multiple nuclei, e.g. (1)H and (13)C, and results in two 3D-data sets simultaneously. These yield complete backbone resonance assignment ((1)H(N), (15)N, (13)CO, (1)Hα/(13)Cα, and (1)Hβ/(13)Cβ chemical shifts) and side chain assignment of D, E, N and Q residues. Such an exhaustive assignment has the potential of yielding accurate 3D structures using one or more of several algorithms which calculate structures of the molecules very reliably on the basis of NMR chemical shifts alone. The side chain assignments of D, E, N, and Q will be extremely valuable for interaction studies with different ligands; D and E side chains are known to be involved in majority of catalytic activities. Utility of this experiment has been demonstrated with Ca(2+) bound M-crystallin, which contains largely D, E, N and Q residues at the metal binding sites.

  11. Application of nitrogen and carbon stable isotopes (δ(15)N and δ(13)C) to quantify food chain length and trophic structure.

    PubMed

    Perkins, Matthew J; McDonald, Robbie A; van Veen, F J Frank; Kelly, Simon D; Rees, Gareth; Bearhop, Stuart

    2014-01-01

    Increasingly, stable isotope ratios of nitrogen (δ(15)N) and carbon (δ(13)C) are used to quantify trophic structure, though relatively few studies have tested accuracy of isotopic structural measures. For laboratory-raised and wild-collected plant-invertebrate food chains spanning four trophic levels we estimated nitrogen range (NR) using δ(15)N, and carbon range (CR) using δ(13)C, which are used to quantify food chain length and breadth of trophic resources respectively. Across a range of known food chain lengths we examined how NR and CR changed within and between food chains. Our isotopic estimates of structure are robust because they were calculated using resampling procedures that propagate variance in sample means through to quantified uncertainty in final estimates. To identify origins of uncertainty in estimates of NR and CR, we additionally examined variation in discrimination (which is change in δ(15)N or δ(13)C from source to consumer) between trophic levels and among food chains. δ(15)N discrimination showed significant enrichment, while variation in enrichment was species and system specific, ranged broadly (1.4‰ to 3.3‰), and importantly, propagated variation to subsequent estimates of NR. However, NR proved robust to such variation and distinguished food chain length well, though some overlap between longer food chains infers a need for awareness of such limitations. δ(13)C discrimination was inconsistent; generally no change or small significant enrichment was observed. Consequently, estimates of CR changed little with increasing food chain length, showing the potential utility of δ(13)C as a tracer of energy pathways. This study serves as a robust test of isotopic quantification of food chain structure, and given global estimates of aquatic food chains approximate four trophic levels while many food chains include invertebrates, our use of four trophic level plant-invertebrate food chains makes our findings relevant for a majority of

  12. The structures and properties of the new two-dimensional inorganic-organic hybrid materials based on the molybdate chains

    NASA Astrophysics Data System (ADS)

    Li, Na; Mu, Bao; Cao, Xinyu; Huang, Rudan

    2014-09-01

    A series of inorganic organic hybrid materials based on polyoxometalates(POMs), namely, [MII(HL)2(H2O)2][MoVI6O20] [M=Co (1), Ni (2), Cu (3), Zn (4)], [MnIVL2(H2O)2][MoVI6O20] (5), and (HL)3PMO12O40 (6) [L=3-(4-pyridyl)pyrazole], have been synthesized. The compounds have been characterized by elemental analysis, powder X-ray diffraction (PXRD) and single-crystal X-ray diffraction. The results from single-crystal X-ray diffraction indicate that 1-5 are isostructural. It is worth noting that the polyanions are bridged by Mo-O-Mo to form 1D inorganic chains, which are further connected via M ions to form 2D nets. In compound 6, the ligands are used as the positive ions to balance the charge of the compound. Moreover, the magnetic properties of compound 5 have also been investigated in detail.

  13. Tctex1d2 Is a Negative Regulator of GLUT4 Translocation and Glucose Uptake.

    PubMed

    Shimoda, Yoko; Okada, Shuichi; Yamada, Eijiro; Pessin, Jeffrey E; Yamada, Masanobu

    2015-10-01

    Tctex1d2 (Tctex1 domain containing 2) is an open reading frame that encodes for a functionally unknown protein that contains a Tctex1 domain found in dynein light chain family members. Examination of gene expression during adipogenesis demonstrated a marked increase in Tctex1d2 protein expression that was essentially undetectable in preadipocytes and markedly induced during 3T3-L1 adipocyte differentiation. Tctex1d2 overexpression significantly inhibited insulin-stimulated glucose transporter 4 (GLUT4) translocation and 2-deoxyglucose uptake. In contrast, Tctex1d2 knockdown significantly increased insulin-stimulated GLUT4 translocation and 2-deoxyglucose uptake. However, acute insulin stimulation (up to 30 min) in 3T3-L1 adipocytes with overexpression or knockdown of Tctex1d2 had no effect on Akt phosphorylation, a critical signal transduction target required for GLUT4 translocation. Although overexpression of Tctex1d2 had no significant effect on GLUT4 internalization, Tctex1d2 was found to associate with syntaxin 4 in an insulin-dependent manner and inhibit Doc2b binding to syntaxin 4. In addition, glucose-dependent insulinotropic polypeptide rescued the Tctex1d2 inhibition of insulin-stimulated GLUT4 translocation by suppressing the Tctex1d2-syntaxin 4 interaction and increasing Doc2b-Synatxin4 interactions. Taking these results together, we hypothesized that Tctex1d2 is a novel syntaxin 4 binding protein that functions as a negative regulator of GLUT4 plasma membrane translocation through inhibition of the Doc2b-syntaxin 4 interaction.

  14. Examining Prebiotic Chemistry Using O(^1D) Insertion Reactions

    NASA Astrophysics Data System (ADS)

    Hays, Brian M.; Laas, Jacob C.; Weaver, Susanna L. Widicus

    2013-06-01

    Aminomethanol, methanediol, and methoxymethanol are all prebiotic molecules expected to form via photo-driven grain surface chemistry in the interstellar medium (ISM). These molecules are expected to be precursors for larger, biologically-relevant molecules in the ISM such as sugars and amino acids. These three molecules have not yet been detected in the ISM because of the lack of available rotational spectra. A high resolution (sub)millimeter spectrometer coupled to a molecular source is being used to study these molecules using O(^1D) insertion reactions. The O(^1D) chemistry is initiated using an excimer laser, and the products of the insertion reactions are adiabatically cooled using a supersonic expansion. Experimental parameters are being optimized by examination of methanol formed from O(^1D) insertion into methane. Theoretical studies of the structure and reaction energies for aminomethanol, methanediol, and methoxymethanol have been conducted to guide the laboratory studies once the methanol experiment has been optimized. The results of the calculations and initial experimental results will be presented.

  15. Ab initio quantum transport in atomic carbon chains

    NASA Astrophysics Data System (ADS)

    Botello-Méndez, Andrés R.; Charlier, Jean-Christophe; Banhart, Florian; NAPS Team; Carbyne Collaboration

    2015-03-01

    Carbyne, the sp-hybridized phase of carbon, is still a missing link in the family of carbon allotropes. Recently, detailed electrical measurements and first-principles electronic transport calculations have been performed on monoatomic carbon chains. When the 1D system is under strain, the current-voltage curves exhibit a semiconducting behavior, which corresponds to the polyyne structure of the atomic chain with alternating single and triple bonds. Conversely, when the chain is unstrained, the ohmic behavior is observed in agreement with the metallic cumulene structure with double bonds, confirming recent theoretical predictions, namely that a metal-insulator transition can be induced by adjusting the strain. The key role of the contacting leads is also scrutinized by ab initio quantum conductance calculations, explaining the rectifying behavior measured in monoatomic carbon chains in a non-symmetric contact configuration.

  16. Two new Co(II)-MOFs based on polymeric chain building units: Crystal structures, and magnetic properties

    SciTech Connect

    Han, Min-Le; Wu, Ya-Pan; Zhao, Jun; Li, Dong-Sheng; Wang, Yao-Yu

    2015-10-15

    Two new Co(II) metal-organic frameworks, namely [Co{sub 2}(bpm)(H{sub 2}O){sub 3}(L)]{sub n} (1) and ([Co(bpe)(H{sub 2}O)(H{sub 2}L)]·(bpe){sub 0.5}·(H{sub 2}O)){sub n} (2), (H{sub 4}L=1,1′:2′,1″-terphenyl-3,3″,4′,5′-tetracarboxylic acid, bpm=bis(4-pyridyl)amine, bpe=1,2-bis(4-pyridyl)ethene), have been obtained under hydrothermal conditions. Both complexes 1 and 2 have been characterized by elemental analysis, IR spectra, single-crystal X-ray diffraction, powder X-ray diffraction (PXRD), and thermogravimetric analysis (TGA). Complexes 1 and 2 consist of 1D Co(II) chains bridging by carboxylate groups in syn-anti fashion. 1 shows a novel 3D tri-nodal (4,6,10)-connected net with a (3.4{sup 3}.5{sup 2}){sub 2}(3{sup 2}.4{sup 14}.5{sup 12}.6{sup 12}.7{sup 4}.8)(3{sup 2}.4{sup 2}.5{sup 5}.6{sup 4}.7{sup 2}) topology. While 2 exhibits a 2D sql layer. Magnetic susceptibility measurements indicate that both 1 and 2 show weak antiferromagnetic interactions between the adjacent Co(II) ions in 300–8 K for 1 and 300–16 K for 2, respectively, and then 2 also displays ferromagnetic coupling at lower temperatures. - Graphical abstract: Two Co(II) coordination polymers with similar metal chain bridging by carboxylates in syn-anti fashion have been synthesized. Both 1 and 2 show weak antiferromagnetic interactions in high temperature, and then 2 also displays ferromagnetic coupling at lower temperatures. - Highlights: • Two Co(II) coordination polymers with similar metal chain bridging by carboxylates. • A novel 3D (4,6,10)-connected net and a 2D sql layers. • A antiferromagnetic coupling at high temperature for 1 and 2. • A ferromagnetic coupling at lower temperature for 2.

  17. Unique [(1)infinityNi(8)Bi(8)S] metallic wires in a novel quasi-1D compound. Synthesis, crystal and electronic structure, and properties of Ni(8)Bi(8)SI.

    PubMed

    Baranov, A I; Kloo, L; Olenev, A V; Popovkin, B A; Romanenko, A I; Shevelkov, A V

    2001-12-12

    A new quasi-one-dimensional compound Ni(8)Bi(8)SI has been synthesized and its crystal structure determined from single-crystal X-ray diffraction data. The structure of Ni(8)Bi(8)SI consists of [(1)infinityNi(8)Bi(8)S] columns separated by iodine atoms. Conductivity and magnetic susceptibility measurements (down to 4.2 K) show that Ni(8)Bi(8)SI is a one-dimensional metal and exhibits Pauli paramagnetic properties. These observations are in good agreement with the results from electronic structure calculations. An analysis of the chemical bonding employing difference electron charge density maps reveals strong multicenter Ni-Bi bonds and pair Ni-S interactions within the [(1)infinityNi(8)Bi(8)S] columns. Only electrostatic interactions are inferred between the columns and iodine atoms.

  18. Molecular structure of an alkyl-side-chain polymer-water interface: origins of contact angle hysteresis.

    PubMed

    Rangwalla, Hasnain; Schwab, Alexander D; Yurdumakan, Betül; Yablon, Dalia G; Yeganeh, Mohsen S; Dhinojwala, Ali

    2004-09-28

    A new and direct approach to verify surface heterogeneity as the microscopic origin of contact-angle hysteresis is demonstrated. IR-visible sum-frequency-generation spectroscopy (SFG) was used to selectively probe the molecules at the interface of an alkyl-side-chain polymer [poly(vinyl n-octadecyl carbamate-co-vinyl acetate)] with water. The spectra indicate that in contact with water, the polymer surface is heterogeneous (having areas of differing surface energies). This evidence of surface heterogeneity supports the hysteresis observed in the advancing and receding contact angles of the polymer surface with water. The same measurements made for the chemically and structurally similar surface of an octadecyltrichlorosilane self-assembled monolayer indicates a homogeneous surface at the water interface. In this case, contact-angle hysteresis measurements implicate surface roughness as the cause of hysteresis. Atomic force microscopy measurements of roughness for these surfaces further support our conclusions. The polymer-water interface was probed using SFG at above-ambient temperatures, and an order-to-disorder transition (ODT) of alkyl side chains at the interface was observed, which closely follows the melting of crystalline side chains in the bulk. This transition explains the increased wettability of the polymer, by water, when the temperature is raised above the bulk melting temperature. Furthermore, the irreversibility of this ODT suggests that the disordered polymer-water interface is the thermodynamic equilibrium state, whereas the before-heating structure of this interface is a kinetically hindered metastable state.

  19. Relevance of structural segregation and chain compaction for the thermodynamics of folding of a hydrophobic protein model.

    PubMed

    Barbosa, Marco Aurélio A; de Araújo, Antônio F Pereira

    2003-05-01

    The relevance of inside-outside segregation and chain compaction for the thermodynamics of folding of a hydrophobic protein model is probed by complete enumeration of two-dimensional chains of up to 18 monomers in the square lattice. The exact computation of Z scores for uniquely designed sequences confirms that Z tends to decrease linearly with sigma square root of N, as previously suggested by theoretical analysis and Monte Carlo simulations, where sigma, the standard deviation of the number of contacts made by different monomers in the target structure, is a measure of structural segregation and N is the chain length. The probability that the target conformation is indeed the unique global energy minimum of the designed sequence is found to increase dramatically with sigma, approaching unity at maximal segregation. However, due to the huge number of conformations with sub-maximal values of sigma, which correspond to intermediate, only mildly discriminative, values of Z, in addition to significant oscillations of Z around its estimated value, the probability that a correctly designed sequence corresponds to a maximally segregated conformation is small. This behavior of Z also explains the observed relation between sigma and different measures of folding cooperativity of correctly designed sequences.

  20. Phase behavior and hydrated solid structure in lysophospholipid/long-chain alcohol/water system and effect of cholesterol addition.

    PubMed

    Konno, Yoshikazu; Naito, Noboru; Yoshimura, Akio; Aramaki, Kenji

    2010-01-01

    Phase behavior in lysophospholipid/long-chain alcohol/water system at 80°C was investigated using hexanol and oleyl alcohol as the long-chain alcohol. Similarly to hydrophilic surfactant, a micellar phase in a lysophospholipid/water system transitioned to a lamellar liquid-crystalline phase by the addition of long-chain alcohol. In the oleyl alcohol system the lamellar liquid-crystalline phase was observed in wider region compared to the hexanol system. The effect of cholesterol addition on the phase behavior was also studied. The region of liquid-crystalline phase and (reverse micellar + liquid-crystalline + water) phase shifted towards higher lysophospholipid concentrations. The structure of hydrated solid as well as the transition between lamellar liquid-crystalline phase and hydrated solid was analyzed by X-ray scattering measurement and differential scanning calorimetry measurement. It was revealed that the hydrated solid was α-type crystals with lamellar structure. The hydrated solid (gel)-liquid crystal transition temperature gradually decreased with increasing oleyl alcohol concentration and the decrement was enhanced by the addition of cholesterol.

  1. Calculation of monolayer structures of hydrocarbon chains on transition metal dichalcogenides: Dotriacontane on MoSe2

    NASA Astrophysics Data System (ADS)

    Cincotti, S.; Burda, J.; Hentschke, R.; Rabe, J. P.

    1995-03-01

    In situ scanning tunneling microscopy at the interface between atomically flat solid surfaces and solutions containing alkyl chains or alkyl derivatives show that the solute molecules often adsorb from solution to form dense crystalline monolayers at the liquid-solid interface. The structure of these layers depends on the nature of the substrate, and thus cannot be predicted from simple packing considerations alone. As an example of a theoretical approach to this problem on the atomic level, we present a calculation of the monolayer structure of dotriacontane on MoSe2. We carry out energy minimizations of periodic clusters of dotriacontane on MoSe2, where the potential energy is based on ab initio second-order Mo/ller-Plesset perturbation calculations of the adsorbate-substrate interactions combined with a phenomenological force field description of the intra-adsorbate interactions. The resulting adsorbate structure is in excellent agreement with the experimentally observed structure.

  2. 1D-VAR Retrieval Using Superchannels

    NASA Technical Reports Server (NTRS)

    Liu, Xu; Zhou, Daniel; Larar, Allen; Smith, William L.; Schluessel, Peter; Mango, Stephen; SaintGermain, Karen

    2008-01-01

    Since modern ultra-spectral remote sensors have thousands of channels, it is difficult to include all of them in a 1D-var retrieval system. We will describe a physical inversion algorithm, which includes all available channels for the atmospheric temperature, moisture, cloud, and surface parameter retrievals. Both the forward model and the inversion algorithm compress the channel radiances into super channels. These super channels are obtained by projecting the radiance spectra onto a set of pre-calculated eigenvectors. The forward model provides both super channel properties and jacobian in EOF space directly. For ultra-spectral sensors such as Infrared Atmospheric Sounding Interferometer (IASI) and the NPOESS Airborne Sounder Testbed Interferometer (NAST), a compression ratio of more than 80 can be achieved, leading to a significant reduction in computations involved in an inversion process. Results will be shown applying the algorithm to real IASI and NAST data.

  3. Structural basis of light chain amyloidogenicity: comparison of the thermodynamic properties, fibrillogenic potential and tertiary structural features of four vλ6 proteins

    SciTech Connect

    Wall, J.S.; Gupta, V.; Wilkerson, M.; Schell, M.; Loris, R.; Adams, P.; Solomon, A.; Stevens, F.; Dealwis, C.

    2004-04-01

    Primary (AL) amyloidosis results from the pathologic deposition of monoclonal light chains as amyloid fibrils. Studies of recombinant-derived variable region (V{sub L}) fragments of these proteins have shown an inverse relationship between thermodynamic stability and fibrillogenic potential. Further, ionic interactions within the V{sub L} domain were predicted to influence the kinetics of light chain fibrillogenicity, as evidenced from our analyses of a relatively stable V{sub {lambda}}6 protein (Jto) with a long range electrostatic interaction between Asp and Arg side chains at position 29 and 68, respectively, and an unstable, highly fibrillogenic V{sub {lambda}}6 protein (Wil) that had neutral amino acids at these locations. To test this hypothesis, we have generated two Jto-related mutants designed to disrupt the interaction between Asp 29 and Arg 68 (JtoD29A and JtoR68S). Although the thermodynamic stabilities of unfolding for these two molecules were identical, they exhibited very different kinetics of fibril formation: the rate of JtoD29A fibrillogenesis was slow and comparable to the parent molecule, whereas that of JtoR68S was significantly faster. High-resolution X-ray diffraction analyses of crystals prepared from the two mutants having the same space group and unit cell dimensions revealed no significant main-chain conformational changes. However, several notable side-chain alterations were observed in JtoR68S, as compared with JtoD29A, that resulted in the solvent exposure of a greater hydrophobic surface and modifications in the electrostatic potential surface. We posit that these differences contributed to the enhanced fibrillogenic potential of the Arg 68 mutant, since both Jto mutants lacked the intrachain ionic interaction and were equivalently unstable. The information gleaned from our studies has provided insight into structural parameters that in addition to overall thermodynamic stability, contribute to the fibril forming propensity of

  4. Single-chain structure of human ceruloplasmin: the complete amino acid sequence of the whole molecule.

    PubMed Central

    Takahashi, N; Ortel, T L; Putnam, F W

    1984-01-01

    We have determined the amino acid sequence of the amino-terminal 67,000-dalton (67-kDa) fragment of human ceruloplasmin and have established overlapping sequences between the 67-kDa and 50-kDa fragments and between the 50-kDa and 19-kDa fragments. The 67-kDa fragment contains 480 amino acid residues and three glucosamine oligosaccharides. These results together with our previous sequence data for the 50-kDa and 19-kDa fragments complete the amino acid sequence of human ceruloplasmin. The polypeptide chain has a total of 1,046 amino acid residues (Mr 120,085) and has attachment sites for four glucosamine oligosaccharides; together these account for the total molecular mass of human ceruloplasmin (132 kDa). The sequence analysis of the peptides overlapping the fragments showed that one additional amino acid, arginine, is present between the 67-kDa and 50-kDa fragments, and another, lysine, is between the 50-kDa and 19-kDa fragments. Only two apparent sites of amino acid interchange have been identified in the polypeptide chain. Both involve a single-point interchange of glycine and lysine that would result in a difference in charge. The results of the complete sequence analysis verified that human ceruloplasmin is composed of a single polypeptide chain and that the subunit-like fragments are produced by proteolytic cleavage during purification (and possibly also in vivo). PMID:6582496

  5. Experimental investigation of a linear-chain structure in the nucleus 14C

    NASA Astrophysics Data System (ADS)

    Yamaguchi, H.; Kahl, D.; Hayakawa, S.; Sakaguchi, Y.; Abe, K.; Nakao, T.; Suhara, T.; Iwasa, N.; Kim, A.; Kim, D. H.; Cha, S. M.; Kwag, M. S.; Lee, J. H.; Lee, E. J.; Chae, K. Y.; Wakabayashi, Y.; Imai, N.; Kitamura, N.; Lee, P.; Moon, J. Y.; Lee, K. B.; Akers, C.; Jung, H. S.; Duy, N. N.; Khiem, L. H.; Lee, C. S.

    2017-03-01

    It is a well-known fact that a cluster of nucleons can be formed in the interior of an atomic nucleus, and such clusters may occupy molecular-like orbitals, showing characteristics similar to normal molecules consisting of atoms. Chemical molecules having a linear alignment are commonly seen in nature, such as carbon dioxide. A similar linear alignment of the nuclear clusters, referred to as linear-chain cluster state (LCCS), has been studied since the 1950s, however, up to now there is no clear experimental evidence demonstrating the existence of such a state. Recently, it was proposed that an excess of neutrons may offer just such a stabilizing mechanism, revitalizing interest in the nuclear LCCS, specifically with predictions for their emergence in neutron-rich carbon isotopes. Here we present the experimental observation of α-cluster states in the radioactive 14C nucleus. Using the 10Be + α resonant scattering method with a radioactive beam, we observed a series of levels which completely agree with theoretically predicted levels having an explicit linear-chain cluster configuration. We regard this as the first strong indication of the linear-chain clustered nucleus.

  6. Structure effects in the region of superheavy elements via the α-decay chain of 293118

    NASA Astrophysics Data System (ADS)

    Gupta, Raj K.; Kumar, Sushil; Kumar, Rajesh; Balasubramaniam, M.; Scheid, W.

    2002-11-01

    The α-decay chain of 293118, first proposed in the Berkeley cold fusion experiment 208Pb(86Kr, 1n) and now retracted, is calculated by using the preformed cluster model (PCM) of one of the authors (RKG). Also, the possible branchings of α-decays to heavier cluster decays of all the parents in this chain are calculated for the first time. The calculated Q-values, penetrabilities and preformation factors for α-decays suggest that the 285114 nucleus with Z = 114, N = 171 is a magic nucleus, either due to the magicity of Z = 114, or N = 172 or both. The N = 172 is proposed to be a magic number in certain relativistic mean-field calculations, but with Z = 120. The calculated cluster decays point to new interesting possibilities of 14C decay of the 281112 parent, giving rise to a (reasonably) deformed Z = 106, N = 161, 267106 daughter (N = 162 being now established as the deformed magic shell) or to a doubly magic 48Ca cluster emitted from any of the parent nucleus in the α-decay chain. Apparently, these are exciting new directions for future experiments.

  7. Structure predictions of two Bauhinia variegata lectins reveal patterns of C-terminal properties in single chain legume lectins.

    PubMed

    Moreira, Gustavo M S G; Conceição, Fabricio R; McBride, Alan J A; Pinto, Luciano da S

    2013-01-01

    Bauhinia variegata lectins (BVL-I and BVL-II) are single chain lectins isolated from the plant Bauhinia variegata. Single chain lectins undergo post-translational processing on its N-terminal and C-terminal regions, which determines their physiological targeting, carbohydrate binding activity and pattern of quaternary association. These two lectins are isoforms, BVL-I being highly glycosylated, and thus far, it has not been possible to determine their structures. The present study used prediction and validation algorithms to elucidate the likely structures of BVL-I and -II. The program Bhageerath-H was chosen from among three different structure prediction programs due to its better overall reliability. In order to predict the C-terminal region cleavage sites, other lectins known to have this modification were analysed and three rules were created: (1) the first amino acid of the excised peptide is small or hydrophobic; (2) the cleavage occurs after an acid, polar, or hydrophobic residue, but not after a basic one; and (3) the cleavage spot is located 5-8 residues after a conserved Leu amino acid. These rules predicted that BVL-I and -II would have fifteen C-terminal residues cleaved, and this was confirmed experimentally by Edman degradation sequencing of BVL-I. Furthermore, the C-terminal analyses predicted that only BVL-II underwent α-helical folding in this region, similar to that seen in SBA and DBL. Conversely, BVL-I and -II contained four conserved regions of a GS-I association, providing evidence of a previously undescribed X4+unusual oligomerisation between the truncated BVL-I and the intact BVL-II. This is the first report on the structural analysis of lectins from Bauhinia spp. and therefore is important for the characterisation C-terminal cleavage and patterns of quaternary association of single chain lectins.

  8. Structure Predictions of Two Bauhinia variegata Lectins Reveal Patterns of C-Terminal Properties in Single Chain Legume Lectins

    PubMed Central

    Moreira, Gustavo M. S. G.; Conceição, Fabricio R.; McBride, Alan J. A.; Pinto, Luciano da S.

    2013-01-01

    Bauhinia variegata lectins (BVL-I and BVL-II) are single chain lectins isolated from the plant Bauhinia variegata. Single chain lectins undergo post-translational processing on its N-terminal and C-terminal regions, which determines their physiological targeting, carbohydrate binding activity and pattern of quaternary association. These two lectins are isoforms, BVL-I being highly glycosylated, and thus far, it has not been possible to determine their structures. The present study used prediction and validation algorithms to elucidate the likely structures of BVL-I and -II. The program Bhageerath-H was chosen from among three different structure prediction programs due to its better overall reliability. In order to predict the C-terminal region cleavage sites, other lectins known to have this modification were analysed and three rules were created: (1) the first amino acid of the excised peptide is small or hydrophobic; (2) the cleavage occurs after an acid, polar, or hydrophobic residue, but not after a basic one; and (3) the cleavage spot is located 5-8 residues after a conserved Leu amino acid. These rules predicted that BVL-I and –II would have fifteen C-terminal residues cleaved, and this was confirmed experimentally by Edman degradation sequencing of BVL-I. Furthermore, the C-terminal analyses predicted that only BVL-II underwent α-helical folding in this region, similar to that seen in SBA and DBL. Conversely, BVL-I and -II contained four conserved regions of a GS-I association, providing evidence of a previously undescribed X4+unusual oligomerisation between the truncated BVL-I and the intact BVL-II. This is the first report on the structural analysis of lectins from Bauhinia spp. and therefore is important for the characterisation C-terminal cleavage and patterns of quaternary association of single chain lectins. PMID:24260572

  9. Breakdown of 1D water wires inside charged carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Pant, Shashank

    2016-11-01

    Using molecular dynamics approach we investigated the structure and dynamics of water confined inside pristine and charged 6,6 carbon nanotubes (CNTs). This study reports the breakdown of 1D water wires and the emergence of triangular faced water on incorporating charges in 6,6 CNTs. Incorporation of charges results in high potential barriers to flipping of water molecules due to the formation of large number of hydrogen bonds. The PMF analyses show the presence of ∼2 kcal/mol barrier for the movement of water inside pristine CNT and almost negligible barrier in charged CNTs.

  10. Tunability and Sensing Properties of Plasmonic/1D Photonic Crystal

    NASA Astrophysics Data System (ADS)

    Shaban, Mohamed; Ahmed, Ashour M.; Abdel-Rahman, Ehab; Hamdy, Hany

    2017-02-01

    Gold/one-dimensional photonic crystal (Au/1D-PC) is fabricated and applied for sensitive sensing of glucose and different chemical molecules of various refractive indices. The Au layer thickness is optimized to produce surface plasmon resonance (SPR) at the right edge of the photonic band gap (PBG). As the Au deposition time increased to 60 sec, the PBG width is increased from 46 to 86 nm in correlation with the behavior of the SPR. The selectivity of the optimized Au/1D-PC sensor is tested upon the increase of the environmental refractive index of the detected molecules. The resonance wavelength and the PBG edges increased linearly and the transmitted intensity increased nonlinearly as the environment refractive index increased. The SPR splits to two modes during the detection of chloroform molecules based on the localized capacitive coupling of Au particles. Also, this structure shows high sensitivity at different glucose concentrations. The PBG and SPR are shifted to longer wavelengths, and PBG width is decreased linearly with a rate of 16.04 Å/(μg/mm3) as the glucose concentration increased. The proposed structure merits; operation at room temperature, compact size, and easy fabrication; suggest that the proposed structure can be efficiently used for the biomedical and chemical application.

  11. Tunability and Sensing Properties of Plasmonic/1D Photonic Crystal

    PubMed Central

    Shaban, Mohamed; Ahmed, Ashour M.; Abdel-Rahman, Ehab; Hamdy, Hany

    2017-01-01

    Gold/one-dimensional photonic crystal (Au/1D-PC) is fabricated and applied for sensitive sensing of glucose and different chemical molecules of various refractive indices. The Au layer thickness is optimized to produce surface plasmon resonance (SPR) at the right edge of the photonic band gap (PBG). As the Au deposition time increased to 60 sec, the PBG width is increased from 46 to 86 nm in correlation with the behavior of the SPR. The selectivity of the optimized Au/1D-PC sensor is tested upon the increase of the environmental refractive index of the detected molecules. The resonance wavelength and the PBG edges increased linearly and the transmitted intensity increased nonlinearly as the environment refractive index increased. The SPR splits to two modes during the detection of chloroform molecules based on the localized capacitive coupling of Au particles. Also, this structure shows high sensitivity at different glucose concentrations. The PBG and SPR are shifted to longer wavelengths, and PBG width is decreased linearly with a rate of 16.04 Å/(μg/mm3) as the glucose concentration increased. The proposed structure merits; operation at room temperature, compact size, and easy fabrication; suggest that the proposed structure can be efficiently used for the biomedical and chemical application. PMID:28176799

  12. Tunability and Sensing Properties of Plasmonic/1D Photonic Crystal.

    PubMed

    Shaban, Mohamed; Ahmed, Ashour M; Abdel-Rahman, Ehab; Hamdy, Hany

    2017-02-08

    Gold/one-dimensional photonic crystal (Au/1D-PC) is fabricated and applied for sensitive sensing of glucose and different chemical molecules of various refractive indices. The Au layer thickness is optimized to produce surface plasmon resonance (SPR) at the right edge of the photonic band gap (PBG). As the Au deposition time increased to 60 sec, the PBG width is increased from 46 to 86 nm in correlation with the behavior of the SPR. The selectivity of the optimized Au/1D-PC sensor is tested upon the increase of the environmental refractive index of the detected molecules. The resonance wavelength and the PBG edges increased linearly and the transmitted intensity increased nonlinearly as the environment refractive index increased. The SPR splits to two modes during the detection of chloroform molecules based on the localized capacitive coupling of Au particles. Also, this structure shows high sensitivity at different glucose concentrations. The PBG and SPR are shifted to longer wavelengths, and PBG width is decreased linearly with a rate of 16.04 Å/(μg/mm(3)) as the glucose concentration increased. The proposed structure merits; operation at room temperature, compact size, and easy fabrication; suggest that the proposed structure can be efficiently used for the biomedical and chemical application.

  13. Bi(3n+1)Ti7Fe(3n-3)O(9n+11) Homologous Series: Slicing Perovskite Structure with Planar Interfaces Containing Anatase-like Chains.

    PubMed

    Batuk, Dmitry; Tsirlin, Alexander A; Filimonov, Dmitry S; Zakharov, Konstantin V; Volkova, Olga S; Vasiliev, Alexander; Hadermann, Joke; Abakumov, Artem M

    2016-02-01

    The n = 3-6 members of a new perovskite-based homologous series Bi(3n+1)Ti7Fe(3n-3)O(9n+11) are reported. The crystal structure of the n = 3 Bi10Ti7Fe6O38 member is refined using a combination of X-ray and neutron powder diffraction data (a = 11.8511(2) Å, b = 3.85076(4) Å, c = 33.0722(6) Å, S.G. Immm), unveiling the partially ordered distribution of Ti(4+) and Fe(3+) cations and indicating the presence of static random displacements of the Bi and O atoms. All Bi(3n+1)Ti7Fe(3n-3)O(9n+11) structures are composed of perovskite blocks separated by translational interfaces parallel to the (001)p perovskite planes. The thickness of the perovskite blocks increases with n, while the atomic arrangement at the interfaces remains the same. The interfaces comprise chains of double edge-sharing (Fe,Ti)O6 octahedra connected to the octahedra of the perovskite blocks by sharing edges and corners. This configuration shifts the adjacent perovskite blocks relative to each other over a vector ½[110]p and creates S-shaped tunnels along the [010] direction. The tunnels accommodate double columns of the Bi(3+) cations, which stabilize the interfaces owing to the stereochemical activity of their lone electron pairs. The Bi(3n+1)Ti7Fe(3n-3)O(9n+11) structures can be formally considered either as intergrowths of perovskite modules and polysynthetically twinned modules of the Bi2Ti4O11 structure or as intergrowths of the 2D perovskite and 1D anatase fragments. Transmission electron microscopy (TEM) on Bi10Ti7Fe6O38 reveals that static atomic displacements of Bi and O inside the perovskite blocks are not completely random; they are cooperative, yet only short-range ordered. According to TEM, the interfaces can be laterally shifted with respect to each other over ±1/3a, introducing an additional degree of disorder. Bi10Ti7Fe6O38 is paramagnetic in the 1.5-1000 K temperature range due to dilution of the magnetic Fe(3+) cations with nonmagnetic Ti(4+). The n = 3, 4 compounds demonstrate a

  14. 75 FR 27411 - Airworthiness Directives; Turbomeca Arriel 1B, 1D, 1D1, and 1S1 Turboshaft Engines

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-17

    ... (that incorporate Turbomeca Modification (mod) TU 148), Arriel 1D, 1D1, and 1S1 turboshaft engines that do not incorporate mod TU 347. That AD also requires initial and repetitive replacements of 2nd stage... incorporate mod TU 148), 1D, 1D1, and 1S1 turboshaft engines that do not incorporate mod TU 347. We...

  15. Synthesis, structure, and magnetic properties of regular alternating μ-bpm/di-μ-X copper(II) chains (bpm = 2,2'-bipyrimidine; X = OH, F).

    PubMed

    Marino, Nadia; Armentano, Donatella; De Munno, Giovanni; Cano, Joan; Lloret, Francesc; Julve, Miguel

    2012-04-02

    The preparation and X-ray crystal structure of four 2,2'-bipyrimidine (bpm)-containing copper(II) complexes of formula {[Cu(2)(μ-bpm)(H(2)O)(4)(μ-OH)(2)][Mn(H(2)O)(6)](SO(4))(2)}(n) (1), {[Cu(2)(μ-bpm)(H(2)O)(4)(μ-OH)(2)]SiF(6)}(n) (2), {Cu(2)(μ-bpm)(H(2)O)(2)(μ-F)(2)F(2)}(n) (3), and [Cu(bpm)(H(2)O)(2)F(NO(3))][Cu(bpm)(H(2)O)(3)F]NO(3)·2H(2)O (4) are reported. The structures of 1-3 consist of chains of copper(II) ions with regular alternation of bis-bidentate bpm and di-μ-hydroxo (1 and 2) or di-μ-fluoro (3) groups, the electroneutrality being achieved by either hexaaqua manganese(II) cations plus uncoordinated sulfate anions (1), uncoordinated hexafluorosilicate anions (2), or terminally bound fluoride ligands (3). Each copper(II) ion in 1-4 is six-coordinated in elongated octahedral surroundings. 1 and 2 show identical, linear chain motifs with two bpm-nitrogen atoms and two hydroxo groups building the equatorial plane at each copper(II) ion and the axial position being filled by water molecules. In the case of 3, the axial sites at the copper atom are occupied by a bpm-nitrogen atom and a bis-monodentate fluoride anion, producing a "step-like" chain motif. The values of the angle at the hydroxo and fluoro bridges are 94.11(6) (1), 94.75(4) (2), and 101.43(4)° (3). In each case, the copper-copper separation through the bis-bidentate bpm [5.428(1) (1), 5.449(1) (2), and 5.9250(4) Å (3)] is considerably longer than that through the di-μ-hydroxo [2.8320(4) (1) and 2.824(1) Å (2)] or di-μ-fluoro [3.3027(4) Å (3)] bridges. Compound 4 is a mononuclear species whose structure is made up of neutral [Cu(bpm)(H(2)O)(2)F(NO(3))] units, [Cu(bpm)(H(2)O)(3)F](+) cations, uncoordinated nitrate anions, and crystallization water molecules, giving rise to a pseudo-helical, one-dimensional (1D) supramolecular motif. The magnetic properties of 1-3 have been investigated in the temperature range 1.9-300 K. Relatively large, alternating antiferro- [J = -149 (1) and

  16. Phase behavior of binary mixture systems of saturated-unsaturated mixed-acid triacylglycerols: effects of glycerol structures and chain-chain interactions.

    PubMed

    Bayés-García, Laura; Calvet, Teresa; Cuevas-Diarte, Miquel Àngel; Ueno, Satoru; Sato, Kiyotaka

    2015-03-26

    We systematically examined the phase behavior of binary mixtures of mixed-acid triacylglycerols (TAGs) containing palmitic and oleic acid moieties 1,3-dioleoyl-2-palmitoyl-glycerol (OPO), 1,2-dipalmitoyl-3-oleoyl-rac-glycerol (PPO), and 1,2-dioleoyl-3-palmitoyl-rac-glycerol (OOP), which are widely present in natural fats and are employed in the food, pharmaceutical, and cosmetic industries. Differential scanning calorimetry and X-ray diffraction methods were applied to observe the mixing behavior of PPO/OPO, OOP/OPO, and PPO/OOP under metastable and stable conditions. The results led to three conclusions: (1) Eutectic behavior was observed in PPO/OPO. (2) Molecular compound (MC) crystals were formed in the mixtures of OOP/OPO and PPO/OOP. (3) However, the MC crystals occurred only under metastable conditions and tended to separate into component TAGs to form eutectic mixture systems after 17 months of incubation. These results were contrary to those of previous studies on 1,3-dipalmitoyl-2-oleoyl glycerol (POP)/OPO and POP/PPO in which the MC crystals were thermodynamically stable. We determined that specific molecular interactions may cause this different phase behavior (stability of POP/OPO and POP/PPO MC crystals and metastability of OOP/OPO and PPO/OOP MC crystals). All results confirm the significant effects of molecular structures of glycerol groups, interactions of fatty acid chains, and polymorphism of the component TAGs on the mixing behavior of mixed-acid TAGs.

  17. Crystal structure analysis of auromomycin apoprotein (macromomycin) shows importance of protein side chains to chromophore binding selectivity.

    PubMed Central

    Van Roey, P; Beerman, T A

    1989-01-01

    The crystal structure of macromomycin, the apoprotein of the antitumor antibiotic auromomycin, has been determined and refined at 1.6-A resolution. The overall structure is composed of a flattened seven-stranded antiparallel beta-barrel and two antiparallel beta-sheet ribbons. The barrel and the ribbons define a deep cleft that is the chromophore binding site. The cleft is very accessible and in this structure is occupied by two 2-methyl-2,4-pentanediol and two water molecules. The overall shape of the binding site is similar to that of the analogue actinoxanthin. Highly specific side chains that are not conserved between different analogues extend into the binding site and may be important to the chromophore binding specificity. PMID:2771945

  18. Surface functionalization of quantum dots with fine-structured pH-sensitive phospholipid polymer chains.

    PubMed

    Liu, Yihua; Inoue, Yuuki; Ishihara, Kazuhiko

    2015-11-01

    To add novel functionality to quantum dots (QDs), we synthesized water-soluble and pH-responsive block-type polymers by reversible addition-fragmentation chain transfer (RAFT) polymerization. The polymers were composed of cytocompatible 2-methacryloyloxyethyl phosphorylcholine (MPC) polymer segments, which contain a small fraction of active ester groups and can be used to conjugate biologically active compounds to the polymer, and pH-responsive poly(2-(N,N-diethylamino) ethyl methacrylate (DEAEMA)) segments. One terminal of the polymer chain had a hydrophobic alkyl group that originated from the RAFT initiator. This hydrophobic group can bind to the hydrophobic layer on the QD surface. A fluorescent dye was conjugated to the polymer chains via the active ester group. The block-type polymers have an amphiphilic nature in aqueous medium. The polymers were thus easily bound to the QD surface upon evaporation of the solvent from a solution containing the block-type polymer and QDs, yielding QD/fluorescence dye-conjugated polymer hybrid nanoparticles. Fluorescence resonance energy transfer (FRET) between the QDs (donors) and the fluorescent dye molecules (acceptors) was used to obtain information on the conformational dynamics of the immobilized polymers. Higher FRET efficiency of the QD/fluorescent dye-conjugated polymer hybrid nanoparticles was observed at pH 7.4 as compared to pH 5.0 due to a stretching-shrinking conformational motion of the poly(DEAEMA) segments in response to changes in pH. We concluded that the block-type MPC polymer-modified nanoparticles could be used to evaluate the pH of cells via FRET fluorescence based on the cytocompatibility of the MPC polymer.

  19. Effects of chain length, chlorination degree, and structure on the octanol-water partition coefficients of polychlorinated n-alkanes.

    PubMed

    Hilger, Bettina; Fromme, Hermann; Völkel, Wolfgang; Coelhan, Mehmet

    2011-04-01

    Log octanol-water partition coefficients (log Kow) of 40 synthesized polychlorinated n-alkanes (PCAs) with different chlorination degrees were determined using reversed-phase high performance liquid chromatography (RP-HPLC). In addition, log Kow values of a technical mixture namely Cereclor 63L as well as 15 individual in house synthesized C10, C11, and C12 chloroalkanes with known chlorine positions were estimated. Based on these results, the effects of chain length, chlorination degree, and structure were explored. The estimated log Kow values ranged from 4.10 (polychlorinated n-decanes with 50.2% chlorine content) to 11.34 (polychlorinated n-octacosanes with 54.8% chlorine content) for PCAs and from 3.82 (1,2,5,6,9,10-hexachlorodecane) to 7.75 (1,1,1,3,9,11,11,11-octachlorododecane) for the individual chloroalkanes studied. The results showed that log Kow value was influenced linearly at a given chlorine content by chain length, while a polynominal effect was observed in dependence on the chlorination degree of an alkane chain. Chlorine substitution pattern influenced markedly the log Kow value of chloroalkanes.

  20. Zero temperature non-plateau magnetization and magnetocaloric effect in an Ising-XYZ diamond chain structure

    NASA Astrophysics Data System (ADS)

    Torrico, J.; Rojas, M.; de Souza, S. M.; Rojas, Onofre

    2016-10-01

    Zero temperature non-plateau magnetization is a peculiar property of a quantum spin chain and it sometimes appears due to different gyromagnetic factors. In this study, we illustrate a quite unusual non-plateau magnetization property driven by XY-anisotropy in an Ising-XYZ diamond chain. Two particles with spin-1/2 are bonded by XYZ coupling and they are responsible for the emergence of non-plateau magnetization. These two quantum operator spins are bonded to two nodal Ising spins and this process is repeated infinitely to yield a diamond chain structure. Due to the non-plateau magnetization property, we focus our discussion on the magnetocaloric effect of this model by presenting the isentropic curves and the Grüneisen parameters, as well as showing the regions where the model exhibits an efficient magnetocaloric effect. Due to the existence of two phases located very close to each other, the strong XY-anisotropy exhibits a particular behavior with a magnetocaloric effect, with a wider interval in the magnetic field, where the magnetocaloric effect is efficient.

  1. Monoclonal antibodies to kinesin heavy and light chains stain vesicle- like structures, but not microtubules, in cultured cells

    PubMed Central

    1989-01-01

    Kinesin, a microtubule-activated ATPase and putative motor protein for the transport of membrane-bounded organelles along microtubules, was purified from bovine brain and used as an immunogen for the production of murine monoclonal antibodies. Hybridoma lines that secreted five distinct antikinesin IgGs were cloned. Three of the antibodies reacted on immunoblots with the 124-kD heavy chain of kinesin, while the other two antibodies recognized the 64-kD light chain. When used for immunofluorescence microscopy, the antibodies stained punctate, cytoplasmic structures in a variety of cultured mammalian cell types. Consistent with the identification of these structures as membrane- bounded organelles was the observation that cells which had been extracted with Triton X-100 before fixation contained little or no immunoreactive material. Staining of microtubules in the interphase cytoplasm or mitotic spindle was never observed, nor were associated structures, such as centrosomes and primary cilia, labeled by any of the antibodies. Nevertheless, in double-labeling experiments using antibodies to kinesin and tubulin, kinesin-containing particles were most abundant in regions where microtubules were most highly concentrated and the particles often appeared to be aligned on microtubules. These results constitute the first direct evidence for the association of kinesin with membrane-bounded organelles, and suggest a molecular mechanism for organelle motility based on transient interactions of organelle-bound kinesin with the microtubule surface. PMID:2522455

  2. Catalytic Features of the Botulinum Neurotoxin A Light Chain Revealed by High Resolution Structure of an Inhibitory Peptide Complex

    SciTech Connect

    Silvaggi,N.; Wilson, D.; Tzipori, S.; Allen, K.

    2008-01-01

    The Clostridium botulinum neurotoxin serotype A light chain (BoNT/A-LC) is a Zn(II)-dependent metalloprotease that blocks the release of acetylcholine at the neuromuscular junction by cleaving SNAP-25, one of the SNARE proteins required for exocytosis. Because of the potential for use of the toxin in bioterrorism and the increasingly widespread application of the toxin in the medical field, there is significant interest in the development of small-molecule inhibitors of the metalloprotease. Efforts to design such inhibitors have not benefited from knowledge of how peptides bind to the active site since the enzyme-peptide structures available previously either were not occupied in the vicinity of the catalytic Zn(II) ion or did not represent the product of SNAP-25 substrate cleavage. Herein we report the 1.4 Angstroms-resolution X-ray crystal structure of a complex between the BoNT/A-LC and the inhibitory peptide N-Ac-CRATKML, the first structure of the light chain with an inhibitory peptide bound at the catalytic Zn(II) ion. The peptide is bound with the Cys S? atom coordinating the metal ion. Surprisingly, the cysteine sulfur is oxidized to the sulfenic acid form. Given the unstable nature of this species in solution, is it likely that oxidation occurs on the enzyme. In addition to the peptide-bound structure, we report two structures of the unliganded light chain with and without the Zn(II) cofactor bound at 1.25 and 1.20 Angstroms resolution, respectively. The two structures are nearly identical, confirming that the Zn(II) ion plays a purely catalytic role. Additionally, the structure of the Zn(II)-bound uncomplexed enzyme allows identification of the catalytic water molecule and a second water molecule that occupies the same position as the peptidic oxygen in the tetrahedral intermediate. This observation suggests that the enzyme active site is prearranged to stabilize the tetrahedral intermediate of the protease reaction.

  3. Structure-property optimizations in donor polymers via electronics, substituents, and side chains toward high efficiency solar cells.

    PubMed

    Uy, Rycel L; Price, Samuel C; You, Wei

    2012-07-26

    Many advances in organic photovoltaic efficiency are not yet fully understood and new insight into structure-property relationships is required to push this technology into broad commercial use. The aim of this article is not to comprehensively review recent work, but to provide commentary on recent successes and forecast where researchers should look to enhance the efficiency of photovoltaics. By lowering the LUMO level, utilizing electron-withdrawing substituents advantageously, and employing appropriate side chains on donor polymers, researchers can elucidate further aspects of polymer-PCBM interactions while ultimately developing materials that will push past 10% efficiency.

  4. Two novel CPs with double helical chains based rigid tripodal ligands: Syntheses, crystal structures, magnetic susceptibility and fluorescence properties

    NASA Astrophysics Data System (ADS)

    Wang, Xiao; Hou, Xiang-Yang; Zhai, Quan-Guo; Hu, Man-Cheng

    2016-11-01

    Two three-dimensional coordination polymers (CPs), namely [Cd(bpydb)- (H2bpydb)]n·0.5nH2O (1), and [Cu2(bpydb)2]n (2) (2,6-di-p-carboxyphenyl-4,4'- bipyridine1 = H2bpydb), containing a novel double-helical chains, which have been solvothermal synthesized, characterized, and structure determination. CPs 1-2 reveal the new (3,5)-net and (3,6)-net alb topology, respectively. The fluorescence properties of CPs 1-2 were investigated, and magnetic susceptibility measurements indicate that compound 1 has dominating antiferromagnetic couplings between metal ions.

  5. Mechanically durable and highly conductive elastomeric composites from long single-walled carbon nanotubes mimicking the chain structure of polymers.

    PubMed

    Ata, Seisuke; Kobashi, Kazufumi; Yumura, Motoo; Hata, Kenji

    2012-06-13

    By using long single-walled carbon nanotubes (SWNTs) as a filler possessing the highest aspect ratio and small diameter, we mimicked the chain structure of polymers in the matrix and realized a highly conductive elastomeric composite (30 S/cm) with an excellent mechanical durability (4500 strain cycles until failure), far superior to any other reported conductive elastomers. This exceptional mechanical durability was explained by the ability of long and traversing SWNTs to deform in concert with the elastomer with minimum stress concentration at their interfaces. The conductivity was sufficient to operate many active electronics components, and thus this material would be useful for practical stretchable electronic devices.

  6. Isostructural 1D coordination polymers of Zn(II), Cd(II) and Cu(II) with phenylpropynoic acid and DABCO as organic linkers

    NASA Astrophysics Data System (ADS)

    Saravanakumar, Rajendran; Varghese, Babu; Sankararaman, Sethuraman

    2014-11-01

    Using phenylpropynoic acid (PPA) and 1,4-diazabicyclo[2.2.2]octane (DABCO) as organic spacers, isostructural coordination polymers of Zn(II), Cd(II) and Cu(II) were synthesized by solvothermal method and structurally characterized using single crystal XRD, powder XRD, 13C CP-MAS NMR spectroscopy. Single crystal XRD data revealed four PPA units coordinating with two metal ions forming a paddle wheel secondary building unit (SBU). The paddle wheel units are connected through coordination of DABCO nitrogen to the metal centers from the axial positions leading to the formation of the 1D coordination polymers along the c axis. Intermolecular π stacking and Csbnd H…π interactions between the adjacent polymer chains convert the 1D coordination polymer into an interesting 3D network with the Csbnd H…π bonds running along the crystallographic a and b axes. Thermal and nitrogen adsorption studies of these coordination polymers are reported.

  7. Avian community responses to vegetation structure within chained and hand-cut pinyon-juniper woodlands on the Colorado Plateau

    USGS Publications Warehouse

    Van Riper, Charles; Crow, Claire

    2012-01-01

    We investigated relationships between breeding birds and vegetation characteristics in fuels-reduction treatment areas within pinyon-juniper woodlands at locations over the Colorado Plateau. The goal of this study was to document differences in avian community responses to two types of pinyon-juniper fuels-reduction treatments (chained vs. hand-cut), relative to control sites. We selected 73 vegetation plots in southern Utah and northern Arizona, of which 33 had been previously thinned by handcutting or chaining, and 40 control plots in untreated pinyon-juniper woodlands. At the 73 locations we documented vegetation structure and counted birds within 3.1 ha circular plots during the 2005 and 2006 breeding seasons. We focused in particular on the effects of fuels-reduction treatments to 16 bird species that are considered pinyon-juniper obligates. We found that density of pinyon pines was the most important variable in predicting bird species richness in all treatments and at control sites. Abundance of Brewer’s Sparrow (Spizella breweri) was negatively related to chained, but positively related to hand cut areas. Vesper Sparrow (Poocetes graminius) abundance was negatively related to both chaining and handcutting. Within 16 pinyon-juniper obligate bird species, abundance of five was positively related to pinyon-pine density, while two were positively related to juniper density. These responses, along with other bird-vegetation relationships influenced by treatment type, need to be considered by land managers when planning fuels reduction treatments in pinyon-juniper woodland habitat in the Colorado Plateau.

  8. On the origin of multi-step spin transition behaviour in 1D nanoparticles

    NASA Astrophysics Data System (ADS)

    Chiruta, Daniel; Jureschi, Catalin-Maricel; Linares, Jorge; Dahoo, Pierre Richard; Garcia, Yann; Rotaru, Aurelian

    2015-09-01

    To investigate the spin state switching mechanism in spin crossover (SCO) nanoparticles, a special attention is given to three-step thermally induced SCO behavior in 1D chains. An additional term is included in the standard Ising-like Hamiltonian to account for the border interaction between SCO molecules and its local environment. It is shown that this additional interaction, together with the short range interaction, drives the multi-steps thermal hysteretic behavior in 1D SCO systems. The relation between a polymeric matrix and this particular multi-step SCO phenomenon is discussed accordingly. Finally, the environmental influence on the SCO system's size is analyzed as well.

  9. Automotive Lithium-ion Cell Manufacturing: Regional Cost Structures and Supply Chain Considerations

    SciTech Connect

    Chung, Donald; Elgqvist, Emma; Santhanagopalan, Shriram

    2016-04-08

    Manufacturing capacity for lithium-ion batteries (LIBs)--which power many consumer electronics and are increasingly used to power electric vehicles--is heavily concentrated in east Asia. Currently, China, Japan, and Korea collectively host 88% of all LIB cell and 79% of automotive LIB cell manufacturing capacity. Mature supply chains and strong cumulative production experience suggest that most LIB cell production will remain concentrated in Asia. However, other regions--including North America--could be competitive in the growing automotive LIB cell market under certain conditions. To illuminate the factors that drive regional competitiveness in automotive LIB cell production, this study models cell manufacturing cost and minimum sustainable price, and examines development of LIB supply chains and current LIB market conditions. Modeled costs are for large format, 20-Ah stacked pouch cells with lithium-nickel-manganese-cobalt-oxide (NMC) cathodes and graphite anodes suitable for automotive application. Production volume is assumed to be at commercial scale, 600 MWh per year.

  10. Structure-activity relationship study of vitamin D analogs with oxolane group in their side chain.

    PubMed

    Belorusova, Anna Y; Martínez, Andrea; Gándara, Zoila; Gómez, Generosa; Fall, Yagamare; Rochel, Natacha

    2017-04-02

    Synthetic analogs of 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3) have been developed with the goal of improving the biological profile of the natural hormone for therapeutic applications. Derivatives of 1,25(OH)2D3 with the oxolane moiety branched in the side chain at carbon C20, act as Vitamin D nuclear Receptor (VDR) superagonists being several orders of magnitude more active than the natural ligand. Here, we describe the synthesis and biological evaluation of three diastereoisomers of (1S, 3R)-Dihydroxy-(20S)-[(2″-hydroxy-2″-propyl)-tetrahydrofuryl]-22,23,24,25,26,27-hexanor-1α-hydroxyvitamin D3, with different stereochemistry at positions C2 and C5 of the oxolane ring branched at carbon C22 (1, C2RC5S; 2, C2SC5R; 3, C2SC5S). These compounds act as weak VDR agonist in transcriptional assays with compound 3 being the most active. X-ray crystallographic analysis of the VDR ligand-binding domain accommodating the three compounds indicates that the oxolane group branched at carbon C22 is not constrained as in case of compound with oxolane group branched at C20 leading to the loss of interactions of the triene group and increased flexibility of the C/D-rings and of the side chain.

  11. The influence of interchain coupling on intramolecular oscillation mobility in coupled macromolecular chains: The case of coplanar parallel chains

    NASA Astrophysics Data System (ADS)

    Čevizović, D.; Petković, S.; Galović, S.; Chizhov, A.; Reshetnyak, A.

    2015-10-01

    We enlarge our results from the study of the hopping mechanism of the oscillation excitation transport in 1D model of one biologica-likel macromolecular chain to the case of a system composed from two 1D parallel macromolecular chains with consideration of the properties of intramolecular oscillation excitations. We suppose, that due to the exciton interaction with thermal oscillation (generated by mechanical phonon subsystem) of structural elements (consisting of the peptide group) of the chains, the exciton becomes by self trapped and forms the polaron state. We suggest a model which generalizes the modified Holstein polaron model to the case of two macromolecular chains and find that because of the interchain coupling, the exciton energy band is splitted into two subbands. The hopping process of exciton migration along the macromolecular chains is studied in dependence of system parameters and temperature. We pay an special attention to the temperature range (near T = 300 K) in which living cells operate. It is found that for the certain values of the system parameters there exists the abrupt change of the exciton migration nature from practically free (light) exciton motion to an immobile (heavy, dressed by phonon cloud) quasiparticle We discuss an application of the obtained results to the exciton transport both within deoxyribonucleic acid molecule and in the 2D polymer films organized from such macromolecular chains.

  12. Surface structures of poly(methyl methacrylate) films influenced by chain entanglement in the corresponding film-formation solution.

    PubMed

    Xu, Jianquan; Liu, Yingjun; He, Jinsheng; Zhang, Rongping; Zuo, Biao; Wang, Xinping

    2014-11-28

    The effects of the properties of casting solution on the surface structure of poly(methyl methacrylate) (PMMA) films were systematically investigated. It was observed that the hydrophobicity of PMMA films increased with increasing viscosity of the corresponding polymer solution regardless of the film-formation techniques that were utilized. The ratio of the C-H symmetric stretching vibrations of methylene groups (hydrophobic components, with a peak at 2910 cm(-1)) to those of the ester methyl groups (relative hydrophilic components, with a peak at 2955 cm(-1)) from sum frequency generation (SFG) vibrational spectra, A2910/A2955, was used as a parameter to evaluate the structure on the film surface, which was related to the surface wettability of the films. The results showed that A2910/A2955 of cast PMMA films increased linearly with ηsp(0.3) (ηsp, the specific viscosity of the casting solution), whereas that of the corresponding spin-coated films showed a linear relationship defined as ηsp(0.3)E(0.26), where E is the average number of entanglement points per molecule (E = Mw/Me). These results indicate that a relative equilibrium conformation on the PMMA film surface, adopted from the perspective of thermodynamics, was easily achieved during film formation, when the conformation of the polymer chains in the corresponding casting solution was close to that in the bulk. For the spin-coated films, the chain entanglement structure in the casting solution was a more important factor for the resulting film to reach a relative equilibrium state, since this structure was in favor of maintaining the pristine conformation in casting solution under centrifugal force during spin-coating. This work may help to enhance the fundamental understanding of the formation of the film surface structure from polymer solution to the resulting solid film, which will affect not only the corresponding surface properties, but also the dynamics of the resulting thin films.

  13. Acyl chain length and saturation modulate interleaflet coupling in asymmetric bilayers: effects on dynamics and structural order.

    PubMed

    Chiantia, Salvatore; London, Erwin

    2012-12-05

    A long-standing question about membrane structure and function is the degree to which the physical properties of the inner and outer leaflets of a bilayer are coupled to one another. Using our recently developed methods to prepare asymmetric vesicles, coupling was investigated for vesicles containing phosphatidylcholine (PC) in the inner leaflet and sphingomyelin (SM) in the outer leaflet. The coupling of both lateral diffusion and membrane order was monitored as a function of PC and SM acyl chain structure. The presence in the outer leaflet of brain SM, which decreased outer-leaflet lateral diffusion, had little effect upon lateral diffusion in inner leaflets composed of dioleoyl PC (i.e., diffusion was only weakly coupled in the two leaflets) but did greatly reduce lateral diffusion in inner leaflets composed of PC with one saturated and one oleoyl acyl chain (i.e., diffusion was strongly coupled in these cases). In addition, reduced outer-leaflet diffusion upon introduction of outer-leaflet milk SM or a synthetic C24:0 SM, both of which have long interdigitating acyl chains, also greatly reduce diffusion of inner leaflets composed of dioleoyl PC, indicative of strong coupling. Strikingly, several assays showed that the ordering of the outer leaflet induced by the presence of SM was not reflected in increased lipid order in the inner leaflet, i.e., there was no detectable coupling between inner and outer leaflet membrane order. We propose a model for how lateral diffusion can be coupled in opposite leaflets and discuss how this might impact membrane function.

  14. 10B+α states with chain-like structures in 14N

    NASA Astrophysics Data System (ADS)

    Kanada-En'yo, Yoshiko

    2015-12-01

    I investigate 10B+α -cluster states of 14N with a 10B+α -cluster model. Near the α -decay threshold energy, I obtain Kπ=3+ and Kπ=1+ rotational bands having 10B(3+) +α and 10B(1+) +α components, respectively. I assign the bandhead state of the Kπ=3+ band to the experimental 3+ at Ex=13.19 MeV of 14N observed in α scattering reactions by 10B and show that the calculated α -decay width is consistent with the experimental data. I discuss an α -cluster motion around the 10B cluster and show that the Kπ=3+ and Kπ=1+ rotational bands contain an enhanced component of a linear-chain 3 α configuration, in which an α cluster is localized in the longitudinal direction around the deformed 10B cluster.

  15. Sibship reconstruction in hierarchical population structures using Markov chain Monte Carlo techniques.

    PubMed

    Thomas, Stuart C; Hill, William G

    2002-06-01

    Markov chain Monte Carlo procedures allow the reconstruction of full-sibships using data from genetic marker loci only. In this study, these techniques are extended to allow the reconstruction of nested full- within half-sib families, and to present an efficient method for calculating the likelihood of the observed marker data in a nested family. Simulation is used to examine the properties of the reconstructed sibships, and of estimates of heritability and common environmental variance of quantitative traits obtained from those populations. Accuracy of reconstruction increases with increasing marker information and with increasing size of the nested full-sibships, but decreases with increasing population size. Estimates of variance component are biased, with the direction and magnitude of bias being dependent upon the underlying errors made during pedigree reconstruction.

  16. Exploring the use of concept chains to structure teacher trainees' understanding of science

    NASA Astrophysics Data System (ADS)

    Machin, Janet; Varleys, Janet; Loxley, Peter

    2004-12-01

    This paper reports on a paper and pencil concept-sorting strategy that enables trainee teachers to restructure their knowledge in any one domain of science. It is used as a self-study tool, mainly to enable them to break down and understand the progression of concepts beyond the level at which they have to teach. The strategy involves listing key ideas in an increasingly complex and inclusive fashion such that a 'chain' is developed where the initial statements are simple and the final ones more complex. Evaluation of the strategy with trainees over a five-year period revealed promising potential for the strategy as a self-study tool, as well as an audit tool, enabling tutors to more easily identify misconceptions. There was some evidence that trainees found the strategy useful in preparing themselves to teach in the classroom, possibly by enabling meaningful learning to take place according to the Ausubel-Novak-Gowin theory.

  17. Alkyl Chain Length and Temperature Effects on Structural Properties of Pyrrolidinium-Based Ionic Liquids: A Combined Atomistic Simulation and Small-Angle X-ray Scattering Study

    SciTech Connect

    Li, Song; Bañuelos, José Leobardo; Guo, Jianchang; Anovitz, Lawrence; Rother, Gernot; Shaw, Robert W.; Hillesheim, Patrick C.; Dai, Sheng; Baker, Gary A.; Cummings, Peter T.

    2011-12-21

    Molecular dynamics (MD) simulations of 1-alkyl-1-methylpyrrolidinium bis(trifluoromethanesulfonyl)imide ([CnMPy][Tf₂N], n = 3, 4, 6, 8, 10) were conducted using an all-atom model. Radial distribution functions (RDF) were computed and structure functions were generated to compare with new X-ray scattering experimental results, reported herein. The scattering peaks in the structure functions generally shift to lower Q values with increased temperature for all the liquids in this series. However, the first sharp diffraction peak (FSDP) in the longer alkyl chain liquids displays a marked shift to higher Q values with increasing temperature. Alkyl chain-dependent ordering of the polar groups and increased tail aggregation with increasing alkyl chain length were observed in the partial pair correlation functions and the structure functions. The reasons for the observed alkyl chain-dependent phenomena and temperature effects were explored.

  18. Alkyl Chain Length and Temperature Effects on Structural Properties of Pyrrolidinium-Based Ionic Liquids: A Combined Atomistic Simulation and Small-Angle X-ray Scattering Study.

    SciTech Connect

    Li, Song; Banuelos, Jose Leo; Guo, Jianchang; Anovitz, Lawrence {Larry} M; Rother, Gernot; Shaw, Robert W; Hillesheim, Patrick C; Dai, Sheng; Baker, Gary A; Cummings, Peter T

    2011-01-01

    Molecular dynamics (MD) simulations of 1-alkyl-1-methylpyrrolidinium 12 bis(trifluoromethanesulfonyl)imide ([CnMPy][Tf2N], n = 3, 4, 6, 8, 10) were conducted 13 using an all-atom model. Radial distribution functions (RDF) were computed and structure 14 functions were generated to compare with new X-ray scattering experimental results, 15 reported herein. The scattering peaks in the structure functions generally shift to lower Q 16 values with increased temperature for all the liquids in this series. However, the first sharp 17 diffraction peak (FSDP) in the longer alkyl chain liquids displays a marked shift to higher Q 18 values with increasing temperature. Alkyl chain-dependent ordering of the polar groups and 19 increased tail aggregation with increasing alkyl chain length were observed in the partial pair 20 correlation functions and the structure functions. The reasons for the observed alkyl chain- 21 dependent phenomena and temperature effects were explored.

  19. Thermoplastic biodegradable polyurethanes: the effect of chain extender structure on properties and in-vitro degradation.

    PubMed

    Tatai, Lisa; Moore, Tim G; Adhikari, Raju; Malherbe, François; Jayasekara, Ranjith; Griffiths, Ian; Gunatillake, Pathiraja A

    2007-12-01

    Biodegradable polyurethanes are typically prepared from polyester polyols, aliphatic diisocyanates and chain extenders. We have developed a degradable chain extender (DCE) based on dl-lactic acid and ethylene glycol to accelerate hard segment degradation. Three series of polyurethane elastomers were synthesised to investigate the effect of incorporating DCE on synthesis, mechanical and thermal properties and in-vitro degradation. Polyurethane soft segments were based on poly(epsilon-caprolactone) (PCL) polyol. The hard segment was based on either ethyl lysine diisocyanate or hexamethylene diisocyanate in combination with ethylene glycol or DCE. Polyurethanes were characterised by gel permeation chromatography, tensile testing (Instron) and differential scanning calorimetry. Polymer degradation in-vitro (phosphate buffered saline) was tested by measuring mass loss, change in molecular weight and amine concentration in degradation products at three different time points over a 1 year period. Incorporation of DCE did not affect thermal or mechanical properties but had an influence on the in-vitro degradation. All polyurethanes exhibited considerable molecular weight decrease over the test period, and DCE-based polyurethanes showed the highest mass loss. The presence of the DCE and the initial molecular weight of the polyurethane are the key factors responsible for high mass losses. Differential scanning calorimetry, amine group analysis and the observation that mass loss was directly proportional to hard segment weight percentage, strongly supported that the polyurethane hard segment is the most susceptible segment to degradation in these polyurethanes. The PCL-based soft segment appears to undergo little or no degradation under these test conditions.

  20. Structural instability of the CoO4 tetrahedral chain in SrCoO3-δ thin films

    DOE PAGES

    Glamazda, A.; Choi, Kwang-yong; Lemmens, P.; ...

    2015-08-31

    Raman scattering experiments together with detailed lattice dynamic calculations are performed to elucidate crystallographic and electronic peculiarities of SrCoO3-δ films. We observe that the 85 cm-1 phonon mode involving the rotation of a CoO4 tetrahedron undergoes a hardening by 21 cm-1 when the temperature is decreased. In addition, new phonon modes appear at 651.5 and 697.6 cm-1 . The latter modes are attributed to the Jahn-Teller activated modes. Upon cooling from room temperature, all phonons exhibit an exponential-like increase of intensity with a characteristic energy of about 103–107 K. We attribute this phenomenon to an instability of the CoO4 tetrahedralmore » chain structure, which constitutes a key ingredient to understand the electronic and structural properties of the brownmillerite SrCoO2.5.« less

  1. Morphodynamics and sediment tracers in 1-D (MAST-1D): 1-D sediment transport that includes exchange with an off-channel sediment reservoir

    NASA Astrophysics Data System (ADS)

    Lauer, J. Wesley; Viparelli, Enrica; Piégay, Hervé

    2016-07-01

    Bed material transported in geomorphically active gravel bed rivers often has a local source at nearby eroding banks and ends up sequestered in bars not far downstream. However, most 1-D numerical models for gravel transport assume that gravel originates from and deposits on the channel bed. In this paper, we present a 1-D framework for simulating morphodynamic evolution of bed elevation and size distribution in a gravel-bed river that actively exchanges sediment with its floodplain, which is represented as an off-channel sediment reservoir. The model is based on the idea that sediment enters the channel at eroding banks whose elevation depends on total floodplain sediment storage and on the average elevation of the floodplain relative to the channel bed. Lateral erosion of these banks occurs at a specified rate that can represent either net channel migration or channel widening. Transfer of material out of the channel depends on a typical bar thickness and a specified lateral exchange rate due either to net channel migration or narrowing. The model is implemented using an object oriented framework that allows users to explore relationships between bank supply, bed structure, and lateral change rates. It is applied to a ∼50-km reach of the Ain River, France, that experienced significant reduction in sediment supply due to dam construction during the 20th century. Results are strongly sensitive to lateral exchange rates, showing that in this reach, the supply of sand and gravel at eroding banks and the sequestration of gravel in point bars can have strong influence on overall reach-scale sediment budgets.

  2. Structural features of macrocyclic cobalt complexes - catalysts of chain transfer to a monomer in radical polymerization

    SciTech Connect

    Gridnev, A.A.; Lampeka, Ya.D.; Smirnov, B.R.; Yatsimirskii, K.B.

    1987-11-01

    Data are given on the catalytic activity of a series of cobalt coordination compounds with macrocyclic and acyclic ligsnds of different structures in radical polymerization reactions of methacrylic monomers. The influence of various factors (especially the structure of the ligand) on the manifestation of catalytic properties of the compounds studied is discussed.

  3. 1D-1D Coulomb drag in a 6 Million Mobility Bi-layer Heterostructure

    NASA Astrophysics Data System (ADS)

    Bilodeau, Simon; Laroche, Dominique; Xia, Jian-Sheng; Lilly, Mike; Reno, John; Pfeiffer, Loren; West, Ken; Gervais, Guillaume

    We report Coulomb drag measurements in vertically-coupled quantum wires. The wires are fabricated in GaAs/AlGaAs bilayer heterostructures grown from two different MBE chambers: one at Sandia National Laboratories (1.2M mobility), and the other at Princeton University (6M mobility). The previously observed positive and negative drag signals are seen in both types of devices, demonstrating the robustness of the result. However, attempts to determine the temperature dependence of the drag signal in the 1D regime proved challenging in the higher mobility heterostructure (Princeton), in part because of difficulties in aligning the wires within the same transverse subband configuration. Nevertheless, this work, performed at the Microkelvin laboratory of the University of Florida, is an important proof-of-concept for future investigations of the temperature dependence of the 1D-1D drag signal down to a few mK. Such an experiment could confirm the Luttinger charge density wave interlocking predicted to occur in the wires. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under Contract DE-AC04-94AL8500.

  4. Structural reconstruction and spontaneous formation of Fe polynuclears: a self-assembly of Fe-porphyrin coordination chains on Au(111) revealed by scanning tunneling microscopy.

    PubMed

    Wang, Yuxu; Zhou, Kun; Shi, Ziliang; Ma, Yu-Qiang

    2016-06-07

    A self-assembled Fe-porphyrin coordination chain structure on a Au(111) surface is investigated by scanning tunneling microscopy (STM), revealing structural reconstruction resulting from an alternative change of molecular orientations and spontaneous formation of uniformly sized Fe polynuclears. The alternation of the molecular orientations is ascribed to the cooperation of the attractive coordination and the intermolecular steric repulsion as elucidated by high-resolution STM observations. Furthermore, chemical control experiments are carried out to determine the number of atoms in an Fe polynuclear, suggesting a tentative Fe dinuclear-module that serves not only as a coordination center to link porphyrin units together but also as a "dangling" site for further functionalization by a guest terpyridine ligand. The chain structure and the Fe polynuclears are stable up to 320 K as revealed by real-time STM scanning. Annealing at higher temperatures converts the chain structure into a two-dimensional coordination structure.

  5. Structural Insights into the Drosophila melanogaster Retinol Dehydrogenase, a Member of the Short-Chain Dehydrogenase/Reductase Family

    PubMed Central

    Hofmann, Lukas; Tsybovsky, Yaroslav; Alexander, Nathan S.; Babino, Darwin; Leung, Nicole Y.; Montell, Craig; Banerjee, Surajit; von Lintig, Johannes; Palczewski, Krzysztof

    2016-01-01

    The 11-cis-retinylidene chromophore of visual pigments isomerizes upon interaction with a photon, initiating a downstream cascade of signaling events that ultimately lead to visual perception. 11-cis-Retinylidene is regenerated through enzymatic transformations collectively called the visual cycle. The first and rate-limiting enzymatic reaction within this cycle, i.e., the reduction of all-trans-retinal to all-trans-retinol, is catalyzed by retinol dehydrogenases. Here, we determined the structure of Drosophila melanogaster photoreceptor retinol dehydrogenase (PDH) isoform C that belongs to the short-chain dehydrogenase/reductase (SDR) family. This is the first reported structure of a SDR that possesses this biologically important activity. Two crystal structures of the same enzyme grown under different conditions revealed a novel conformational change of the NAD+ cofactor, likely representing a change during catalysis. Amide hydrogen–deuterium exchange of PDH demonstrated changes in the structure of the enzyme upon dinucleotide binding. In D. melanogaster, loss of PDH activity leads to photoreceptor degeneration that can be partially rescued by transgenic expression of human RDH12. Based on the structure of PDH, we analyzed mutations causing Leber congenital amaurosis 13 in a homology model of human RDH12 to obtain insights into the molecular basis of RDH12 disease-causing mutations. PMID:27809489

  6. Structures of Clostridium Botulinum Neurotoxin Serotype A Light Chain Complexed with Small-Molecule Inhibitors Highlight Active-Site Flexibility

    SciTech Connect

    Silvaggi,N.; Boldt, G.; Hixon, M.; Kennedy, J.; Tzipori, S.; Janda, K.; Allen, K.

    2007-01-01

    The potential for the use of Clostridial neurotoxins as bioweapons makes the development of small-molecule inhibitors of these deadly toxins a top priority. Recently, screening of a random hydroxamate library identified a small-molecule inhibitor of C. botulinum Neurotoxin Serotype A Light Chain (BoNT/A-LC), 4-chlorocinnamic hydroxamate, a derivative of which has been shown to have in vivo efficacy in mice and no toxicity. We describe the X-ray crystal structures of BoNT/A-LC in complexes with two potent small-molecule inhibitors. The structures of the enzyme with 4-chlorocinnamic hydroxamate or 2,4-dichlorocinnamic hydroxamate bound are compared to the structure of the enzyme complexed with L-arginine hydroxamate, an inhibitor with modest affinity. Taken together, this suite of structures provides surprising insights into the BoNT/A-LC active site, including unexpected conformational flexibility at the S1' site that changes the electrostatic environment of the binding pocket. Information gained from these structures will inform the design and optimization of more effective small-molecule inhibitors of BoNT/A-LC.

  7. Kinematics of an oblique deformation front using paleomagnetic data; the Altomira-Loranca structures (Iberian Chain, Central Spain)

    NASA Astrophysics Data System (ADS)

    Valcarcel, M.

    2013-05-01

    Manoel Valcárcel1, 5, Ruth Soto2, Elisabet Beamud3, Belén Oliva-Urcia4 and Josep Anton Muñoz5 1 IGME, Departamento de Investigación y Prospección Geocientífica. C/ La Calera, 1, 28760 Tres Cantos; m.valcarcel@igme.es 2 IGME, Unidad de Zaragoza, C/ Manuel Lasala 44, 9 B, 50006 Zaragoza, Spain 3 Lab. Paleomagnetisme (CCiT UB-CSIC). ICT "Jaume Almera", Solé i Sabarís, s/n, 08028 Barcelona, Spain. 4 IPE-CSIC, Avda. Montañana 1005, 50059 Zaragoza, Spain 5 Grup Geodinàmica i Anàlisi de Conques, Universitat de Barcelona, Zona Universitària Pedralbes, 08028 Barcelona, Spain The Altomira and Loranca structures consist of a fold-and-thrust system detached on Triassic evaporites. They are oriented N-S to NNE-SSW and NNW-SSE at its northern and southern end, respectively, forming a subtle arc, oblique with respect to the general NW-SE trend of the Iberian Chain. The aim of this work is to characterize with paleomagnetic data the kinematic evolution of the the Altomira Range, located at the southwestern deformation front of the Iberian Chain, and of the structures within its associated piggy-back basin, the Loranca basin. This approach will also give clues regarding the primary and/or secondary origin of these structures to better characterize them in further studies (3D reconstruction and restoration, fault pattern). A total of 180 samples were obtained from 19 sites in Eocene, Oligocene and Miocene rocks (including clays, fine sandstones and limestones). They were analyzed by means of stepwise thermal demagnetization and subsequent measurement of the natural remanent magnetization (NRM). Although fold tests are not statistically significant, a primary origin of the magnetization is deduced by samples showing either normal or reverse polarity after bedding correction of the calculated characteristic components. Declinations of the site mean directions appear scattered after bedding correction suggesting differential vertical-axis rotations. Sites located at the

  8. Strain-induced metal–semiconductor transition observed in atomic carbon chains

    PubMed Central

    La Torre, A.; Botello-Mendez, A.; Baaziz, W.; Charlier, J. -C.; Banhart, F.

    2015-01-01

    Carbyne, the sp1-hybridized phase of carbon, is still a missing link in the family of carbon allotropes. While the bulk phases of carbyne remain elusive, the elementary constituents, that is, linear chains of carbon atoms, have already been observed using the electron microscope. Isolated atomic chains are highly interesting one-dimensional conductors that have stimulated considerable theoretical work. Experimental information, however, is still very limited. Here we show electrical measurements and first-principles transport calculations on monoatomic carbon chains. When the 1D system is under strain, the chains are semiconducting corresponding to the polyyne structure with alternating bond lengths. Conversely, when the chain is unstrained, the ohmic behaviour of metallic cumulene with uniform bond lengths is observed. This confirms the recent prediction of a metal–insulator transition that is induced by strain. The key role of the contacting leads explains the rectifying behaviour measured in monoatomic carbon chains in a nonsymmetric contact configuration. PMID:25818506

  9. Strain-induced metal-semiconductor transition observed in atomic carbon chains

    NASA Astrophysics Data System (ADS)

    La Torre, A.; Botello-Mendez, A.; Baaziz, W.; Charlier, J.-C.; Banhart, F.

    2015-03-01

    Carbyne, the sp1-hybridized phase of carbon, is still a missing link in the family of carbon allotropes. While the bulk phases of carbyne remain elusive, the elementary constituents, that is, linear chains of carbon atoms, have already been observed using the electron microscope. Isolated atomic chains are highly interesting one-dimensional conductors that have stimulated considerable theoretical work. Experimental information, however, is still very limited. Here we show electrical measurements and first-principles transport calculations on monoatomic carbon chains. When the 1D system is under strain, the chains are semiconducting corresponding to the polyyne structure with alternating bond lengths. Conversely, when the chain is unstrained, the ohmic behaviour of metallic cumulene with uniform bond lengths is observed. This confirms the recent prediction of a metal-insulator transition that is induced by strain. The key role of the contacting leads explains the rectifying behaviour measured in monoatomic carbon chains in a nonsymmetric contact configuration.

  10. From structural push to chain migration: notes on the persistence of migration to Ciudad Juarez, Mexico.

    PubMed

    Zoomers, E B

    1986-01-01

    "Spatial differentiation in regional welfare is often assumed to be one of the most important explanatory factors in individual migration behaviour. By the weight of 'push' against 'pull', migrants walk in step with the unequal distribution of socio-economic opportunities. In the case of Ciudad Juarez [Mexico], these 'structural factors' only appear to have determined migration in its first stages; especially recently 'non-structural' factors seem to be at the root of the ever-increasing process."

  11. The Effect of Side-Chain Length on the Solid-State Structure and Optical Properties of F8BT: A DFT Study

    NASA Astrophysics Data System (ADS)

    Javad Eslamibidgoli, Mohammad; Lagowski, Jolanta B.

    2012-02-01

    Using the long-range corrected hybrid density functional theory (DFT/B97D) approach, we have performed bulk solid state calculations to investigate the influence of side-chain length on the molecular packing and optical properties of poly (9,9-di-n-octylfluorene-alt-benzothiadiazole) or F8BT. Two different packing structures, the lamellar and nearly hexagonal, were obtained corresponding to longer and shorter side-chains respectively. This behavior can be attributed to the micro-phase separations between the flexible side-chains and the rigid backbones and is in agreement with previous investigations for other hairy-rod polymers. In addition, as a result of the efficient inter-chain interactions for the lamellar structure, the dihedral angle between the F8 and BT units is reduced providing a more planar configuration for the backbone which leads to the decreased band gap (by 0.2-0.3 eV) in comparison to the hexagonal phase and the gas phase with no side-chain. Time-dependent DFT (TDDFT/B3LYP) was also used to study the excited states of the monomer of F8BT optimized in solid-state structures with different side-chain lengths. It is found that the absorption spectrum is red shifted for the polymers with lamellar structure relative to the polymers in hexagonal and gas phases.

  12. Effect of chain structure on hydrogen bonding in vinyl acetate - vinyl alcohol copolymers

    NASA Astrophysics Data System (ADS)

    Merekalova, Nadezhda D.; Bondarenko, Galina N.; Denisova, Yuliya I.; Krentsel, Liya B.; Litmanovich, Arkadiy D.; Kudryavtsev, Yaroslav V.

    2017-04-01

    FTIR spectroscopy and semi-empirical AM1 method are used to study hydrogen bonding in multiblock and random equimolar copolymers of vinyl acetate and vinyl alcohol. An energetically beneficial zip-holder complex, built on multiple inter- and intrachain hydroxyl-hydroxyl bonds and an intrachain hydroxyl-acetyloxy bond, can be formed between two vinyl alcohol sequences. As a result, multiblock copolymers reveal stronger degree of association that affects crystallinity, as well as various rheological and relaxation properties discussed in the literature. Macromolecular complexes in random copolymers are weak and tend to be destroyed in the presence of residual DMF solvent and adsorbed water. Nevertheless, a rather stable interchain quaternary complex can be formed that includes vinyl alcohol and vinyl acetate units and DMF and water molecules. For a single chain it is shown that an H-bond between neighboring vinyl alcohol and vinyl acetate monomer units mostly engages a carbonyl oxygen atom of the vinyl acetate, if the vinyl alcohol belongs to a short (<5 units) sequence, and an ether oxygen atom in the other case. On the whole, the quantum chemistry calculations shed much light on the origin of distinctions in the copolymer FTIR spectra, which may seem subtle when considered standalone.

  13. Structure-activity study on the Phe side chain arrangement of endomorphins using conformationally constrained analogues.

    PubMed

    Tömböly, Csaba; Kövér, Katalin E; Péter, Antal; Tourwé, Dirk; Biyashev, Dauren; Benyhe, Sándor; Borsodi, Anna; Al-Khrasani, Mahmoud; Rónai, András Z; Tóth, Géza

    2004-01-29

    Endomorphins-1 and -2 were substituted with all the beta-MePhe stereoisomers in their Phe residues to generate a conformationally constrained peptide set. This series of molecules was subjected to biological assays, and for beta-MePhe(4)-endomorphins-2, a conformational analysis was performed. Incorporation of (2S,3S)-beta-MePhe(4) resulted in the most potent analogues of both endomorphins with enhanced enzymatic stability. Their micro opioid affinities were 4-times higher than the parent peptides, they stimulated [(35)S]GTPgammaS binding, and they were found to be full agonists. NMR experiments revealed that C-terminal (2S,3S)-beta-MePhe in endomorphin-2 strongly favored the gauche (-) spatial orientation which implies the presence of the chi(1) = -60 degrees rotamer of Phe(4) in the binding conformer of endomorphins. Our results emphasize that the appropriate orientation of the C-terminal aromatic side chain of endomorphins is substantial for binding to the micro opioid receptor.

  14. Evaluating 1d Seismic Models of the Lunar Interior

    NASA Astrophysics Data System (ADS)

    Yao, Y.; Thorne, M. S.; Weber, R. C.; Schmerr, N. C.

    2012-12-01

    A four station seismic network was established on the Moon from 1969 to 1977 as part of the Apollo Lunar Surface Experiment Package (ALSEP). A total of nine 1D seismic velocity models were generated using a variety of different techniques. In spite of the fact that these models were generated from the same data set, significant differences exist between them. We evaluate these models by comparing predicted travel-times to published catalogs of lunar events. We generate synthetic waveform predictions for 1D lunar models using a modified version of the Green's Function of the Earth by Minor Integration (GEMINI) technique. Our results demonstrate that the mean square errors between predicted and measured P-wave travel times are smaller than those for S-wave travel times in all cases. Moreover, models fit travel times for artificial and meteoroid impacts better than for shallow and deep moonquakes. Overall, models presented by Nakamura [Nakamura, 1983] and Garcia et al. [Garcia et al., 2011] predicted the observed travel times better than all other models and were comparable in their explanation of travel-times. Nevertheless, significant waveform differences exist between these models. In particular, the seismic velocity structure of the lunar crust and regolith strongly affect the waveform characteristics predicted by these models. Further complexity is added by possible mantle discontinuity structure that exists in a subset of these models. We show synthetic waveform predictions for these models demonstrating the role that crustal structure has in generating long duration seismic coda inherent in the lunar waveforms.

  15. Novel Familial Dilated Cardiomyopathy Mutation in MYL2 Affects the Structure and Function of Myosin Regulatory Light Chain

    PubMed Central

    Huang, Wenrui; Liang, Jingsheng; Yuan, Chen-Ching; Kazmierczak, Katarzyna; Zhou, Zhiqun; Morales, Ana; McBride, Kim L.; Fitzgerald-Butt, Sara M.; Hershberger, Ray E.; Szczesna-Cordary, Danuta

    2015-01-01

    Dilated Cardiomyopathy (DCM) is a disease of the myocardium characterized by left ventricular dilatation and diminished contractile function. In this report we describe a novel DCM mutation identified for the first time in the myosin regulatory light chain (RLC), replacing Aspartic Acid at position 94 with Alanine (D94A). The mutation was identified by exome sequencing of three adult first-degree relatives who met formal criteria for idiopathic DCM. To gain insight into the functional significance of this pathogenic MYL2 variant, we have cloned and purified the human ventricular RLC wild-type (WT) and D94A-mutant proteins and performed in vitro experiments using RLC-exchanged porcine cardiac preparations. The mutation was observed to induce a reduction in the α-helical content of the RLC and imposed intra-molecular rearrangements. The Ca2+-calmodulin-activated myosin light chain kinase phosphorylation of RLC was not affected by D94A. The mutation was seen to impair the binding of RLC to the MHC (myosin heavy chain), and its incorporation into the RLC-depleted porcine myosin. The actin-activated ATPase activity of mutant-reconstituted porcine cardiac myosin was significantly higher compared to ATPase of WT. No changes in myofibrillar ATPase-pCa relationship were observed in WT- or D94A-reconstituted preparations. Measurements of contractile force showed a slightly reduced maximal tension per cross-section of muscle with no change in calcium sensitivity of force in D94A-reconstituted skinned porcine papillary muscle strips compared with WT. Our data indicate that subtle structural rearrangements in the RLC molecule followed by its impaired interaction with the MHC may trigger functional abnormalities contributing to the DCM phenotype. PMID:25825243

  16. Simulations of Edge Effect in 1D Spin Crossover Compounds by Atom-Phonon Coupling Model

    NASA Astrophysics Data System (ADS)

    Linares, J.; Chiruta, D.; Jureschi, C. M.; Alayli, Y.; Turcu, C. O.; Dahoo, P. R.

    2016-08-01

    We used the atom-phonon coupling model to explain and illustrate the behaviour of a linear nano-chain of molecules. The analysis of the system's behaviour was performed using Free Energy method, and by applying Monte Carlo Metropolis (MCM) method which take into account the phonon contribution. In particular we tested both the MCM algorithm and the dynamic-matrix method and we expose how the thermal behaviour of a 1D spin crossover system varies as a function of different factors. Furthermore we blocked the edge atoms of the chain in its high spin state to study the effect on the system's behaviour.

  17. Microwave-Assisted Extraction, Chemical Structures, and Chain Conformation of Polysaccharides from a Novel Cordyceps Sinensis Fungus UM01.

    PubMed

    Cheong, Kit-Leong; Wang, Lan-Ying; Wu, Ding-Tao; Hu, De-Jun; Zhao, Jing; Li, Shao-Ping

    2016-09-01

    Cordyceps sinensis is a well-known tonic food with broad medicinal properties. The aim of the present study was to investigate the optimization of microwave-assisted extraction (MAE) and characterize chemical structures and chain conformation of polysaccharides from a novel C. sinensis fungus UM01. Ion-exchange and gel filtration chromatography were used to purify the polysaccharides. The chemical structure of purified polysaccharide was determined through gas chromatography-mass spectrometry. Moreover, high performance size exclusion chromatography combined with refractive index detector and multiangle laser light scattering were conducted to analyze the molecular weight (Mw ) and chain conformation of purified polysaccharide. Based on the orthogonal design L9 , optimal MAE conditions could be obtained through 1300 W of microwave power, with a 5-min irradiation time at a solid to water ratio of 1:60, generating the highest extraction yield of 6.20%. Subsequently, the polysaccharide UM01-S1 was purified. The UM01-S1 is a glucan-type polysaccharide with a (1→4)-β-d-glucosyl backbone and branching points located at O-3 of Glcp with a terminal-d-Glcp. The Mw , radius of gyration (Rg ) and hydrodynamic radius (Rh ) of UM01-S1 were determined as 5.442 × 10(6)  Da, 21.8 and 20.2 nm, respectively. Using the polymer solution theory, the exponent (ν) value of the power law function was calculated as 0.38, and the shape factor (ρ = Rg /Rh ) was 1.079, indicating that UM01-S1 has a sphere-like conformation with a branched structure in an aqueous solution. These results provide fundamental information for the future application of polysaccharides from cultured C. sinensis in health and functional food area.

  18. The Compact and Biologically Relevant Structure of Inter-α-inhibitor Is Maintained by the Chondroitin Sulfate Chain and Divalent Cations*

    PubMed Central

    Scavenius, Carsten; Nikolajsen, Camilla Lund; Stenvang, Marcel; Thøgersen, Ida B.; Wyrożemski, Łukasz; Wisniewski, Hans-Georg; Otzen, Daniel E.; Sanggaard, Kristian W.; Enghild, Jan J.

    2016-01-01

    Inter-α-inhibitor is a proteoglycan of unique structure. The protein consists of three subunits, heavy chain 1, heavy chain 2, and bikunin covalently joined by a chondroitin sulfate chain originating at Ser-10 of bikunin. Inter-α-inhibitor interacts with an inflammation-associated protein, tumor necrosis factor-inducible gene 6 protein, in the extracellular matrix. This interaction leads to transfer of the heavy chains from the chondroitin sulfate of inter-α-inhibitor to hyaluronan and consequently to matrix stabilization. Divalent cations and heavy chain 2 are essential co-factors in this transfer reaction. In the present study, we have investigated how divalent cations in concert with the chondroitin sulfate chain influence the structure and stability of inter-α-inhibitor. The results showed that Mg2+ or Mn2+, but not Ca2+, induced a conformational change in inter-α-inhibitor as evidenced by a decrease in the Stokes radius and a bikunin chondroitin sulfate-dependent increase of the thermodynamic stability. This structure was shown to be essential for the ability of inter-α-inhibitor to participate in extracellular matrix stabilization. In addition, the data revealed that bikunin was positioned adjacent to both heavy chains and that the two heavy chains also were in close proximity. The chondroitin sulfate chain interacted with all protein components and inter-α-inhibitor dissociated when it was degraded. Conventional purification protocols result in the removal of the Mg2+ found in plasma and because divalent cations influence the conformation and affect function it is important to consider this when characterizing the biological activity of inter-α-inhibitor. PMID:26728454

  19. Investigation of the structure of anti-human seminal plasma protein single-chain antibody and its association with linker peptide length.

    PubMed

    Jiang, Xin; Zhai, Jun; Song, Dongkui; Qu, Qingshan; Li, Ming; Xing, Li; Miao, Shuzhai

    2015-09-01

    To enhance the activity of seminoprotein single‑chain variable fragment (γ‑Sm‑ScFv) antibodies, modulation of the length of the linker peptide, which connects the variable region of the heavy chain (VH) and the light chain (VL) of single‑chain antibodies, was performed in the present study. Homologous modeling of single VH and VL were performed, respectively. Subsequently, modeling of the whole ScFv sequence, which was previously modified with added linkers of different lengths was also performed, and the (Gly4Ser)n peptide chain structure was used as the linker. The similarities between VH and VL prior to and following the addition of the linker were compared by applying the algorithm of protein similarity, based on spherical coordinates layering. In addition, changes in the fore and aft distance, and diffusion radius were calculated using a MATLAB tool, based on which changes in structural stability were analyzed. Finally, the single‑chain antibody was assessed in a nude mouse model. When n=3 or n=6, the similarity between the original distance and VH and VL were the highest, and the fore and aft distance and diffusion radius were relatively close. In addition, the nude mouse model indicated that, when n=3 or n=6, the inhibitory rate of the single‑chain antibody against tumor cells was significantly higher, compared with the other linker peptides of different lengths. The effect of structural changes of the linker peptides in the single‑chain antibodies on the whole antibody molecule was examined at different levels using a combination of mathematical modeling, bioinformatics methods and biological experiments. The findings of the present study may provide a foundation for further investigation into the preparation of single‑chain antibodies.

  20. Modeling an electric motor in 1-D

    NASA Technical Reports Server (NTRS)

    Butler, Thomas G.

    1991-01-01

    Quite often the dynamicist will be faced with having an electric drive motor as a link in the elastic path of a structure such that the motor's characteristics must be taken into account to properly represent the dynamics of the primary structure. He does not want to model it so accurately that he could get detailed stress and displacements in the motor proper, but just sufficiently to represent its inertia loading and elastic behavior from its mounting bolts to its drive coupling. Described here is how the rotor and stator of such a motor can be adequately modeled as a colinear pair of beams.

  1. Hemoglobins of reptiles. The primary structures of the alpha I- and beta I-chains of common iguana (Iguana iguana) hemoglobin.

    PubMed

    Rücknagel, K P; Braunitzer, G; Wiesner, H

    1988-10-01

    The primary structures of alpha I- and beta I-chains from the hemoglobins of the Common Iguana (Iguana iguana) are presented. The globin chains were separated on CM-cellulose in 8 M urea buffer. The amino-acid sequences were established by automatic Edman degradation of the native chains, the tryptic peptides and a peptide obtained by cyanogen bromide cleavage. The sequences are compared with human hemoglobin. Amino-acid replacements at positions critical for structure and function of the hemoglobin are discussed. The requirements for binding of ATP and also of DPG as allosteric effectors at the beta-chains seem to be fulfilled. Comparison of the alpha-chains with those of the Viper (Vipera aspis) shows 66 amino-acid substitutions. This number is in the same order of magnitude as the ones found by comparison with alpha-chains of crocodiles and mammals as well as with alpha A-chains of a turtle and birds. This result points towards a period of independent evolution of the reptile lines leading to the Common Iguana on one hand and to the Viper on the other. This time span is comparable to the one separating mammals from reptiles.

  2. Structure and Mechanism of Receptoe Sharing by the IL-10R2 Common Chain

    SciTech Connect

    Yoon, Sung-il; Jones, Brandi C.; Logsdon, Naomi J.; Harris, Bethany D.; Deshpande, Ashlesha; Radaeva, Svetlana; Halloran, Brian A.; Gao, Bin; Walter, Mark R.

    2010-06-14

    IL-10R2 is a shared cell surface receptor required for the activation of five class 2 cytokines (IL-10, IL-22, IL-26, IL-28, and IL-29) that play critical roles in host defense. To define the molecular mechanisms that regulate its promiscuous binding, we have determined the crystal structure of the IL-10R2 ectodomain at 2.14 {angstrom} resolution. IL-10R2 residues required for binding were identified by alanine scanning and used to derive computational models of IL-10/IL-10R1/IL-10R2 and IL-22/IL-22R1/IL-10R2 ternary complexes. The models reveal a conserved binding epitope that is surrounded by two clefts that accommodate the structural and chemical diversity of the cytokines. These results provide a structural framework for interpreting IL-10R2 single nucleotide polymorphisms associated with human disease.

  3. Structure and Mechanism of Receptor Sharing by the IL-10R2 Common Chain

    SciTech Connect

    Yoon, Sung-il; Jones, Brandi C.; Logsdon, Naomi J.; Harris, Bethany D.; Deshpande, Ashlesha; Radaeva, Svetlana; Halloran, Brian A.; Gao, Bin; Walter, Mark R.

    2010-07-19

    IL-10R2 is a shared cell surface receptor required for the activation of five class 2 cytokines (IL-10, IL-22, IL-26, IL-28, and IL-29) that play critical roles in host defense. To define the molecular mechanisms that regulate its promiscuous binding, we have determined the crystal structure of the IL-10R2 ectodomain at 2.14 {angstrom} resolution. IL-10R2 residues required for binding were identified by alanine scanning and used to derive computational models of IL-10/IL-10R1/IL-10R2 and IL-22/IL-22R1/IL-10R2 ternary complexes. The models reveal a conserved binding epitope that is surrounded by two clefts that accommodate the structural and chemical diversity of the cytokines. These results provide a structural framework for interpreting IL-10R2 single nucleotide polymorphisms associated with human disease.

  4. Crystal Structure of FadA Adhesin from Fusobacterium nucleatum Reveals a Novel Oligomerization Motif, the Leucine Chain

    SciTech Connect

    Nithianantham, Stanley; Xu, Minghua; Yamada, Mitsunori; Ikegami, Akihiko; Shoham, Menachem; Han, Yiping W.

    2009-04-07

    Many bacterial appendages have filamentous structures, often composed of repeating monomers assembled in a head-to-tail manner. The mechanisms of such linkages vary. We report here a novel protein oligomerization motif identified in the FadA adhesin from the Gram-negative bacterium Fusobacterium nucleatum. The 2.0 {angstrom} crystal structure of the secreted form of FadA (mFadA) reveals two antiparallel {alpha}-helices connected by an intervening 8-residue hairpin loop. Leucine-leucine contacts play a prominent dual intra- and intermolecular role in the structure and function of FadA. First, they comprise the main association between the two helical arms of the monomer; second, they mediate the head-to-tail association of monomers to form the elongated polymers. This leucine-mediated filamentous assembly of FadA molecules constitutes a novel structural motif termed the 'leucine chain.' The essential role of these residues in FadA is corroborated by mutagenesis of selected leucine residues, which leads to the abrogation of oligomerization, filament formation, and binding to host cells.

  5. Structural insight into MtmC, a bifunctional ketoreductase-methyltransferase involved in the assembly of the mithramycin trisaccharide chain.

    PubMed

    Chen, Jhong-Min; Hou, Caixia; Wang, Guojun; Tsodikov, Oleg V; Rohr, Jürgen

    2015-04-21

    More and more post-PKS tailoring enzymes are recognized as being multifunctional and codependent on other tailoring enzymes. One of the recently discovered intriguing examples is MtmC, a bifunctional TDP-4-keto-d-olivose ketoreductase-methyltransferase, which-in codependence with glycosyltransferase MtmGIV-is a key contributor to the biosynthesis of the critical trisaccharide chain of the antitumor antibiotic mithramycin (MTM), produced by Streptomyces argillaceus. We report crystal structures of three binary complexes of MtmC with its methylation cosubstrate SAM, its coproduct SAH, and a nucleotide TDP as well as crystal structures of two ternary complexes, MtmC-SAH-TDP-4-keto-d-olivose and MtmC-SAM-TDP, in the range of 2.2-2.7 Å resolution. The structures reveal general and sugar-specific recognition and catalytic structural features of MtmC. Depending on the catalytic function that is conducted by MtmC, it must bind either NADPH or SAM in the same cofactor binding pocket. A tyrosine residue (Tyr79) appears as a lid covering the sugar moiety of the substrate during the methyl transfer reaction. This residue swings out of the active site by ~180° in the absence of the substrate. This unique conformational change likely serves to release the methylated product and, possibly, to open the active site for binding the bulkier cosubstrate NADPH prior to the reduction reaction.

  6. Effects of odd-even side chain length of alkyl-substituted diphenylbithiophenes on first monolayer thin film packing structure.

    PubMed

    Akkerman, Hylke B; Mannsfeld, Stefan C B; Kaushik, Ananth P; Verploegen, Eric; Burnier, Luc; Zoombelt, Arjan P; Saathoff, Jonathan D; Hong, Sanghyun; Atahan-Evrenk, Sule; Liu, Xueliang; Aspuru-Guzik, Alán; Toney, Michael F; Clancy, Paulette; Bao, Zhenan

    2013-07-31

    Because of their preferential two-dimensional layer-by-layer growth in thin films, 5,5'bis(4-alkylphenyl)-2,2'-bithiophenes (P2TPs) are model compounds for studying the effects of systematic chemical structure variations on thin-film structure and morphology, which in turn, impact the charge transport in organic field-effect transistors. For the first time, we observed, by grazing incidence X-ray diffraction (GIXD), a strong change in molecular tilt angle in a monolayer of P2TP, depending on whether the alkyl chain on the P2TP molecules was of odd or even length. The monolayers were deposited on densely packed ultrasmooth self-assembled alkane silane modified SiO2 surfaces. Our work shows that a subtle change in molecular structure can have a significant impact on the molecular packing structure in thin film, which in turn, will have a strong impact on charge transport of organic semiconductors. This was verified by quantum-chemical calculations that predict a corresponding odd-even effect in the strength of the intermolecular electronic coupling.

  7. Crystal structures of ricin toxin's enzymatic subunit (RTA) in complex with neutralizing and non-neutralizing single-chain antibodies.

    PubMed

    Rudolph, Michael J; Vance, David J; Cheung, Jonah; Franklin, Matthew C; Burshteyn, Fiana; Cassidy, Michael S; Gary, Ebony N; Herrera, Cristina; Shoemaker, Charles B; Mantis, Nicholas J

    2014-08-26

    Ricin is a select agent toxin and a member of the RNA N-glycosidase family of medically important plant and bacterial ribosome-inactivating proteins. In this study, we determined X-ray crystal structures of the enzymatic subunit of ricin (RTA) in complex with the antigen binding domains (VHH) of five unique single-chain monoclonal antibodies that differ in their respective toxin-neutralizing activities. None of the VHHs made direct contact with residues involved in RTA's RNA N-glycosidase activity or induced notable allosteric changes in the toxin's subunit. Rather, the five VHHs had overlapping structural epitopes on the surface of the toxin and differed in the degree to which they made contact with prominent structural elements in two folding domains of the RTA. In general, RTA interactions were influenced most by the VHH CDR3 (CDR, complementarity-determining region) elements, with the most potent neutralizing antibody having the shortest and most conformationally constrained CDR3. These structures provide unique insights into the mechanisms underlying toxin neutralization and provide critically important information required for the rational design of ricin toxin subunit vaccines.

  8. Modification of soy protein hydrolysates by Maillard reaction: Effects of carbohydrate chain length on structural and interfacial properties.

    PubMed

    Li, Weiwei; Zhao, Haibo; He, Zhiyong; Zeng, Maomao; Qin, Fang; Chen, Jie

    2016-02-01

    This study investigated the effects of carbohydrate chain length on the structural and interfacial properties of the Maillard reaction conjugates of soy protein hydrolysates (Mw>30 kDa). The covalent attachment of sugars to soy peptides was confirmed by amino acid analysis and examination of the Fourier-transform infrared spectra. The results suggested that the emulsion stability of the conjugates increased as the length of the carbohydrate chains increased. The surface activity measurement revealed that the soy peptide-dextran conjugates were closely packed and that each molecule occupied a small area of the interface. It was further confirmed that the soy peptide-dextran conjugates formed a thick adsorbed layer at the oil-water interface, as observed in the confocal laser scanning micrographs. The interfacial layer of soy peptides was rheologically complex with broad linear viscoelastic region and strong elastic modulus, and the soy peptide-dextran conjugates might form multilayer adsorption at the interface. This study suggested that the improved surface properties of the soy peptide-dextran conjugates were a result of the strong membrane formed by the closely packed molecular and multilayer adsorption at the interface, which provided steric hindrance to flocculation.

  9. Solubilisation of different medium chain esters in zwitterionic surfactant solutions--effects on phase behaviour and structure.

    PubMed

    Barth, A; Prévost, S; Popig, J; Dzionara, M; Hedicke, G; Gradzielski, M

    2011-12-01

    We studied the effect of solubilisation of methyl esters with different chains of medium length into the binary surfactant system tetradecyldimethylamine oxide/water at constant surfactant concentration of 200 mM. As esters we employed valeric, capronic, enanthic, and pelargonic methyl ester, thereby decreasing the polarity. Always a phase sequence L(1)-L(α)-L(1) is observed with increasing ester concentration, where the L(α)-phase increases in extent and goes to much lower temperatures with increasing chain length of the ester. Viscosity measurements show a maximum at intermediate concentrations of additive that is independent of the type of ester. From SANS measurements detailed information about the structural changes occurring during the rod-to-sphere transition in the system of the shortest additive is deduced, which proceeds first through a pronounced rod growth. Interestingly, for the different esters an almost constant value of the volumic solubilisation capacity is observed, in agreement with the relatively constant interfacial tension. For the different esters no effect on the radius and the area requirement at the amphiphilic interface is observed at the solubilisation boundary. The microemulsions present here are spherical aggregates where the ester is partitioned between core and shell. From the SANS and interfacial tension data the effective bending constants of the surfactant monolayers were deduced and they show that the extension of the L(α)-phase is directly related to a corresponding increase in the bending constants of the surfactant/ester monolayers.

  10. Effect of Chain Structure on the Miscibility of Cellulose Acetate Blends. A Small-Angle Neutron Scattering Study

    SciTech Connect

    Dyer, Caleb W.; Jiang, Zhe; Bozell, Joseph J.; Rials, Timothy G.; Heller, William T.; Dadmun, Mark D.

    2013-02-12

    The miscibility of cellulose ester blends with varying degree of substitution (DS) of acetates along the chain backbone has been investigated using small-angle neutron scattering. The difference in degree of substitution (ΔDS) between the two components in the blend was systematically varied from 0.06 to 0.63 where each blend was found to be a partially miscible, two-phase system. Miscibility between the two components initially decreases as ΔDS of the blends increases. The Flory interaction parameter, χ, concurrently increases with increasing ΔDS as a result of diminishing van der Waals forces between components. The cellulose acetates with lower degree of substitution, which contain more hydroxyl substituents, however, demonstrate greater miscibility even at higher ΔDS. This is interpreted to be the result of favorable hydrogen bonding between blend components that are possible in the presence of more hydroxyl groups. FT-IR data support this interpretation, indicating an increase in hydrogen bonding in a blend having a lower DS component. These results indicate that while an increase in structural differences between cellulose acetate blend components limits miscibility, the presence of hydroxyl groups on the chain promotes mixing. This competition accentuates the significant impact specific interactions have on blend miscibility for these copolymers.

  11. Paleoseismological analysis of an intraplate extensional structure: the Concud fault (Iberian Chain, eastern Spain)

    NASA Astrophysics Data System (ADS)

    Lafuente, P.; Arlegui, L. E.; Liesa, C. L.; Simón, J. L.

    2011-10-01

    The Concud fault is a 13.5 km long, NW-SE striking normal fault at the eastern Iberian Chain. Its recent (Late Pleistocene) slip history is characterized from mapping and trench analysis and discussed in the context of the accretion/incision history of the Alfambra River. The fault has been active since Late Pliocene times, with slip rates ranging from 0.07 to 0.33 mm/year that are consistent with its present-day geomorphologic expression. The most likely empirical correlation suggests that the associated paleoseisms have potential magnitudes close to 6.8, coseismic displacements of 2.0 m, and recurrence intervals from 6.1 to 28.9 ka. At least six paleoseismic events have been identified between 113 and 32 ka. The first three events (U to W) involved displacement along the major fault plane. The last three events (X to Z) encompassed downthrow and hanging-wall synthetic bending prompting fissure opening. This change is accompanied by a decrease in slip rate (from 0.63 to 0.08-0.17 mm/year) and has been attributed to activation of a synthetic blind fault at the hanging wall. The average coseismic displacement (1.9-2.0 m) and recurrence period (6.7-7.9 ka) inferred from this paleoseismic succession are within the ranges predicted from empirical correlation. Such paleoseismic activity contrasts with the moderate present-day seismicity of the area (maximum instrumental Mb = 4.4), which can be explained by the long recurrence interval that characterizes intraplate regions.

  12. Untying a nanoscale knotted polymer structure to linear chains for efficient gene delivery in vitro and to the brain

    NASA Astrophysics Data System (ADS)

    Newland, B.; Aied, A.; Pinoncely, A. V.; Zheng, Y.; Zhao, T.; Zhang, H.; Niemeier, R.; Dowd, E.; Pandit, A.; Wang, W.

    2014-06-01

    The purpose of this study was to develop a platform transfection technology, for applications in the brain, which could transfect astrocytes without requiring cell specific functionalization and without the common cause of toxicity through high charge density. Here we show that a simple and scalable preparation technique can be used to produce a ``knot'' structured cationic polymer, where single growing chains can crosslink together via disulphide intramolecular crosslinks (internal cyclizations). This well-defined knot structure can thus ``untie'' under reducing conditions, showing a more favorable transfection profile for astrocytes compared to 25 kDa-PEI (48-fold), SuperFect® (39-fold) and Lipofectamine®2000 (18-fold) whilst maintaining neural cell viability at over 80% after four days of culture. The high transfection/lack of toxicity of this knot structured polymer in vitro, combined with its ability to mediate luciferase transgene expression in the adult rat brain, demonstrates its use as a platform transfection technology which should be investigated further for neurodegenerative disease therapies.The purpose of this study was to develop a platform transfection technology, for applications in the brain, which could transfect astrocytes without requiring cell specific functionalization and without the common cause of toxicity through high charge density. Here we show that a simple and scalable preparation technique can be used to produce a ``knot'' structured cationic polymer, where single growing chains can crosslink together via disulphide intramolecular crosslinks (internal cyclizations). This well-defined knot structure can thus ``untie'' under reducing conditions, showing a more favorable transfection profile for astrocytes compared to 25 kDa-PEI (48-fold), SuperFect® (39-fold) and Lipofectamine®2000 (18-fold) whilst maintaining neural cell viability at over 80% after four days of culture. The high transfection/lack of toxicity of this knot

  13. The intermolecular hydrogen-hydrogen structure of chain-molecule liquids from neutron diffraction

    NASA Astrophysics Data System (ADS)

    Londono, J. D.; Annis, B. K.; Turner, J. Z.; Soper, A. K.

    1994-11-01

    Neutron diffraction isotopic substitution experiments on liquid n-decane (C10H22) and n-eicosane (C20H42) are described. The intermolecular H-H structure function hHH(Q) and the intermolecular H-H correlation function ginterHH(r) are obtained without recourse to models of the intramolecular structure. The structure of the ginterHH(r) found at 2.5, 5.0, and 7.0 Å corresponds to different shells in the H-H pair correlation function. In addition, ginterHH(r)<1 for a considerable range, due to the screening of intermolecular correlations by intramolecular correlations. This ``correlation hole'' effect is accentuated by extrapolation of the structure functions to the expected infinite wavelength limit, and shows good agreement with values determined from small-angle neutron scattering (SANS) data. All of these features are in good agreement with the results of molecular dynamics simulations for the closely related system C13H28.

  14. Chain-branching control of the atomic structure of alkanethiol-based gold-sulfur interfaces.

    PubMed

    Wang, Yun; Chi, Qijin; Zhang, Jingdong; Hush, Noel S; Reimers, Jeffrey R; Ulstrup, Jens

    2011-09-28

    Density functional theory structure calculations at 0 K and simulations at 300 K of observed high-resolution in situ scanning tunneling microscopy (STM) images reveal three different atomic-interface structures for the self-assembled monolayers (SAMs) of three isomeric butanethiols on Au(111): direct binding to the Au(111) surface without pitting, binding to adatoms above a regular surface with extensive pitting, and binding to adatoms with local surface vacancies and some pitting. Thermal motions are shown to produce some observed STM features, with a very tight energy balance controlling the observed structures. Variation of the degree of substitution on the α carbon is found to significantly change the relative energies for interaction of the different types of adatom structures with the surface, while the nature of the surface cell, controlled primarily by inter-adsorbate steric interactions, controls substrate reorganization energies and adsorbate distortion energies. Most significantly, by manipulating these features, chemical control of the adsorbate can produce stable interfaces with surface pitting eliminated, providing new perspectives for technological applications of SAMs.

  15. Structure-function study of gemini derivatives with two different side chains at C-20, Gemini-0072 and Gemini-0097.

    PubMed

    Huet, Tiphaine; Maehr, Hubert; Lee, Hong Jin; Uskokovic, Milan R; Suh, Nanjoo; Moras, Dino; Rochel, Natacha

    2011-01-01

    Derivatives of vitamin D(3) containing a second side-chain emanating at C-20 are known as gemini and act as vitamin D receptor agonists. Recently, two of these, namely Gemini-0072 and the epimeric Gemini-0097, were selected for further studies in view of their high biological activities and lack of hypercalcemic effects. We now show that the two analogs recruit coactivator SRC-1 better than the parental gemini and act as VDR superagonists. The crystal structures of complexes of zVDR with Gemini-0072 and Gemini-0097 indicate that these ligands induce an extra cavity within the ligand-binding pocket similar to gemini and that their superagonistic activity is due to an increased stabilization of helix H12.

  16. Molecular structure stability of short-chain chlorinated paraffins (SCCPs): Evidence from lattice compatibility and Simha-Somcynsky theories

    NASA Astrophysics Data System (ADS)

    Yumak, A.; Boubaker, K.; Petkova, P.; Yahsi, U.

    2015-10-01

    In is known that short-chain chlorinated paraffins (SCCPs) are highly complex technical mixtures of polychlorinated n-alkanes with single chlorine content. Due to their physical properties (viscosity, flame resistance) they are used in many different applications, such as lubricant additives, metal processing, leather fat-liquoring, plastics softening, PVC plasticizing and flame retardants in paints, adhesives and sealants. SCCPs are studied here in terms of processing-linked molecular structure stability, under Simha and Somcynsky-EOS theory calculations and elements from Simha-Somcynsky-related Lattice Compatibility Theory. Analyses were carried out on 1-chloropropane, 2-chloropropane, 1-chlorobutane, 2-chlorobutane, 1-chloro 2-methylane, and 2-chloro 2-methylane as (SCCPs) universal representatives. This paper gives evidence to this stability and reviews the current state of knowledge and highlights the need for further research in order to improve future (SCCPs) monitoring efforts.

  17. Towards a systematic analysis of human short-chain dehydrogenases/reductases (SDR): Ligand identification and structure-activity relationships.

    PubMed

    Bhatia, Chitra; Oerum, Stephanie; Bray, James; Kavanagh, Kathryn L; Shafqat, Naeem; Yue, Wyatt; Oppermann, Udo

    2015-06-05

    Short-chain dehydrogenases/reductases (SDRs) constitute a large, functionally diverse branch of enzymes within the class of NAD(P)(H) dependent oxidoreductases. In humans, over 80 genes have been identified with distinct metabolic roles in carbohydrate, amino acid, lipid, retinoid and steroid hormone metabolism, frequently associated with inherited genetic defects. Besides metabolic functions, a subset of atypical SDR proteins appears to play critical roles in adapting to redox status or RNA processing, and thereby controlling metabolic pathways. Here we present an update on the human SDR superfamily and a ligand identification strategy using differential scanning fluorimetry (DSF) with a focused library of oxidoreductase and metabolic ligands to identify substrate classes and inhibitor chemotypes. This method is applicable to investigate structure-activity relationships of oxidoreductases and ultimately to better understand their physiological roles.

  18. Structure control for fine tuning fluorescence emission from side-chain azobenzene polymers.

    PubMed

    Smitha, P; Asha, S K

    2007-06-14

    New fluorescent azobenzene dyes and side-chain polymers have been synthesized and characterized and their photophysical properties studied. A series of azobenzene dyes having different fluorophores such as phenol (S1), phenylphenol (S2) and naphthol (S3) incorporated in them were synthesized. S2 had unusually high fluorescence with a quantum yield of phi f = 0.2 recorded in dichloromethane (DCM), whereas S1 and S3 were found to be weakly fluorescent. The azobenzene dyes were converted into methacrylate monomers having short ethyleneoxy spacers and then free radically polymerized. Phenylphenol-based azobenzene polymer (P2) continued to show fluorescence, whereas fluorescence was completely quenched in the case of phenol (P1)- and naphthol (P3)-based polymers. Phenylphenol, though twisted in the ground state is known to have a more planar geometry in the excited state--a factor that enables it to retain its fluorescence behavior even when it is incorporated as part of an azobenzene unit. In contrast, naphthol, which is a better fluorophore compared to phenylphenol, loses much of its emissive behavior upon coupling to the azobenzene unit. The extent of trans to cis photoisomerization in solution was very low (approximately 17%) for P2 after 30 min of continuous irradiation using 365 nm light, in contrast to approximately 40% for P1 under identical conditions. This is attributed to the steric repulsion brought about by the bulky phenylphenol units that restrict rotation. A 2-fold enhancement in fluorescence emission was observed for P2 upon irradiation by UV light at 360 nm, which relaxed to the original intensity in about 7 day's time. The higher emission of the cis azobenzenes is generally attributed to an inhibition of photoinduced electron transfer (PET) mechanism. The emission of P2 showed a concentration dependence which increased initially and then decreased in intensity with the formation of a new red-shifted peak at higher concentration due to aggregation

  19. The four-spinon dynamical structure factor of the Heisenberg chain

    NASA Astrophysics Data System (ADS)

    Caux, Jean-Sébastien; Hagemans, Rob

    2006-12-01

    We compute the exact four-spinon contribution to the zero-temperature dynamical structure factor of the spin-1/2 Heisenberg isotropic antiferromagnet in zero magnetic field, directly in the thermodynamic limit. We make use of the expressions for matrix elements of local spin operators obtained by Jimbo and Miwa using the quantum affine symmetry of the model, and of their adaptation to the isotropic case by Abada, Bougourzi and Si-Lakhal (correcting some overall factors). The four-spinon contribution to the first frequency moment sum rule at fixed momentum is calculated. This shows, as expected, that most of the remaining correlation weight above the known two-spinon part is carried by four-spinon states. Our results therefore provide an extremely accurate description of the exact structure factor.

  20. Changes in the physical structure and chain dynamics of elastin network in homocysteine-cultured arteries.

    PubMed

    Samouillan, Valérie; Lamy, Edouard; Dandurand, Jany; Foucault-Bertaud, Alexandrine; Chareyre, Corinne; Lacabanne, Colette; Charpiot, Philippe

    2010-05-01

    The thermal and dielectric properties of the elastin network were investigated in arteries cultured with physiological and pathological concentrations of homocysteine, an aminoacid responsible of histological impairments in human arteries. The physical structure of this amorphous protein was investigated by differential scanning calorimetry (DSC). To explore the molecular dynamics of the elastin network in the nanometer range, we used thermally stimulated currents (TSC), a dielectric technique running at low frequency, and measuring the dipolar reorientations in proteins subjected to a static electrical field. Combining DSC and TSC experiments reveals the molecular mobility of the proteins, both in the glassy state and in the liquid state. Significant differences are evidenced in the physical structure and relaxation behavior of elastin network in cultured arteries (physiological and pathological concentrations of homocysteine) and discussed.

  1. Protein Tertiary Structure Prediction Based on Main Chain Angle Using a Hybrid Bees Colony Optimization Algorithm

    NASA Astrophysics Data System (ADS)

    Mahmood, Zakaria N.; Mahmuddin, Massudi; Mahmood, Mohammed Nooraldeen

    Encoding proteins of amino acid sequence to predict classified into their respective families and subfamilies is important research area. However for a given protein, knowing the exact action whether hormonal, enzymatic, transmembranal or nuclear receptors does not depend solely on amino acid sequence but on the way the amino acid thread folds as well. This study provides a prototype system that able to predict a protein tertiary structure. Several methods are used to develop and evaluate the system to produce better accuracy in protein 3D structure prediction. The Bees Optimization algorithm which inspired from the honey bees food foraging method, is used in the searching phase. In this study, the experiment is conducted on short sequence proteins that have been used by the previous researches using well-known tools. The proposed approach shows a promising result.

  2. Crystal structure of 2,3-di-methyl-maleic anhydride: continuous chains of electrostatic attraction.

    PubMed

    Wiscons, Ren A; Zeller, Matthias; Rowsell, Jesse L C

    2015-08-01

    In the crystal structure of 2,3-di-methyl-maleic anhydride, C6H6O3, the closest non-bonding inter-molecular distances, between the carbonyl C and O atoms of neighboring mol-ecules, were measured as 2.9054 (11) and 3.0509 (11) Å, which are well below the sum of the van der Waals radii for these atoms. These close contacts, as well as packing motifs similar to that of the title compound, were also found in the crystal structure of maleic anhydride itself and other 2,3-disubstituted maleic anhydrides. Computational modeling suggests that this close contact is caused by strong electrostatic inter-actions between the carbonyl C and O atoms.

  3. Structures of sugar chains of the subunits of an alpha-amylase inhibitor from Phaseolus vulgaris white kidney beans.

    PubMed

    Yamaguchi, H; Funaoka, H; Iwamoto, H

    1992-03-01

    The structures of asparagine-linked oligosaccharides in the subunits of an alpha-amylase inhibitor from the white kidney bean (Phaseolus vulgaris) were determined. Glycopeptides obtained from each subunit were treated with hydrazine, then N-acetylated. The oligosaccharides thus liberated were labeled with 2-aminopyridine at their reducing ends and purified by gel-permeation, reverse-phase, and size-fractionation HPLC. The structures of seven oligosaccharides from the alpha-subunit and eight oligosaccharides from the beta-subunit were determined by a combination of composition and molecular size analyses, exo- and endoglycosidase digestions, partial acetolysis, and 1H-NMR spectroscopy. The major glycan chains in the alpha-subunit were Man alpha 1-6(Man alpha 1-3)Man alpha 1-6(Man alpha 1-2Man alpha 1-3)-Man beta 1-4GlcNAc beta 1-4GlcNAc and (Man alpha 1-2)Man alpha 1-6(Man alpha 1-2Man alpha 1-3)Man alpha 1-6 (Man alpha 1-2Man alpha 1-2Man alpha 1-3)Man beta 1-4GlcNAc beta 1-4GlcNAc, while a glycan chain Man alpha 1-6(Man alpha 1-3)(Xyl beta 1-2)Man beta 1-4GlcNAc beta 1-4GlcNAc comprised more than 70% of the sugar moiety of the beta-subunit.

  4. Structural transformations, composition anomalies and a dramatic collapse of linear polymer chains in dilute ethanol-water mixtures.

    PubMed

    Banerjee, Saikat; Ghosh, Rikhia; Bagchi, Biman

    2012-03-29

    Water-ethanol mixtures exhibit many interesting anomalies, such as negative excess partial molar volume of ethanol, excess sound absorption coefficient at low concentrations, and positive deviation from Raoult's law for vapor pressure, to mention a few. These anomalies have been attributed to different, often contradictory origins, but a quantitative understanding is still lacking. We show by computer simulation and theoretical analyses that these anomalies arise from the sudden emergence of a bicontinuous phase that occurs at a relatively low ethanol concentration of x(eth) ≈ 0.06-0.10 (that amounts to a volume fraction of 0.17-0.26, which is a significant range!). The bicontinuous phase is formed by aggregation of ethanol molecules, resulting in a weak phase transition whose nature is elucidated. We find that the microheterogeneous structure of the mixture gives rise to a pronounced nonmonotonic composition dependence of local compressibility and nonmonotonic dependence in the peak value of the radial distribution function of ethyl groups. A multidimensional free energy surface of pair association is shown to provide a molecular explanation of the known negative excess partial volume of ethanol in terms of parallel orientation and hence better packing of the ethyl groups in the mixture due to hydrophobic interactions. The energy distribution of the ethanol molecules indicates additional energy decay channels that explain the excess sound attenuation coefficient in aqueous alcohol mixtures. We studied the dependence of the solvation of a linear polymer chain on the composition of the water-ethanol solvent. We find that there is a sudden collapse of the polymer at x(eth) ≈ 0.05-a phenomenon which we attribute to the formation of the microheterogeneous structures in the binary mixture at low ethanol concentrations. Together with recent single molecule pulling experiments, these results provide new insight into the behavior of polymer chain and foreign solutes

  5. The FC-1D: The profitable alternative Flying Circus Commercial Aviation Group

    NASA Technical Reports Server (NTRS)

    Meza, Victor J.; Alvarez, Jaime; Harrington, Brook; Lujan, Michael A.; Mitlyng, David; Saroughian, Andy; Silva, Alex; Teale, Tim

    1994-01-01

    The FC-1D was designed as an advanced solution for a low cost commercial transport meeting or exceeding all of the 1993/1994 AIAA/Lockheed request for proposal requirements. The driving philosophy behind the design of the FC-1D was the reduction of airline direct operating costs. Every effort was made during the design process to have the customer in mind. The Flying Circus Commercial Aviation Group targeted reductions in drag, fuel consumption, manufacturing costs, and maintenance costs. Flying Circus emphasized cost reduction throughout the entire design program. Drag reduction was achieved by implementation of the aft nacelle wing configuration to reduce cruise drag and increase cruise speeds. To reduce induced drag, rather than increasing the wing span of the FC-1D, spiroids were included in the efficient wing design. Profile and friction drag are reduced by using riblets in place of paint around the fuselage and empennage of the FC-1D. Choosing a single aisle configuration enabled the Flying Circus to optimize the fuselage diameter. Thus, reducing fuselage drag while gaining high structural efficiency. To further reduce fuel consumption a weight reduction program was conducted through the use of composite materials. An additional quality of the FC-1D is its design for low cost manufacturing and assembly. As a result of this design attribute, the FC-1D will have fewer parts which reduces weight as well as maintenance and assembly costs. The FC-1D is affordable and effective, the apex of commercial transport design.

  6. [THE MODEL OF NUCLEOSOME STRUCTURE BASED ON THE LOCAL ROTATION OF THE NUCLEOHISTONE CHAIN, WHICH INDUCES ITS FOLDING].

    PubMed

    Priyatkina, T N

    2015-01-01

    An alternative model to the "double turn of DNA on the histone core" approach is forwarded based on the biochemical, cytological, and crystallographic data on the structural organization of the chromatin units--nucleosomes. The model assumes that the initial structure is a linear nucleohistone cord with a repeating symmetrical histone sequence. The compact (core) particle (a minimal nucleosome) is forming upon a stepwise rotation of DNA (kinks) at the centre and at two symmetrical sites into each repeating fragment stemming from the electrostatic binding of the lysine ε-NH2-groups with the followed one by one phosphates of the sugar-phosphate chain. As a result, we have a rhomboid structure composed of two counter-symmetrical DNA folds stabilized by histone-histone interactions. Based on disposable data, the histone sequence along nucleosome DNA is deduced. The following characteristics of the sequence are considered: continuity, non-overlapping, versatility, and dyadic symmetry in dispose of two every kind histone molecules and the sequence on the whole. The model is in agreement with a topology of nucleosome DNA, as well as the pattern of DNA-histone and histone-histone interactions in chromatin.

  7. All-electron and pseudo-potential studies of structural and electronic properties of Si chains and nanowires

    NASA Astrophysics Data System (ADS)

    Li, Jun; Williamson, Andrew

    2005-03-01

    Recent experimentsootnotetextY. Wu, et.al., Nature 430, 61 (2004); and references therein invoke Si nanowires as promising materials for nanoscale electronic and optical devices. We carried out electronic structure calculations of silicon chains and nanowires, by using both the full-potential linearized augmented plane wave (FLAPW) methodootnotetextE.Wimmer, H.Krakauer, M.Weinert, AJ Freeman, PRB 24, 864 (1981) and the pseudopotential plane wave method. We studied two sets of H-terminated one nanometer silicon wires, one oriented along (001) and the other along(111); both show direct band gaps, with the (111) oriented wires showing a smaller gap (˜2.1 eV) than (001) (˜2.5 eV). This trend differs from that reported in the literature ootnotetextF. Buda, et.al., PRL 69, 1272 (1992); A. M. Saitta, et.al., PRB 53, 1446 (1996), but it is the same in both our all-electron and well converged pseudopotential calculations. We also found that structural relaxations induce different effects on the band structure of differently oriented wires; the band gap change is nearly 0.2 eV between the ideal and relaxed models for (001) while it is negligible for (111) wires.

  8. Comparative Study on Sequence-Structure-Function Relationship of the Human Short-chain Dehydrogenases/Reductases Protein Family.

    PubMed

    Tang, Nu Thi Ngoc; Le, Ly

    2014-01-01

    Human short-chain dehydrogenases/reductases (SDRs) protein family has been the subject of recent studies for its critical role in human metabolism. Studies also found that single nucleotide polymorphisms of the SDR protein family were responsible for a variety of genetic diseases, including type II diabetes. This study reports the effect of sequence variation on the structural and functional integrities of human SDR protein family using phylogenetics and correlated mutation analysis tools. Our results indicated that (i) tyrosine, serine, and lysine are signature protein residues that have direct contribution to the structural and functional stabilities of the SDR protein family, (ii) subgroups of SDR protein family have their own signature protein combination that represent their unique functionality, and (iii) mutations of the human SDR protein family showed high correlation in terms of evolutionary history. In combination, the results inferred that over evolutionary history, the SDR protein family was able to diverge itself in order to adapt with the changes in human nutritional demands. Our study reveals understanding of structural and functional scaffolds of specific SDR subgroups that may facilitate the design of specific inhibitor.

  9. Structural