Unraveling metamaterial properties in zigzag-base folded sheets.

PubMed

Eidini, Maryam; Paulino, Glaucio H

2015-09-01

Creating complex spatial objects from a flat sheet of material using origami folding techniques has attracted attention in science and engineering. In the present work, we use the geometric properties of partially folded zigzag strips to better describe the kinematics of known zigzag/herringbone-base folded sheet metamaterials such as Miura-ori. Inspired by the kinematics of a one-degree of freedom zigzag strip, we introduce a class of cellular folded mechanical metamaterials comprising different scales of zigzag strips. This class of patterns combines origami folding techniques with kirigami. Using analytical and numerical models, we study the key mechanical properties of the folded materials. We show that our class of patterns, by expanding on the design space of Miura-ori, is appropriate for a wide range of applications from mechanical metamaterials to deployable structures at small and large scales. We further show that, depending on the geometry, these materials exhibit either negative or positive in-plane Poisson's ratios. By introducing a class of zigzag-base materials in the current study, we unify the concept of in-plane Poisson's ratio for similar materials in the literature and extend it to the class of zigzag-base folded sheet materials.

A Two-Dimensional 'Zigzag' Silica Polymorph on a Metal Support.

PubMed

Kuhness, David; Yang, Hyun Jin; Klemm, Hagen W; Prieto, Mauricio; Peschel, Gina; Fuhrich, Alexander; Menzel, Dietrich; Schmidt, Thomas; Yu, Xin; Shaikhutdinov, Shamil; Lewandowski, Adrian; Heyde, Markus; Kelemen, Anna; Włodarczyk, Radosław; Usvyat, Denis; Schütz, Martin; Sauer, Joachim; Freund, Hans-Joachim

2018-05-16

We present a new polymorph of the two-dimensional (2D) silica film with a characteristic 'zigzag' line structure and a rectangular unit cell which forms on a Ru(0001) metal substrate. This new silica polymorph may allow for important insights into growth modes and transformations of 2D silica films as a model system for the study of glass transitions. Based on scanning tunneling microscopy, low energy electron diffraction, infrared reflection absorption spectroscopy, and X-ray photoelectron spectroscopy measurements on the one hand, and density functional theory calculations on the other, a structural model for the 'zigzag' polymorph is proposed. In comparison to established monolayer and bilayer silica, this 'zigzag' structure system has intermediate characteristics in terms of coupling to the substrate and stoichiometry. The silica 'zigzag' phase is transformed upon reoxidation at higher annealing temperature into a SiO 2 silica bilayer film which is chemically decoupled from the substrate.

Spin-polarized currents generated by magnetic Fe atomic chains.

PubMed

Lin, Zheng-Zhe; Chen, Xi

2014-06-13

Fe-based devices are widely used in spintronics because of high spin-polarization and magnetism. In this work, freestanding Fe atomic chains, the thinnest wires, were used to generate spin-polarized currents due to the spin-polarized energy bands. By ab initio calculations, the zigzag structure was found to be more stable than the wide-angle zigzag structure and had a higher ratio of spin-up and spin-down currents. By our theoretical prediction, Fe atomic chains have a sufficiently long thermal lifetime only at T ≦̸ 150 K, while C atomic chains are very stable even at T = 1000 K. This means that the spintronic devices based on Fe chains could work only at low temperatures. A system constructed by a short Fe chain sandwiched between two graphene electrodes could be used as a spin-polarized current generator, while a C chain could not be used in this way. The present work may be instructive and meaningful to further practical applications based on recent technical developments on the preparation of metal atomic chains (Proc. Natl. Acad. Sci. USA 107 9055 (2010)).

Optimization of the nanotwin-induced zigzag surface of copper by electromigration

NASA Astrophysics Data System (ADS)

Chen, Hsin-Ping; Huang, Chun-Wei; Wang, Chun-Wen; Wu, Wen-Wei; Liao, Chien-Neng; Chen, Lih-Juann; Tu, King-Ning

2016-01-01

By adding nanotwins to Cu, the surface electromigration (EM) slows down. The atomic mobility of the surface step-edges is retarded by the triple points where a twin meets a free surface to form a zigzag-type surface. We observed that EM can alter the zigzag surface structure to optimize the reduction of EM, according to Le Chatelier's principle. Statistically, the optimal alternation is to change an arbitrary (111)/(hkl) zigzag pair to a pair having a very low index (hkl) plane, especially the (200) plane. Using in situ ultrahigh vacuum and high-resolution transmission electron microscopy, we examined the effects of different zigzag surfaces on the rate of EM. The calculated rate of surface EM can be decreased by a factor of ten.By adding nanotwins to Cu, the surface electromigration (EM) slows down. The atomic mobility of the surface step-edges is retarded by the triple points where a twin meets a free surface to form a zigzag-type surface. We observed that EM can alter the zigzag surface structure to optimize the reduction of EM, according to Le Chatelier's principle. Statistically, the optimal alternation is to change an arbitrary (111)/(hkl) zigzag pair to a pair having a very low index (hkl) plane, especially the (200) plane. Using in situ ultrahigh vacuum and high-resolution transmission electron microscopy, we examined the effects of different zigzag surfaces on the rate of EM. The calculated rate of surface EM can be decreased by a factor of ten. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr05418d

First principles study on the electronic structures and transport properties of armchair/zigzag edge hybridized graphene nanoribbons

NASA Astrophysics Data System (ADS)

Yi, Xiuying; Long, Mengqiu; Liu, Anhua; Li, Mingjun; Xu, Hui

2018-05-01

Graphene nanoribbons (GNRs) can be mainly classified into armchair graphene nanoribbons (aGNRs) and zigzag graphene nanoribbons (zGNRs) by different edge chiral directions. In this work, by introducing Stone-Wales defects on the edges of the V-shaped aGNRs, we propose a kind of armchair/zigzag edge hybridized GNRs (a/zHGNRs) and using the density functional theory and the nonequilibrium Green's function method, the band structures and electronic transport properties of the a/zHGNRs have been calculated. Our results show that an indirect bandgap appears in the band structures of the a/zHGNRs, which is very different from the direct bandgap of aGNRs and gapless of zGNRs. We also find that the valance band is mainly derived from the armchair partial atoms on the hybridized edge, while the conduction band comes mainly from the zigzag partial atoms of the hybridized edge. Meanwhile, the bandgap also oscillates with a period of three when the ribbon width increases. In addition, our quantum transport calculations show that there is a remarkable transition between the semiconductor and the metal with different ribbon widths in the a/zHGNRs devices, and the corresponding physical analysis is given.

Band-selective filter in a zigzag graphene nanoribbon.

PubMed

Nakabayashi, Jun; Yamamoto, Daisuke; Kurihara, Susumu

2009-02-13

Electric transport of a zigzag graphene nanoribbon through a steplike potential and a barrier potential is investigated by using the recursive Green's function method. In the case of the steplike potential, we demonstrate numerically that scattering processes obey a selection rule for the band indices when the number of zigzag chains is even; the electrons belonging to the "even" ("odd") bands are scattered only into the even (odd) bands so that the parity of the wave functions is preserved. In the case of the barrier potential, by tuning the barrier height to be an appropriate value, we show that it can work as the "band-selective filter", which transmits electrons selectively with respect to the indices of the bands to which the incident electrons belong. Finally, we suggest that this selection rule can be observed in the conductance by applying two barrier potentials.

A Refined Zigzag Beam Theory for Composite and Sandwich Beams

NASA Technical Reports Server (NTRS)

Tessler, Alexander; Sciuva, Marco Di; Gherlone, Marco

2009-01-01

A new refined theory for laminated composite and sandwich beams that contains the kinematics of the Timoshenko Beam Theory as a proper baseline subset is presented. This variationally consistent theory is derived from the virtual work principle and employs a novel piecewise linear zigzag function that provides a more realistic representation of the deformation states of transverse-shear flexible beams than other similar theories. This new zigzag function is unique in that it vanishes at the top and bottom bounding surfaces of a beam. The formulation does not enforce continuity of the transverse shear stress across the beam s cross-section, yet is robust. Two major shortcomings that are inherent in the previous zigzag theories, shear-force inconsistency and difficulties in simulating clamped boundary conditions, and that have greatly limited the utility of these previous theories are discussed in detail. An approach that has successfully resolved these shortcomings is presented herein. Exact solutions for simply supported and cantilevered beams subjected to static loads are derived and the improved modelling capability of the new zigzag beam theory is demonstrated. In particular, extensive results for thick beams with highly heterogeneous material lay-ups are discussed and compared with corresponding results obtained from elasticity solutions, two other zigzag theories, and high-fidelity finite element analyses. Comparisons with the baseline Timoshenko Beam Theory are also presented. The comparisons clearly show the improved accuracy of the new, refined zigzag theory presented herein over similar existing theories. This new theory can be readily extended to plate and shell structures, and should be useful for obtaining relatively low-cost, accurate estimates of structural response needed to design an important class of high-performance aerospace structures.

Evidence for SrHo2O4 and SrDy2O4 as model J1-J2 zigzag chain materials

NASA Astrophysics Data System (ADS)

Fennell, A.; Pomjakushin, V. Y.; Uldry, A.; Delley, B.; Prévost, B.; Désilets-Benoit, A.; Bianchi, A. D.; Bewley, R. I.; Hansen, B. R.; Klimczuk, T.; Cava, R. J.; Kenzelmann, M.

2014-06-01

Neutron diffraction and inelastic spectroscopy is used to characterize the magnetic Hamiltonian of SrHo2O4 and SrDy2O4. Through a detailed computation of the crystal-field levels we find site-dependent anisotropic single-ion magnetism in both materials, and diffraction measurements show the presence of strong one-dimensional spin correlations. Our measurements indicate that competing interactions of the zigzag chain, combined with frustrated interchain interactions, play a crucial role in stabilizing spin-liquid type correlations in this series.

Fabricating and Controlling Silicon Zigzag Nanowires by Diffusion-Controlled Metal-Assisted Chemical Etching Method.

PubMed

Chen, Yun; Zhang, Cheng; Li, Liyi; Tuan, Chia-Chi; Wu, Fan; Chen, Xin; Gao, Jian; Ding, Yong; Wong, Ching-Ping

2017-07-12

Silicon (Si) zigzag nanowires (NWs) have a great potential in many applications because of its high surface/volume ratio. However, fabricating Si zigzag NWs has been challenging. In this work, a diffusion-controlled metal-assisted chemical etching method is developed to fabricate Si zigzag NWs. By tailoring the composition of etchant to change its diffusivity, etching direction, and etching time, various zigzag NWs can be easily fabricated. In addition, it is also found that a critical length of NW (>1 μm) is needed to form zigzag nanowires. Also, the amplitude of zigzag increases as the location approaches the center of the substrate and the length of zigzag nanowire increases. It is also demonstrated that such zigzag NWs can help the silicon substrate for self-cleaning and antireflection. This method may provide a feasible and economical way to fabricate zigzag NWs and novel structures for broad applications.

Effect of edge defects on band structure of zigzag graphene nanoribbons

NASA Astrophysics Data System (ADS)

Wadhwa, Payal; Kumar, Shailesh; Dhilip Kumar, T. J.; Shukla, Alok; Kumar, Rakesh

2018-04-01

In this article, we report band structure studies of zigzag graphene nanoribbons (ZGNRs) on introducing defects (sp3 hybridized carbon atoms) in different concentrations at edges by varying the ratio of sp3 to sp2 hybridized carbon atoms. On the basis of theoretical analyses, bandgap values of ZGNRs are found to be strongly dependent on the relative arrangement of sp3 to sp2 hybridized carbon atoms at the edges for a defect concentration; so the findings would greatly help in understanding the bandgap of nanoribbons for their electronic applications.

Variable Asymmetric Chains in Transition Metal Oxyfluorides: Structure-Second-Harmonic-Generation Property Relationships.

PubMed

Ahmed, Belal; Jo, Hongil; Oh, Seung-Jin; Ok, Kang Min

2018-05-15

Four novel transition metal oxyfluorides, [Zn(pz) 3 ][MoO 2 F 4 ]·0.1H 2 O (1), [Zn(pz) 2 F 2 ][Zn(pz) 3 ] 2 [WO 2 F 4 ] 2 (2), [Cd(pz) 4 ][Cd(pz) 4 (H 2 O)][MoO 2 F 4 ] 2 ·0.625H 2 O (3), and [Zn(mpz) 3 ] 2 [MoO 2 F 4 ] 2 (4) (pz = pyrazole; mpz = 3-methyl pyrazole) have been synthesized. Compounds 1 and 4 contain helical chains. Compound 2 accommodates zigzag chains, and compound 3 has quasi-one-dimensional linear chains. The variable chain structures are found to be attributable to the different structure-directing anionic groups and hydrogen bonding interactions. Compound 4 crystallized in the noncentrosymmetric (NCS) polar space group, Pna2 1 , is nonphase-matchable (Type I), and reveals a moderate second-harmonic-generation (SHG) efficiency (10 × α-SiO 2 ). The observed SHG efficiency of compound 4 is due to the small net polarization occurring from the arrangement of ZnN 3 F 2 trigonal bipyramids. Spectroscopic and thermal characterizations along with calculations for the title materials are reported.

Atomistic full-quantum transport model for zigzag graphene nanoribbon-based structures: Complex energy-band method

NASA Astrophysics Data System (ADS)

Chen, Chun-Nan; Luo, Win-Jet; Shyu, Feng-Lin; Chung, Hsien-Ching; Lin, Chiun-Yan; Wu, Jhao-Ying

2018-01-01

Using a non-equilibrium Green’s function framework in combination with the complex energy-band method, an atomistic full-quantum model for solving quantum transport problems for a zigzag-edge graphene nanoribbon (zGNR) structure is proposed. For transport calculations, the mathematical expressions from the theory for zGNR-based device structures are derived in detail. The transport properties of zGNR-based devices are calculated and studied in detail using the proposed method.

Electronic transport across a junction between armchair graphene nanotube and zigzag nanoribbon. Transmission in an armchair nanotube without a zigzag half-line of dimers

NASA Astrophysics Data System (ADS)

Sharma, Basant Lal

2018-05-01

Based on the well known nearest-neighbor tight-binding approximation for graphene, an exact expression for the electronic conductance across a zigzag nanoribbon/armchair nanotube junction is presented for non-interacting electrons. The junction results from the removal of a half-row of zigzag dimers in armchair nanotube, or equivalently by partial rolling of zigzag nanoribbon and insertion of a half-row of zigzag dimers in between. From the former point of view, a discrete form of Dirichlet condition is imposed on a zigzag half-line of dimers assuming the vanishing of wave function outside the physical structure. A closed form expression is provided for the reflection and transmission moduli for the outgoing wave modes for each given electronic wave mode incident from either side of the junction. It is demonstrated that such a contact junction between the nanotube and nanoribbon exhibits negligible backscattering, and the transmission has been found to be nearly ballistic. In contrast to the previously reported studies for partially unzipped carbon nanotubes (CNTs), using the same tight binding model, it is found that due to the "defect" there is certain amount of mixing between the electronic wave modes with even and odd reflection symmetries. But the junction remains a perfect valley filter for CNTs at certain energy ranges. Applications aside from the electronic case, include wave propagation in quasi-one-dimensional honeycomb structures of graphene-like constitution. The paper includes several numerical calculations, analytical derivations, and graphical results, which complement the provision of succinct closed form expressions.

Refined Zigzag Theory for Laminated Composite and Sandwich Plates

NASA Technical Reports Server (NTRS)

Tessler, Alexander; DiSciuva, Marco; Gherlone, Marco

2009-01-01

A refined zigzag theory is presented for laminated-composite and sandwich plates that includes the kinematics of first-order shear deformation theory as its baseline. The theory is variationally consistent and is derived from the virtual work principle. Novel piecewise-linear zigzag functions that provide a more realistic representation of the deformation states of transverse-shear-flexible plates than other similar theories are used. The formulation does not enforce full continuity of the transverse shear stresses across the plate s thickness, yet is robust. Transverse-shear correction factors are not required to yield accurate results. The theory is devoid of the shortcomings inherent in the previous zigzag theories including shear-force inconsistency and difficulties in simulating clamped boundary conditions, which have greatly limited the accuracy of these theories. This new theory requires only C(sup 0)-continuous kinematic approximations and is perfectly suited for developing computationally efficient finite elements. The theory should be useful for obtaining relatively efficient, accurate estimates of structural response needed to design high-performance load-bearing aerospace structures.

Improved Photo-Detection Using Zigzag TiO2 Nanostructures as an Active Medium.

PubMed

Tiwari, A K; Mondal, A; Mahajan, B K; Choudhuri, B; Goswami, T; Sarkar, M B; Chakrabartty, S; Ngangbam, C; Saha, S

2015-07-01

Zigzag TiO2 nanostructures were fabricated using oblique angle deposition technique. The field emission gun-scanning electron microscope (FEG-SEM) image shows that the TiO2 zigzag nanostructures were ~500 nm in length. Averagely two times enhanced UV-Vis absorption was recorded for zigzag structure compared to perpendicular TiO2 nanowires. The main band transition was observed at ~3.4 eV. The zigzag TiO2 exhibited high turn on voltage (+11 V) than that of nanowire (+2 V) detector under dark which were reduced to +0.2 V and +1.0 V under white light illumination, respectively. A maximum ~6 fold photo-responsivity was observed for the zigzag TiO2 compared with nanowire device at + 1.0 V applied potential. The maximum photo-responsivity of 0.36 A/W at 370 nm was measured for the zigzag TiO2 detector. The TiO2 zigzag detector showed slow response with rise time of 10.2 s and fall time of 10.3 s respectively. The UV (370 nm) to visible (450 nm) wavelength rejection ratio of photo-responsivity was recorded ~4 times for the detector.

A GEM readout with radial zigzag strips and linear charge-sharing response

DOE PAGES

Zhang, Aiwu; Hohlmann, Marcus; Azmoun, Babak; ...

2018-01-10

Here, we study the position sensitivity of radial zigzag strips intended to read out large GEM detectors for tracking at future experiments. Zigzag strips can cover a readout area with fewer strips than regular straight strips while maintaining good spatial resolution. Consequently, they can reduce the number of required electronic channels and related cost for large-area GEM detector systems. A non-linear relation between incident particle position and hit position measured from charge sharing among zigzag strips was observed in a previous study. We significantly reduce this non-linearity by improving the interleaving of adjacent physical zigzag strips. Zigzag readout structures aremore » implemented on PCBs and on a flexible foil and are tested using a 10 cm × 10 cm triple-GEM detector scanned with a strongly collimated X-ray gun on a 2D motorized stage. Lastly, angular resolutions of 60–84 μrad are achieved with a 1.37 mrad angular strip pitch at a radius of 784 mm. On a linear scale this corresponds to resolutions below 100 μm.« less

A GEM readout with radial zigzag strips and linear charge-sharing response

NASA Astrophysics Data System (ADS)

Zhang, Aiwu; Hohlmann, Marcus; Azmoun, Babak; Purschke, Martin L.; Woody, Craig

2018-04-01

We study the position sensitivity of radial zigzag strips intended to read out large GEM detectors for tracking at future experiments. Zigzag strips can cover a readout area with fewer strips than regular straight strips while maintaining good spatial resolution. Consequently, they can reduce the number of required electronic channels and related cost for large-area GEM detector systems. A non-linear relation between incident particle position and hit position measured from charge sharing among zigzag strips was observed in a previous study. We significantly reduce this non-linearity by improving the interleaving of adjacent physical zigzag strips. Zigzag readout structures are implemented on PCBs and on a flexible foil and are tested using a 10 cm × 10 cm triple-GEM detector scanned with a strongly collimated X-ray gun on a 2D motorized stage. Angular resolutions of 60-84 μrad are achieved with a 1.37 mrad angular strip pitch at a radius of 784 mm. On a linear scale this corresponds to resolutions below 100 μm.

Patterning monolayer graphene with zigzag edges on hexagonal boron nitride by anisotropic etching

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

Wang, Guole; Wu, Shuang; Zhang, Tingting

2016-08-01

Graphene nanostructures are potential building blocks for nanoelectronic and spintronic devices. However, the production of monolayer graphene nanostructures with well-defined zigzag edges remains a challenge. In this paper, we report the patterning of monolayer graphene nanostructures with zigzag edges on hexagonal boron nitride (h-BN) substrates by an anisotropic etching technique. We found that hydrogen plasma etching of monolayer graphene on h-BN is highly anisotropic due to the inert and ultra-flat nature of the h-BN surface, resulting in zigzag edge formation. The as-fabricated zigzag-edged monolayer graphene nanoribbons (Z-GNRs) with widths below 30 nm show high carrier mobility and width-dependent energy gaps atmore » liquid helium temperature. These high quality Z-GNRs are thus ideal structures for exploring their valleytronic or spintronic properties.« less

Electronic structure and magnetic properties of zigzag blue phosphorene nanoribbons

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

Hu, Tao; Hong, Jisang, E-mail: hongj@pknu.ac.kr

2015-08-07

We investigated the electronic structure and magnetism of zigzag blue phosphorene nanoribbons (ZBPNRs) using first principles density functional theory calculations by changing the widths of ZBPNRs from 1.5 to 5 nm. In addition, the effect of H and O passivation was explored as well. The ZBPNRs displayed intra-edge antiferromagnetic ground state with a semiconducting band gap of ∼0.35 eV; and this was insensitive to the edge structure relaxation effect. However, the edge magnetism of ZBPNRs disappeared with H-passivation. Moreover, the band gap of H-passivated ZBPNRs was greatly enhanced because the calculated band gap was ∼1.77 eV, and this was almost the same asmore » that of two-dimensional blue phosphorene layer. For O-passivated ZBPNRs, we also found an intra-edge antiferromagnetic state. Besides, both unpassivated and O-passivated ZBPNRs preserved almost the same band gap. We predict that the electronic band structure and magnetic properties can be controlled by means of passivation. Moreover, the edge magnetism can be also modulated by the strain. Nonetheless, the intrinsic physical properties are size independent. This feature can be an advantage for device applications because it may not be necessary to precisely control the width of the nanoribbon.« less

Electroosmotic flow mixing in zigzag microchannels.

PubMed

Chen, Jia-Kun; Yang, Ruey-Jen

2007-03-01

In this study we performed numerical and experimental investigations into the mixing of EOFs in zigzag microchannels with two different corner geometries, namely sharp corners and flat corners. In the zigzag microchannel with sharp corners, the flow travels more rapidly near the inner wall of the corner than near the outer wall as a result of the higher electric potential drop. The resulting velocity gradient induces a racetrack effect, which enhances diffusion within the fluid and hence improves the mixing performance. The simulation results reveal that the mixing index is approximately 88.83%. However, the sharp-corner geometry causes residual liquid or bubbles to become trapped in the channel at the point where the flow is almost stationary, when the channel is in the process of cleaning. Accordingly, a zigzag microchannel with flat-corner geometry is developed. The flat-corner geometry forms a convergent-divergent type nozzle which not only enhances the mixing performance in the channel, but also prevents the accumulation of residual liquid or bubbles. Scaling analysis reveals that this corner geometry leads to an effective increase in the mixing length. The experimental results reveal that the mixing index is increased to 94.30% in the flat-corner zigzag channel. Hence, the results demonstrate that the mixing index of the flat-corner zigzag channel is better than that of the conventional sharp-corner microchannel. Finally, the results of Taguchi analysis indicate that the attainable mixing index is determined primarily by the number of corners in the microchannel and by the flow passing height at each corner.

Refinement of Timoshenko Beam Theory for Composite and Sandwich Beams Using Zigzag Kinematics

NASA Technical Reports Server (NTRS)

Tessler, Alexander; DiSciuva, Marco; Gherlone, Marco

2007-01-01

A new refined theory for laminated-composite and sandwich beams that contains the kinematics of the Timoshenko Beam Theory as a proper baseline subset is presented. This variationally consistent theory is derived from the virtual work principle and employs a novel piecewise linear zigzag function that provides a more realistic representation of the deformation states of transverse shear flexible beams than other similar theories. This new zigzag function is unique in that it vanishes at the top and bottom bounding surfaces of a beam. The formulation does not enforce continuity of the transverse shear stress across the beam s cross-section, yet is robust. Two major shortcomings that are inherent in the previous zigzag theories, shear-force inconsistency and difficulties in simulating clamped boundary conditions, and that have greatly limited the utility of these previous theories are discussed in detail. An approach that has successfully resolved these shortcomings is presented herein. This new theory can be readily extended to plate and shell structures, and should be useful for obtaining accurate estimates of structural response of laminated composites.

Stretching of short monatomic gold chains-some model calculations

NASA Astrophysics Data System (ADS)

Sumali, Priyanka, Verma, Veena; Dharamvir, Keya

2012-06-01

The Mechanical properties of zig-zag monatomic gold chains containing 5 and 7 atoms were studied using the Siesta Code (SC), which works within the framework of DFT formalism and Gupta Potential (GP), which is an effective atom-atom potential. The zig-zag chains were stretched by keeping the end atoms fixed while rest of the atoms were relaxed till minimum energy is obtained. Energy, Force and Young's Modulus found using GP and SC were plotted as functions of total length. It is found that the breaking force in case of GP is of order of 1.6nN while for SIESTA is of the order of 2.9nN for both the chains.

Catalyst-free growth of Al-doped SnO2 zigzag-nanobelts for low ppm detection of organic vapours

NASA Astrophysics Data System (ADS)

Sinha, Sudip Kumar; Ghosh, Saptarshi

2016-10-01

In this effort, we report on development of specific sensors dedicated for detection of two of these volatiles, namely ethanol and acetone, below the prescribed statutory limits. Single crystalline Al-doped SnO2 zigzag nanobelt structures were deposited on Si substrate by a catalyst-free thermal evaporation method. The Al-doped SnO2 zigzag nanostructures exhibit high sensitivity and repeatability together with coveted features like fast response and excellent stability. Structural attributes involving the crystal quality and morphology of Al-doped SnO2 zigzag nanobelts were analyzed using X-ray photoelectron spectroscopy (XPS), scanning electron microscopy and transmission electron microscopy. The microscopic images revealed formation of randomly oriented 'zigzag-like' nanobelts with characteristic width between 60 nm and 200 nm and length of 50-300 μm. The Al-doping was observed to have a discerning effect in enhancing the sensitivity in comparison to the pristine nanowires by creating excess oxygen vacancies in the crystal lattice, confirmed through XPS and PL spectra.

Negative differential resistance and rectification effects in zigzag graphene nanoribbon heterojunctions: Induced by edge oxidation and symmetry concept

NASA Astrophysics Data System (ADS)

Nazirfakhr, Maryam; Shahhoseini, Ali

2018-03-01

By applying non-equilibrium Green's functions (NEGF) in combination with tight-binding (TB) model, we investigate and compare the electronic transport properties of H-terminated zigzag graphene nanoribbon (H/ZGNR) and O-terminated ZGNR/H-terminated ZGNR (O/ZGNR-H/ZGNR) heterostructure under finite bias. Moreover, the effect of width and symmetry on the electronic transport properties of both models is also considered. The results reveal that asymmetric H/ZGNRs have linear I-V characteristics in whole bias range, but symmetric H-ZGNRs show negative differential resistance (NDR) behavior which is inversely proportional to the width of the H/ZGNR. It is also shown that the I-V characteristic of O/ZGNR-H/ZGNR heterostructure shows a rectification effect, whether the geometrical structure is symmetric or asymmetric. The fewer the number of zigzag chains, the bigger the rectification ratio. It should be mentioned that, the rectification ratios of symmetric heterostructures are much bigger than asymmetric one. Transmission spectrum, density of states (DOS), molecular projected self-consistent Hamiltonian (MPSH) and molecular eigenstates are analyzed subsequently to understand the electronic transport properties of these ZGNR devices. Our findings could be used in developing nanoscale rectifiers and NDR devices.

Crystal structures and magnetic properties of chiral heterobimetallic chains based on the dicyanoruthenate building block.

PubMed

Ru, Jing; Gao, Feng; Yao, Min-Xia; Wu, Tao; Zuo, Jing-Lin

2014-12-28

By the reaction of chiral Mn(III) Schiff-base complexes with the dicyanoruthenate building block, [Ru(salen)(CN)2](-) (salen(2-) = N,N'-ethylenebis(salicylideneimine) dianion), two couples of enantiomerically pure chiral cyano-bridged heterobimetallic one-dimensional (1D) chain complexes, [Mn((R,R)-salcy)Ru(salen)(CN)2]n (1-(RR)) and [Mn((S,S)-salcy)Ru(salen)(CN)2]n (1-(SS)) (Salcy = N,N'-(1,2-cyclohexanediylethylene)bis(salicylideneiminato) dianion), [Mn((R,R)-salphen)Ru(salen)(CN)2]n (2-(RR)) and [Mn((S,S)-salphen)Ru(salen)(CN)2]n (2-(SS)) (salphen = N,N'-(1,2-diphenylethylene)bis(salicylideneiminato) dianion), were synthesized and structurally characterized. Circular dichroism (CD) and vibrational circular dichroism (VCD) spectra confirm the enantiomeric nature of the optically active complexes. Structural analyses reveal the formation of neutral cyano-bridged zigzag single chains in 1-(RR) and 1-(SS), and double chains in 2-(RR) and 2-(SS). Magnetic studies show that antiferromagnetic coupling is operative between Ru(III) and Mn(III) centers bridged by cyanide. Compounds 1-(RR) and 1-(SS) show metamagnetic behavior with a critical field of about 7.2 kOe at 1.9 K resulting from the intermolecular π∙∙∙π interactions. Additionally, magnetostructural correlation for some typical cyano-bridged heterobimetallic Ru(III)-Mn(III) compounds is discussed.

Solution‐crystallization and related phenomena in 9,9‐dialkyl‐fluorene polymers. II. Influence of side‐chain structure

PubMed Central

Perevedentsev, Aleksandr; Stavrinou, Paul N.; Smith, Paul

2015-01-01

ABSTRACT Solution‐crystallization is studied for two polyfluorene polymers possessing different side‐chain structures. Thermal analysis and temperature‐dependent optical spectroscopy are used to clarify the nature of the crystallization process, while X‐ray diffraction and scanning electron microscopy reveal important differences in the resulting microstructures. It is shown that the planar‐zigzag chain conformation termed the β‐phase, which is observed for certain linear‐side‐chain polyfluorenes, is necessary for the formation of so‐called polymer‐solvent compounds for these polymers. Introduction of alternating fluorene repeat units with branched side‐chains prevents formation of the β‐phase conformation and results in non‐solvated, i.e. melt‐crystallization‐type, polymer crystals. Unlike non‐solvated polymer crystals, for which the chain conformation is stabilized by its incorporation into a crystalline lattice, the β‐phase conformation is stabilized by complexation with solvent molecules and, therefore, its formation does not require specific inter‐chain interactions. The presented results clarify the fundamental differences between the β‐phase and other conformational/crystalline forms of polyfluorenes. © 2015 The Authors. Journal of Polymer Science Part B: Polymer Physics published by Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015, 53, 1492–1506 PMID:27546983

Photo-oxidative doping in π-conjugated zig-zag chain of carbon atoms with sulfur-functional group

NASA Astrophysics Data System (ADS)

Ikeura-Sekiguchi, Hiromi; Sekiguchi, Tetsuhiro

2017-12-01

Photo-oxidative doping processes were studied for the trans-polyacetylene backbone with the -SCH3 side group as a chemically representative of the precisely controlled S-functionalized zig-zag graphene nanoribbon edge. Sulfur K-edge X-ray absorption near edge structure (XANES) spectroscopy indicates that photochemical reaction of S-CH3 with atmospheric O2 forms selectively oxidized products such as -S(O)CH3 and -SO3- bound to the polyacetylene (PA) backbone. Using the correlation between the oxidation states of sulfur and the XANES peak positions, the partial charge distribution of CH3Sδ+-PAδ- has been estimated. Such positively charged sulfur atoms can attract higher electronegative oxygen atoms and expect to enhance the photooxidization capabilities. The formation of the -SO3- side group is evidently responsible for hole doping into the PA backbone. The results can provide some strategy for area-selective and controllable doping processes of atomic-scale molecular systems with the assistance of UV light.

New understanding of photocatalytic properties of zigzag and armchair g-C3N4 nanotubes from electronic structures and carrier effective mass

NASA Astrophysics Data System (ADS)

Liu, Jianjun; Cheng, Bei

2018-02-01

Low-dimensional g-C3N4 nanostructures own distinct electronic structure and remarkable photocatalytic properties, hence their wide application in the photocatalysis field. However, the correlations of structures and photoinduced carrier migrations with the photocatalytic properties of g-C3N4 nanostructures remain unclear. In this study, the geometrical and electronic structures and the photocatalytic properties of zigzag (n, 0) and armchair (n, n) g-C3N4 nanotubes (n = 6, 9, 12) were systematically investigated using hybrid DFT. Results indicated that the differences in geometrical structures of g-C3N4 nanotubes changed the band gaps and effective mass of carriers. Accordingly, the photocatalytic properties of g-C3N4 nanotubes also changed. Notably, the change trends of band gaps and the effective mass of the electrons and holes were the opposite for zigzag (n, 0) and armchair (n, n) g-C3N4 nanotubes. The absolute band edge potential of (n, 0) and (n, n) g-C3N4 nanotubes can split water for hydrogen production. These theoretical results revealed the correlations of structures and carrier effective mass with the photocatalytic properties of g-C3N4 nanotubes, and provided significant guidance for designing low-dimensional g-C3N4 nanostructures.

Zigzag spin structure in layered honeycomb L i3N i2Sb O6 : A combined diffraction and antiferromagnetic resonance study

NASA Astrophysics Data System (ADS)

Kurbakov, A. I.; Korshunov, A. N.; Podchezertsev, S. Yu.; Malyshev, A. L.; Evstigneeva, M. A.; Damay, F.; Park, J.; Koo, C.; Klingeler, R.; Zvereva, E. A.; Nalbandyan, V. B.

2017-07-01

The magnetic structure of L i3N i2Sb O6 has been determined by low-temperature neutron diffraction, and the crystal structure has been refined by a combination of synchrotron and neutron powder diffraction. The monoclinic (C 2 /m ) symmetry, assigned previously to this pseudohexagonal layered structure, has been unambiguously proven by peak splitting in the synchrotron diffraction pattern. The structure is based on essentially hexagonal honeycomb-ordered N i2Sb O6 layers alternating with L i3 layers, all cations and anions being in an octahedral environment. The compound orders antiferromagnetically below TN=15 K , with the magnetic supercell being a 2 a ×2 b multiple of the crystal cell. The magnetic structure within the honeycomb layer consists of zigzag ferromagnetic spin chains coupled antiferromagnetically. The ordered magnetic moment amounts to 1.62 (2 ) μB/Ni , which is slightly lower than the full theoretical value. Upon cooling below TN, the spins tilt from the c axis, with a maximum tilting angle of 15 .6∘ at T =1.5 K . Our data imply non-negligible ferromagnetic interactions between the honeycomb layers. The observed antiferromagnetic resonance modes are in agreement with the two-sublattice model derived from the neutron data. Orthorhombic anisotropy shows up in zero-field splitting of Δ =198 ±4 and 218 ±4 GHz . Above TN, the electron spin resonance data imply short-range antiferromagnetic order up to about 80 K.

Au-induced deep groove nanowire structure on the Ge(001) surface: DFT calculations

NASA Astrophysics Data System (ADS)

Tsay, Shiow-Fon

2016-09-01

The atomic geometry, stability, and electronic properties of self-organized Au induced nanowires on the Ge(001) surface are investigated based on the density-functional theory in GGA and the stoichiometry of Au. A giant Ge zigzag chain structure is suggested for 0.75 ML Au coverage, which displays c(8 × 2) deep groove zigzag nanowire structure simulated STM images. The top layer Ge and Au atomic disorder introduces the chevron units into the zigzag nanowire structure STM image as per the experimental observations. The zigzag Ge nanowire exhibits a semi-metallic characteristic, and the electric transport occurs in between the Ge zigzag nanowire and the subsurface. The system exhibits obvious electronic correlations among the Ge nanowire, the nano-facet Au trimers and the deeper layer Ge atoms, that play an important role in the electronic structure. At surface Brillouin zone boundaries, an anisotropic two-dimensional upward parabolic surface-state band is consistent with the ARPES spectra reported by Nakatsuji et al. [Phys. Rev. B 80, 081406(R) (2009); Phys. Rev. B 84, 115411 (2011)]; this electronic structure is different from the quasi-one-dimensional energy trough reported by Schäfer et al. [Phys. Rev. Lett. 101, 236802 (2008); Phys. Rev. B 83, 121411(R) (2011)].

Capacity improvement of the carbon-based electrochemical capacitor by zigzag-edge introduced graphene

NASA Astrophysics Data System (ADS)

Tamura, Naoki; Tomai, Takaaki; Oka, Nobuto; Honma, Itaru

2018-01-01

The electrochemical properties of graphene edge has been attracted much attention. Especially, zigzag edge has high electrochemical activity because neutral radical exits on edge. However, due to a lack of efficient production method for zigzag graphene, the electrochemical properties of zigzag edge have not been experimentally demonstrated and the capacitance enhancement of carbonaceous materials in energy storage devices by the control in their edge states is still challenge. In this study, we fabricated zigzag-edge-rich graphene by a one-step method combining graphene exfoliation in supercritical fluid and anisotropic etching by catalytic nanoparticles. This efficient production of zigzag-edge-rich graphene allows us to investigate the electrochemical activity of zigzag edge. By cyclic voltammetry, we revealed the zigzag edge-introduced graphene exhibited unique redox reaction in aqueous acid solution. Moreover, by the calculation on the density function theory (DFT), this unique redox potential for zigzag edge-introduced graphene can be attributed to the proton-insertion/-extraction reactions at the zigzag edge. This finding indicates that the graphene edge modification can contribute to the further increase in the capacitance of the carbon-based electrochemical capacitor.

Bandgaps and directional properties of two-dimensional square beam-like zigzag lattices

NASA Astrophysics Data System (ADS)

Wang, Yan-Feng; Wang, Yue-Sheng; Zhang, Chuanzeng

2014-12-01

In this paper we propose four kinds of two-dimensional square beam-like zigzag lattice structures and study their bandgaps and directional propagation of elastic waves. The band structures are calculated by using the finite element method. Both the in-plane and out-of-plane waves are investigated simultaneously via the three-dimensional Euler beam elements. The mechanism of the bandgap generation is analyzed by studying the vibration modes at the bandgap edges. The effects of the geometry parameters of the xy- and z-zigzag lattices on the bandgaps are investigated and discussed. Multiple complete bandgaps are found owing to the separation of the degeneracy by introducing bending arms. The bandgaps are sensitive to the geometry parameters of the periodic systems. The deformed displacement fields of the harmonic responses of a finite lattice structure subjected to harmonic loads at different positions are illustrated to show the directional wave propagation. An extension of the proposed concept to the hexagonal lattices is also presented. The research work in this paper is relevant to the practical design of cellular structures with enhanced vibro-acoustics performance.

Frustrated quantum magnetism in the Kondo lattice on the zigzag ladder

NASA Astrophysics Data System (ADS)

Peschke, Matthias; Rausch, Roman; Potthoff, Michael

2018-03-01

The interplay between the Kondo effect, indirect magnetic interaction, and geometrical frustration is studied in the Kondo lattice on the one-dimensional zigzag ladder. Using the density-matrix renormalization group, the ground-state and various short- and long-range spin- and density-correlation functions are calculated for the model at half filling as a function of the antiferromagnetic Kondo interaction down to J =0.3 t , where t is the nearest-neighbor hopping on the zigzag ladder. Geometrical frustration is shown to lead to at least two critical points: Starting from the strong-J limit, where almost local Kondo screening dominates and where the system is a nonmagnetic Kondo insulator, antiferromagnetic correlations between nearest-neighbor and next-nearest-neighbor local spins become stronger and stronger, until at Jcdim≈0.89 t frustration is alleviated by a spontaneous breaking of translational symmetry and a corresponding transition to a dimerized state. This is characterized by antiferromagnetic correlations along the legs and by alternating antiferro- and ferromagnetic correlations on the rungs of the ladder. A mechanism of partial Kondo screening that has been suggested for the Kondo lattice on the two-dimensional triangular lattice is not realized in the one-dimensional case. Furthermore, within the symmetry-broken dimerized state, there is a magnetic transition to a 90∘ quantum spin spiral with quasi-long-range order at Jcmag≈0.84 t . The quantum-critical point is characterized by a closure of the spin gap (with decreasing J ) and a divergence of the spin-correlation length and of the spin-structure factor S (q ) at wave vector q =π /2 . This is opposed to the model on the one-dimensional bipartite chain, which is known to have a finite spin gap for all J >0 at half filling.

Quantum phase transitions in effective spin-ladder models for graphene zigzag nanoribbons

NASA Astrophysics Data System (ADS)

Koop, Cornelie; Wessel, Stefan

2017-10-01

We examine the magnetic correlations in quantum spin models that were derived recently as effective low-energy theories for electronic correlation effects on the edge states of graphene nanoribbons. For this purpose, we employ quantum Monte Carlo simulations to access the large-distance properties, accounting for quantum fluctuations beyond mean-field-theory approaches to edge magnetism. For certain chiral nanoribbons, antiferromagnetic interedge couplings were previously found to induce a gapped quantum disordered ground state of the effective spin model. We find that the extended nature of the intraedge couplings in the effective spin model for zigzag nanoribbons leads to a quantum phase transition at a large, finite value of the interedge coupling. This quantum critical point separates the quantum disordered region from a gapless phase of stable edge magnetism at weak intraedge coupling, which includes the ground states of spin-ladder models for wide zigzag nanoribbons. To study the quantum critical behavior, the effective spin model can be related to a model of two antiferromagnetically coupled Haldane-Shastry spin-half chains with long-ranged ferromagnetic intrachain couplings. The results for the critical exponents are compared also to several recent renormalization-group calculations for related long-ranged interacting quantum systems.

Synthesis and characterization of silver nanowires with zigzag morphology in N, N-dimethylformamide

NASA Astrophysics Data System (ADS)

He, Xin; Zhao, Xiujian; Chen, Yunxia; Feng, Jinyang; Sun, Zhenya

2007-08-01

Zigzag silver nanowires with a uniform diameter of 20±5 nm were prepared by reducing silver nitrate (AgNO 3) with N, N-dimethylformamide (DMF) in the presence of tetrabutyl titanate (TBT) and acetylacetone (AcAc) at 373 K for 18 h. X-ray and selected area electron diffraction (XRD and SAED) patterns reveal that the prepared product is made of pure silver with face centered cubic structure. Transmission electron microscopy (TEM) investigations suggest that the amount of silver nanowires is enhanced with increase in reaction time, and the end-to-end assemblies of silver nanorods are observed during the reaction process. After 18 h reaction, silver nanowires with zigzag morphology are obtained. In this paper, a possible growth process of silver nanowires with this interesting shape is described. Silver nanoparticles with small sizes were obtained by reducing Ag + ions with DMF, providing seeds for homogeneous growth of silver nanorods. With the extending reaction time, the synthesized silver nanorods were connected in an end-to-end manner, and the interface between the connections of two nanorods gradually disappeared. The final product shows zigzag morphology with various angles. The angles between two connecting straight parts of zigzag nanowires exhibit an alterable range of 74-151°. These silver nanowires show tremendous potential applications in future nanoscale electronic circuits.

Coupling of Armchair and Zigzag Tubes to a Free Electron Metal

NASA Technical Reports Server (NTRS)

Anantram, M. P.; Biegel, Bryan (Technical Monitor)

2001-01-01

The effect of nanotube chirality is of prime importance in determining its electronic properties. We address the issue of how chirality affects the coupling of a nanotube to metal contacts. We model coupling of armchair and zigzag nanotubes to metal contacts, in both the side- and end-contacted geometries. In the side-contacted geometry, the coupling of armchair and metallic-zigzag nanotubes to a free electron metal are significantly different. Namely, it is possible to drive a larger current through a metallic-zigzag nanotube. The predicted difference holds good when both (a) the entire circumference and (b) only a finite sector of the nanotube makes contact to the metal electrode. It might be possible to observe the predicted difference between armchair and zigzag nanotubes using gold contacts.

Polypyrrole polyvinylidene difluoride composite stripe and zigzag actuators for use in facial robotics

NASA Astrophysics Data System (ADS)

Tadesse, Yonas; Priya, Shashank; Ramannair Chenthamarakshan, C.; de Tacconi, Norma R.; Rajeshwar, Krishnan

2008-04-01

Composite stripe and zigzag actuators consisting of a sandwich polypyrrole (PPy)/polyvinylidene difluoride (PVDF)/PPy structure were synthesized using potentiodynamic film growth on gold electrodes. The synthesis was done from an aqueous solution containing tetrabutylammonium perchlorate and pyrrole by polymerization at room temperature. The actuator displacement was modeled using finite element simulations. For depositing thin PPy films and thereby minimizing the response time, experimental optimization of the deposition conditions was performed. The number of current-potential (potentiodynamic) growth cycles and the thickness of the deposited PPy film were highly correlated in the initial stages of polymer film growth. The actuation response measurements indicate that the zigzag shaped actuators provide promising properties to develop artificial muscle.

Effectiveness of zigzag Incision and 1.5-Layer method for frontotemporal craniotomy

PubMed Central

Minami, Noriaki; Kimura, Toshikazu; Kohmura, Eiji

2014-01-01

Background: In this era of minimally invasive treatment, it is important to make operative scars as inconspicuous as possible, and there is a great deal of room for improvement in daily practice. Zigzag incision with coronal incision has been described mainly in the field of plastic surgery, and its applicability for skin incision in general neurosurgery has not been reported. Methods: Zigzag incision with 1.5-layer method was applied to 14 patients with unruptured cerebral aneurysm between April 2011 and August 2012. A questionnaire survey was administered among patients with unruptured aneurysm using SF-36v2 since April 2010. The results were compared between patients with zigzag incision and a previous cohort with traditional incision. Results: There were no cases of complications associated with the operative wound. In the questionnaire survey, all parameters tended to be better in the patients with zigzag incision, and role social component score (RCS) was significantly higher in the zigzag group than in the traditional incision group (P =0.0436). Conclusion: Zigzag incision using the 1.5-layer method with frontotemporal craniotomy seems to represent an improvement over the conventional curvilinear incision with regard to cosmetic outcome and RCS. PMID:24991472

Confinement and Structural Changes in Vertically Aligned Dust Structures

NASA Astrophysics Data System (ADS)

Hyde, Truell

2013-10-01

In physics, confinement is known to influence collective system behavior. Examples include coulomb crystal variants such as those formed from ions or dust particles (classical), electrons in quantum dots (quantum) and the structural changes observed in vertically aligned dust particle systems formed within a glass box placed on the lower electrode of a Gaseous Electronics Conference (GEC) rf reference cell. Recent experimental studies have expanded the above to include the biological domain by showing that the stability and dynamics of proteins confined through encapsulation and enzyme molecules placed in inorganic cavities such as those found in biosensors are also directly influenced by their confinement. In this paper, the self-assembly and subsequent collective behavior of structures formed from n, charged dust particles interacting with one another and located within a glass box placed on the lower, powered electrode of a GEC rf reference cell is discussed. Self-organized formation of vertically aligned one-dimensional 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 one-dimensional chain structures, through a zigzag transition to a two-dimensional, spindle like structures, and then to various three-dimensional, helical structures exhibiting various symmetries. Stable configurations are shown to be strongly dependent upon system confinement. The critical conditions for structural transitions as well as the basic symmetry exhibited by the one-, two-, and three-dimensional structures that subsequently develop will be shown to be in good agreement with molecular dynamics simulations.

Antiferromagnetic S=1/2 spin chain driven by p-orbital ordering in CsO2.

PubMed

Riyadi, Syarif; Zhang, Baomin; de Groot, Robert A; Caretta, Antonio; van Loosdrecht, Paul H M; Palstra, Thomas T M; Blake, Graeme R

2012-05-25

We demonstrate, using a combination of experiment and density functional theory, that orbital ordering drives the formation of a one-dimensional (1D) S=1/2 antiferromagnetic spin chain in the 3D rocksalt structure of cesium superoxide (CsO2). The magnetic superoxide anion (O2(-)) exhibits degeneracy of its 2p-derived molecular orbitals, which is lifted by a structural distortion on cooling. A spin chain is then formed by zigzag ordering of the half-filled superoxide orbitals, promoting a superexchange pathway mediated by the p(z) orbitals of Cs(+) along only one crystal direction. This scenario is analogous to the 3d-orbital-driven spin chain found in the perovskite KCuF3 and is the first example of an inorganic quantum spin system with unpaired p electrons.

A Novel Coordination Polymer Based on Trinuclear Cobalt Building Blocks Cluster: Synthesis, Crystal Structure, and Properties

NASA Astrophysics Data System (ADS)

Lu, J. F.; Tang, Z. H.; Shi, J.; Ge, H. G.; Jiang, M.; Song, J.; Jin, L. X.

2017-12-01

The title compound {[Co3(μ3-OH)(μ2-H2O)2(H2O)5(BTC)2] · 6H2O} n (H3BTC is a 1,3,5-benzenetricarboxylic acid) was prepared and characterized by single crystal and powder X-ray diffraction, Fourier transform infrared spectroscopy, thermogravimetric and elemental analyses. The single crystal X-ray diffraction reveals that the title compound consists of 1D infinite zigzag chains which were constructed by trinuclear cobalt cluster and BTC3- ligand. Neighbouring above-mentioned 1D infinite zigzag chains are further linked by intermolecular hydrogen bonding to form a 3D supermolecular structure. In addition, the luminescent properties of the title compound were investigated.

On the difference between the pyroxenes LiFeSi2O6 and LiFeGe2O6 in their magnetic structures and spin orientations

NASA Astrophysics Data System (ADS)

Lee, Changhoon; Hong, Jisook; Shim, Ji Hoon; Whangbo, Myung-Hwan

2014-03-01

The clinopyroxenes LiFeSi2O6 and LiFeGe2O6, crystallizing in a monoclinic space group P21/c, are isostructural and isoelectronic Their crystal structures are made up of zigzag chains of edge-sharing FeO6 octahedra containing high-spin Fe3 + ions, which run along the c direction. Despite this structural similarity, the two have quite different magnetic structures and spin orientations. In LiFeSi2O6 the Fe spins have a ferromagnetic coupling within the zigzag chains along c and such FM chains have an antiferromagnetic coupling along a. In contrast, in LiFeGe2O6, the spins have an AFM coupling within the zigzag chains along c and such FM chains have an ↑ ↑ ↓ ↓ coupling along a. In addition, the spin orientation is parallel to c in LiFeSi2O6, but is perpendicular to c in LiFeGe2O6. To explain these differences in the magnetic structure and spin orientation, we evaluated the spin exchange parameters by performing energy mapping analysis based on LDA +U and GGA +U calculations and also by evaluating the magnetocrystalline anisotropy energies in terms of GGA +U +SOC and LDA +U +SOC calculations. Our study show that the magnetic structures and spin orientations of LiFeSi2O6 and LiFeGe2O6 are better described by LDA +U and LDA +U +SOC calculations. This research was supported by Basic Science Research Program through the National Research Foundation of Korea(NRF) funded by the Ministry of Education(2013R1A1A2060341).

High power tube solid-state laser with zigzag propagation of pump and laser beam

NASA Astrophysics Data System (ADS)

Savich, Michael

2015-02-01

A novel resonator and pumping design with zigzag propagation of pumping and laser beams permits to design an improved tube Solid State Laser (SSL), solving the problem of short absorption path to produce a high power laser beam (100 - 1000kW). The novel design provides an amplifier module and laser oscillator. The tube-shaped SSL includes a gain element fiber-optically coupled to a pumping source. The fiber optic coupling facilitates light entry at compound Brewster's angle of incidence into the laser gain element and uses internal reflection to follow a "zigzag" path in a generally spiral direction along the length of the tube. Optics are arranged for zigzag propagation of the laser beam, while the cryogenic cooling system is traditional. The novel method of lasing uses advantages of cylindrical geometry to reach the high volume of gain medium with compactness and structural rigidity, attain high pump density and uniformity, and reach a low threshold without excessive increase of the temperature of the crystal. The design minimizes thermal lensing and stress effects, and provides high gain amplification, high power extraction from lasing medium, high pumping and lasing efficiency and a high beam quality.

Iris Segmentation and Normalization Algorithm Based on Zigzag Collarette

NASA Astrophysics Data System (ADS)

Rizky Faundra, M.; Ratna Sulistyaningrum, Dwi

2017-01-01

In this paper, we proposed iris segmentation and normalization algorithm based on the zigzag collarette. First of all, iris images are processed by using Canny Edge Detection to detect pupil edge, then finding the center and the radius of the pupil with the Hough Transform Circle. Next, isolate important part in iris based zigzag collarette area. Finally, Daugman Rubber Sheet Model applied to get the fixed dimensions or normalization iris by transforming cartesian into polar format and thresholding technique to remove eyelid and eyelash. This experiment will be conducted with a grayscale eye image data taken from a database of iris-Chinese Academy of Sciences Institute of Automation (CASIA). Data iris taken is the data reliable and widely used to study the iris biometrics. The result show that specific threshold level is 0.3 have better accuracy than other, so the present algorithm can be used to segmentation and normalization zigzag collarette with accuracy is 98.88%

Magnonic quantum spin Hall state in the zigzag and stripe phases of the antiferromagnetic honeycomb lattice

NASA Astrophysics Data System (ADS)

Lee, Ki Hoon; Chung, Suk Bum; Park, Kisoo; Park, Je-Geun

2018-05-01

We investigated the topological property of magnon bands in the collinear magnetic orders of zigzag and stripe phases for the antiferromagnetic honeycomb lattice and identified Berry curvature and symmetry constraints on the magnon band structure. Different symmetries of both zigzag and stripe phases lead to different topological properties, in particular, the magnon bands of the stripe phase being disentangled with a finite Dzyaloshinskii-Moriya (DM) term with nonzero spin Chern number. This is corroborated by calculating the spin Nernst effect. Our study establishes the existence of a nontrivial magnon band topology for all observed collinear antiferromagnetic honeycomb lattices in the presence of the DM term.

Negative differential resistance in oxidized zigzag graphene nanoribbons.

PubMed

Wang, Min; Li, Chang Ming

2011-01-28

A theoretical study of zigzag graphene nanoribbons (ZGNRs) with an epoxy-pair chain (ZGO) is performed. The electronic transport properties are mainly evaluated by non-equilibrium Green's functions using the TRANSIESTA package. The results indicate that the graphene oxide can have a negative differential resistance (NDR) phenomenon, supported by bias-dependent transmission curves of different spin orientations. Applying non-zero bias voltages makes the density of states (DOS) of the right electrodes shift down. Due to an energy gap between the LUMO and LUMO+1 in ZGOs, with a certain bias, the conduction band of the right electrode cannot match the LUMO of the scattering region, then NDR occurs. With a larger bias, NDR ends when the second conduction band of the right electrode's DOS covers the LUMO of the scattering region. Since most of proposed ZGO systems possess such a gap between the LUMO and LUMO+1, NDR can be widely observed and this discovery may provide great potential applications in NDR-based nanoelectronics by using modified graphene materials.

Nematic liquid crystals on sinusoidal channels: the zigzag instability.

PubMed

Silvestre, Nuno M; Romero-Enrique, Jose M; Telo da Gama, Margarida M

2017-01-11

Substrates which are chemically or topographically patterned induce a variety of liquid crystal textures. The response of the liquid crystal to competing surface orientations, typical of patterned substrates, is determined by the anisotropy of the elastic constants and the interplay of the relevant lengths scales, such as the correlation length and the surface geometrical parameters. Transitions between different textures, usually with different symmetries, may occur under a wide range of conditions. We use the Landau-de Gennes free energy to investigate the texture of nematics in sinusoidal channels with parallel anchoring bounded by nematic-air interfaces that favour perpendicular (hometropic) anchoring. In micron size channels 5CB was observed to exhibit a non-trivial texture characterized by a disclination line, within the channel, which is broken into a zigzag pattern. Our calculations reveal that when the elastic anisotropy of the nematic does not favour twist distortions the defect is a straight disclination line that runs along the channel, which breaks into a zigzag pattern with a characteristic period, when the twist elastic constant becomes sufficiently small when compared to the splay and bend constants. The transition occurs through a twist instability that drives the defect line to rotate from its original position. The interplay between the energetically favourable twist distortions that induce the defect rotation and the liquid crystal anchoring at the surfaces leads to the zigzag pattern. We investigate in detail the dependence of the periodicity of the zigzag pattern on the geometrical parameters of the sinusoidal channels, which in line with the experimental results is found to be non-linear.

Structure and optical properties of several organic-inorganic hybrids containing corner-sharing chains of bismuth iodide octahedra.

PubMed

Mitzi, D B; Brock, P

2001-04-23

Two organic-inorganic bismuth iodides of the form (H3N-R-NH3)BiI5 are reported, each containing long and relatively flexible organic groups, R. The norganic framework in each case consists of distorted BiI6 octahedra sharing cis vertexes to form zigzag chains. Crystals of (H3NC18H24S2NH3)BiI5 were grown from a slowly cooled ethylene glycol/2-butanol solution containing bismuth(III) iodide and AETH.2HI, where AETH = 1,6-bis[5'-(2' '-aminoethyl)-2'-thienyl]hexane. The new compound, (H2AETH)BiI5, adopts an orthorhombic (Aba2) cell with the lattice parameters a = 20.427(3) A, b = 35.078(5) A, c = 8.559(1) A, and Z = 8. The structure consists of corrugated layers of BiI5(2-) chains, with Bi-I bond lengths ranging from 2.942(3) to 3.233(3) A, separated by layers of the organic (H2AETH)(2+) cations. Crystals of the analogous (H3NC12H24NH3)BiI5 compound were also prepared from a concentrated aqueous hydriodic acid solution containing bismuth(III) iodide and the 1,12-dodecanediamine (DDDA) salt, DDDA.2HI. (H2DDDA)BiI5 crystallizes in an orthorhombic (Ibam) cell with a = 17.226(2) A, b = 34.277(4) A, c = 8.654(1) A, and Z = 8. The Bi-I bonds range in length from 2.929(1) to 3.271(1) A. While the inorganic chain structure is nearly identical for the two title compounds, as well as for the previously reported (H3NC6H12NH3)BiI5 [i.e., (H2DAH)BiI5] structure, the packing of the chains is strongly influenced by the choice of organic cation. Optical absorption spectra for thermally ablated thin films of the three organic-inorganic hybrids containing BiI5(2-) chains are reported as a function of temperature (25-290 K). The dominant long-wavelength feature in each case is attributed to an exciton band, which is apparent at room temperature and, despite the similar inorganic chain structure, varies in position from 491 to 541 nm (at 25 K).

Afocal three-mirror anastigmat with zigzag optical axis for widened field of view and enlarged aperture

NASA Astrophysics Data System (ADS)

Li, Qi; Han, Lin; Jin, Yangming; Shen, Weimin

2016-10-01

In order to improve the detection accuracy and range of new generation of Forward Looking Infra-Red (FLIR) system for distant targets, its optical system, which usually consists of a fore afocal telescope and rear imaging lenses, is required to has wide spectral range, large entrance pupil aperture, and wide field of view (FOV). In this paper, a new afocal Three-Mirror Anastigmat (TMA) with widened field of view and high demagnification is suggested. Its mechanical structure remains coaxial, but it has zigzag optical axis through properly and slightly decentering and tilting of the three mirrors to avoid its secondary obscuration due to the third mirror as FOV increase. Compared with conventional off-axis TMA, the suggested zigzag-axis TMA is compact, easy-alignment and low-cost. The design method and optimum result of the suggested afocal TMA is presented. Its initial structural parameters are determined with its first-order relationship and primary aberration theory. Slight and proper decentration and tilt of each mirror is leaded in optimization so that its coaxial mechanical structure is held but attainable FOV and demagnification are respectively as wide and as high as possible. As an example, a 5.5-demagnification zigzag-axis afocal TMA with a wavelength range, an entrance pupil diameter, and FOV respectively from 3μm to 12μm, of 320mm, and 2×3.2 degrees and with a real exit pupil, is designed. Its imaging quality is diffraction limited. It is suitable for fore afocal telescope of the so-called third generation FLIR.

Structural study of quasi-one-dimensional vanadium pyroxene LiVSi{sub 2}O{sub 6} single crystals

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

Ishii, Yuto; Matsushita, Yoshitaka; Oda, Migaku

Single crystals of quasi-one-dimensional vanadium pyroxene LiVSi{sub 2}O{sub 6} were synthesized and the crystal structures at 293 K and 113 K were studied using X-ray diffraction experiments. We found a structural phase transition from the room-temperature crystal structure with space group C2/c to a low-temperature structure with space group P2{sub 1}/c, resulting from a rotational displacement of SiO{sub 4} tetrahedra. The temperature dependence of magnetic susceptibility shows a broad maximum around 116 K, suggesting an opening of the Haldane gap expected for one-dimensional antiferromagnets with S=1. However, an antiferromagnetic long-range order was developed below 24 K, probably caused by amore » weak inter-chain magnetic coupling in the compound. - Graphical abstract: Low temperature crystal structure of LiVSi{sub 2}O{sub 6} and an orbital arrangement within the V-O zig-zag chain along the c-axis. - Highlights: • A low temperature structure of LiVSi{sub 2}O{sub 6} was determined by single crystal X-ray diffraction measurements. • The origin of the structural transition is a rotational displacement of SiO{sub 4} tetrahedra. • The uniform orbital overlap in the V-O zigzag chain makes the system a quasi one-dimensional antiferromagnet.« less

Cd (II) and holodirected lead (II) 3D-supramolecular coordination polymers based on nicotinic acid: Structure, fluorescence property and photocatalytic activity

NASA Astrophysics Data System (ADS)

Etaiw, Safaa El-din H.; Abd El-Aziz, Dina M.; Marie, Hassan; Ali, Elham

2018-05-01

Two new supramolecular coordination polymers namely {[Cd(NA)2(H2O)]}, SCP 1 and {[Pb(NA)2]}, SCP 2, (NA = nicotinate ligand) were synthesized by self-assembly method and structurally characterized by different analytical and spectroscopic methods. Single-crystal X-ray diffraction showed that SCP 1 extend in three dimensions containing bore structure where the 3D- network is constructed via interweaving zigzag chains. The Cd atom coordinates to (O4N2) atoms forming distorted-octahedral configuration. The structure of SCP 2 extend down the projection of the b-axis creating parallel zigzag 1D-chains connected by μ2-O2 atoms and H-bonds forming a holodirected lead (II) hexagonal bi-pyramid configuration. SCP 2 extend to 3D-network via coordinate and hydrogen bonds. The thermal stability, photoluminescence properties, photocatalytic activity for the degradation of methylene blue dye (MB) under UV-irradiation and sunlight irradiation were also studied.

Optical absorption of zigzag single walled boron nitride nanotubes in axial magnetic field

NASA Astrophysics Data System (ADS)

Chegel, Raad; Behzad, Somayeh

2013-11-01

We have investigated the effect of axial magnetic field on the band structure, dipole matrix elements and absorption spectrum in different energy ranges, using tight binding approximation. It is found that magnetic field breaks the degeneracy in the band structure and creates new allowed transitions in the dipole matrix which leads to creation of new peaks in the absorption spectrum. It is found that, unlike to CNTs which show metallic-semiconductor transition, the BNNTs remain semiconductor in any magnetic field strength. By calculation the diameter dependence of peak positions, we found that the positions of three first peaks in the lower energy region (E <5.3 eV) are proportional to n-2. In the middle energy region (7 < E < 7.5 eV) all (n, 0) zigzag BNNTs, with even and odd nanotube index, have two distinct peaks in the absence of magnetic field which these peaks may be used to identify zigzag BNNTs from other tube chiralities. For odd (even) tubes, in the middle energy region, applying the magnetic field leads to splitting of these two peaks into three (five) distinct peaks.

Investigating the edge state of graphene nanoribbons by a chemical approach: Synthesis and magnetic properties of zigzag-edged nanographene molecules

NASA Astrophysics Data System (ADS)

Konishi, Akihito; Hirao, Yasukazu; Kurata, Hiroyuki; Kubo, Takashi

2013-12-01

The edge state, which is a peculiar magnetic state in zigzag-edged graphene nanoribbons (GNRs) originating from an electron-electron correlation in an edge-localized π-state, has promising applications for magnetic and spintronics devices and has attracted much attention of physicists, chemists, and engineers. For deeper understanding the edge state, precise fabrication of edge structures in GNRs has been highly demanded. We focus on [a.b]periacene, which are polycyclic aromatic hydrocarbons (PAHs) that have zigzag and armchair edges on molecular periphery, as a model compound for the understanding and actually prepare and characterize them. This review summarizes our recent studies on the origin of the edge state by investigating [a.b]periacene in terms of the relationship between the molecular structure and spin-localizing character.

Monoclinic crystal structure of α - RuCl 3 and the zigzag antiferromagnetic ground state

DOE PAGES

Johnson, R. D.; Williams, S. C.; Haghighirad, A. A.; ...

2015-12-10

We have proposed the layered honeycomb magnet α - RuCl 3 as a candidate to realize a Kitaev spin model with strongly frustrated, bond-dependent, anisotropic interactions between spin-orbit entangled j eff = 1/2 Ru 3 + magnetic moments. We report a detailed study of the three-dimensional crystal structure using x-ray diffraction on untwinned crystals combined with structural relaxation calculations. We consider several models for the stacking of honeycomb layers and find evidence for a parent crystal structure with a monoclinic unit cell corresponding to a stacking of layers with a unidirectional in-plane offset, with occasional in-plane sliding stacking faults, inmore » contrast with the currently assumed trigonal three-layer stacking periodicity. We also report electronic band-structure calculations for the monoclinic structure, which find support for the applicability of the j eff = 1/2 picture once spin-orbit coupling and electron correlations are included. Of the three nearest-neighbor Ru-Ru bonds that comprise the honeycomb lattice, the monoclinic structure makes the bond parallel to the b axis nonequivalent to the other two, and we propose that the resulting differences in the magnitude of the anisotropic exchange along these bonds could provide a natural mechanism to explain the previously reported spin gap in powder inelastic neutron scattering measurements, in contrast to spin models based on the three-fold symmetric trigonal structure, which predict a gapless spectrum within linear spin wave theory. Our susceptibility measurements on both powders and stacked crystals, as well as magnetic neutron powder diffraction, show a single magnetic transition upon cooling below T N ≈ 13 K. Our analysis of our neutron powder diffraction data provides evidence for zigzag magnetic order in the honeycomb layers with an antiferromagnetic stacking between layers. Magnetization measurements on stacked single crystals in pulsed field up to 60 T show a single transition

Electronic structure and transport properties of zigzag MoS2 nanoribbons

NASA Astrophysics Data System (ADS)

Sharma, Uma Shankar; Shah, Rashmi; Mishra, Pankaj Kumar

2018-05-01

In present study, electronic and transport properties of the 8zigzag MoS2 nanoribbons (8ZMoS2NRs) are investigated using ab-initio density functional theory [DFT]. The calculations were performed using nonequilibrium Green's function (NEGF) formalism based on DFT as implemented in the TranSiesta code. Results show that the defect can introduces few extra states into the energy gap, which lead nanoribbons to reveal a metallic characteristic. The voltage-current (VI) graph of 8ZMoS2NRs show a threshold current increases after introducing Mo defect in the devices. when introducing a Mo vacancy under low biases, the current will be suppressed—whereas under high biases, the current through the defected 8ZMoS2NRs will increases rapidly, due to the other channel being opened, that make possibility of 8ZMoS2NRs application in electronic devices such as voltage regulation.

A distributed parameter electromechanical model for bimorph piezoelectric energy harvesters based on the refined zigzag theory

NASA Astrophysics Data System (ADS)

Chen, Chung-De

2018-04-01

In this paper, a distributed parameter electromechanical model for bimorph piezoelectric energy harvesters based on the refined zigzag theory (RZT) is developed. In this model, the zigzag function is incorporated into the axial displacement, and the zigzag distribution of the displacement between the adjacent layers of the bimorph structure can be considered. The governing equations, including three equations of motions and one equation of circuit, are derived using Hamilton’s principle. The natural frequency, its corresponding modal function and the steady state response of the base excitation motion are given in exact forms. The presented results are benchmarked with the finite element method and two beam theories, the first-order shear deformation theory and the classical beam theory. Comparing examples shows that the RZT provides predictions of output voltage and generated power at high accuracy, especially for the case of a soft middle layer. Variation of the parameters, such as the beam thickness, excitation frequencies and the external electrical loads, is investigated and its effects on the performance of the energy harvesters are studied by using the RZT developed in this paper. Based on this refined theory, analysts and engineers can capture more details on the electromechanical behavior of piezoelectric harvesters.

Study on zigzag maneuver characteristics of V-U very large crude oil (VLCC) tankers

NASA Astrophysics Data System (ADS)

Jaswar, Maimun, A.; Wahid, M. A.; Priyanto, A.; Zamani, Pauzi, Saman

2012-06-01

The Department of Marine Technology at the Faculty of Mechanical Engineering, University Teknologi Malaysia has recently developed an Ship Maneuverability tool which intends to upgrade student's level understanding the application of fluid dynamic on interaction between hull, propeller, and rudder during maneuvering. This paper discusses zigzag maneuver for conventional Very Large Crude Oil (VLCC) ships with the same principal dimensions but different stern flame shape. 10/10 zigzag maneuver characteristics of U and V types of VLCC ships are investigated. Simulation results for U-type show a good agreement with the experimental data, but V-type not good agreement with experimental one. Further study on zigzag maneuver characteristics are required.

Formation of Stone-Wales edge: Multistep reconstruction and growth mechanisms of zigzag nanographene.

PubMed

Dang, Jing-Shuang; Wang, Wei-Wei; Zheng, Jia-Jia; Nagase, Shigeru; Zhao, Xiang

2017-10-05

Although the existence of Stone-Wales (5-7) defect at graphene edge has been clarified experimentally, theoretical study on the formation mechanism is still imperfect. In particular, the regioselectivity of multistep reactions at edge (self-reconstruction and growth with foreign carbon feedstock) is essential to understand the kinetic behavior of reactive boundaries but investigations are still lacking. Herein, by using finite-sized models, multistep reconstructions and carbon dimer additions of a bared zigzag edge are introduced using density functional theory calculations. The zigzag to 5-7 transformation is proved as a site-selective process to generate alternating 5-7 pairs sequentially and the first step with largest barrier is suggested as the rate-determining step. Conversely, successive C 2 insertions on the active edge are calculated to elucidate the formation of 5-7 edge during graphene growth. A metastable intermediate with a triple sequentially fused pentagon fragment is proved as the key structure for 5-7 edge formation. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

A computational NMR study on zigzag aluminum nitride nanotubes

NASA Astrophysics Data System (ADS)

Bodaghi, Ali; Mirzaei, Mahmoud; Seif, Ahmad; Giahi, Masoud

2008-12-01

A computational nuclear magnetic resonance (NMR) study is performed to investigate the electronic structure properties of the single-walled zigzag aluminum nitride nanotubes (AlNNTs). The chemical-shielding (CS) tensors are calculated at the sites of Al-27 and N-15 nuclei in three structural forms of AlNNT including H-saturated, Al-terminated, and N-terminated ones. The structural forms are firstly optimized and then the calculated CS tensors in the optimized structures are converted to chemical-shielding isotropic (CSI) and chemical-shielding anisotropic (CSA) parameters. The calculated parameters reveal that various Al-27 and N-15 nuclei are divided into some layers with equivalent electrostatic properties; furthermore, Al and N can act as Lewis base and acid, respectively. In the Al-terminated and N-terminated forms of AlNNT, in which one mouth of the nanotube is terminated by aluminum and nitrogen nuclei, respectively, just the CS tensors of the nearest nuclei to the mouth of the nanotube are significantly changed due to removal of saturating hydrogen atoms. Density functional theory (DFT) calculations are performed using GAUSSIAN 98 package of program.

Tight binding simulation study on zigzag single-walled carbon nanotubes

NASA Astrophysics Data System (ADS)

Sharma, Deepa; Jaggi, Neena; Gupta, Vishu

2018-01-01

Tight binding simulation studies using the density functional tight binding (DFTB) model have been performed on various zigzag single-walled carbon-nanotubes (SWCNTs) to investigate their electronic properties using DFTB module of the Material Studio Software version 7.0. Various combinations of different eigen-solvers and charge mixing schemes available in the DFTB Module have been tried to chalk out the electronic structure. The analytically deduced values of the bandgap of (9, 0) SWCNT were compared with the experimentally determined value reported in the literature. On comparison, it was found that the tight binding approximations tend to drastically underestimate the bandgap values. However, the combination of Anderson charge mixing method with standard eigensolver when implemented using the smart algorithm was found to produce fairly close results. These optimized model parameters were then used to determine the band structures of various zigzag SWCNTs. (9, 0) Single-walled Nanotube which is extensively being used for sensing NH3, CH4 and NO2 has been picked up as a reference material since its experimental bandgap value has been reported in the literature. It has been found to exhibit a finite energy bandgap in contrast to its expected metallic nature. The study is of utmost significance as it not only probes and validates the simulation route for predicting suitable properties of nanomaterials but also throws light on the comparative efficacy of the different approximation and rationalization quantum mechanical techniques used in simulation studies. Such simulation studies if used intelligently prove to be immensely useful to the material scientists as they not only save time and effort but also pave the way to new experiments by making valuable predictions.

Optical Properties of a Single Carbon Chain-Doped Silicene Nanoribbon

NASA Astrophysics Data System (ADS)

Lu, Dao-Bang; Song, Yu-Ling; Huang, Xiao-yu; Wang, Chong

2018-05-01

Using first-principles spin polarization density function theory calculations, we have studied the electronic and optical properties of zigzag-edge silicene nanoribbons (ZSiNRs) doped with a single carbon chain. Because of the doped carbon chain, there are several defect states in the band structures of ZSiNRs across the Fermi level, and the ferromagnetic ground state is metallic. The dielectric functions in all three dimensions are completely different from each other, and thus the system exhibits strong optical anisotropism. The carbon chain influenced the dielectric functions most at low energy. The first peak in the E//x direction of the dielectric spectrum exhibits a significant blueshift, and its value has changed as well. The main absorption wavelength depends on the polarization direction of the incident light, but occurs within the UV region for all polarization directions. The peaks of the energy loss spectra correspond to the trailing edges in the reflectivity spectrum, and the highest peak corresponds to a plasmon frequency. Our results could be useful for investigating nanodevices based on silicene nanoribbons.

The opposite induced magnetic moment in narrow zigzag graphene nanoribbons

NASA Astrophysics Data System (ADS)

Liu, Hong; Hu, Bian; Liu, Na

2016-11-01

Based on the analysis of band structure and edge states on zigzag graphene nanoribbons (ZGNRs), we can study theoretically the origination of two minimal quantum conductance. At the two energy points - 0.20 eV and 0.15 eV corresponding to the two dips of quantum conductance, the spin-polarized quantum conductance is about 45%. Furthermore, the two types of edge-localized carriers in the opposite transport directions along the two opposite edge sides form the quantum internal loop current, which can generate one big magnetic moment. At these two energy points - 0.17 eV and 0.15 eV the two induced magnetic moments are in opposite signals.

Dense zig-zag microstructures in YSZ thin films by pulsed laser deposition

NASA Astrophysics Data System (ADS)

Stender, Dieter; Schäuble, Nina; Weidenkaff, Anke; Montagne, Alex; Ghisleni, Rudy; Michler, Johann; Schneider, Christof W.; Wokaun, Alexander; Lippert, Thomas

2015-01-01

The very brittle oxygen ion conductor yttria stabilized zirconia (YSZ) is a typical solid electrolyte for miniaturized thin film fuel cells. In order to decrease the fuel cell operating temperature, the thickness of yttria stabilized zirconia thin films is reduced. Often, these thin membranes suffer from mechanical failure and gas permeability. To improve these mechanical issues, a glancing angle deposition approach is used to grow yttria stabilized zirconia thin films with tilted columnar structures. Changes of the material flux direction during the deposition result in a dense, zigzag-like structure with columnar crystallites. This structure reduces the elastic modulus of these membranes as compared to columnar yttria stabilized zirconia thin films as monitored by nano-indentation which makes them more adaptable to applied stress.

Anisotropic thermoelectric behavior in armchair and zigzag mono- and fewlayer MoS2 in thermoelectric generator applications

PubMed Central

Arab, Abbas; Li, Qiliang

2015-01-01

In this work, we have studied thermoelectric properties of monolayer and fewlayer MoS2 in both armchair and zigzag orientations. Density functional theory (DFT) using non-equilibrium Green’s function (NEGF) method has been implemented to calculate the transmission spectra of mono- and fewlayer MoS2 in armchair and zigzag directions. Phonon transmission spectra are calculated based on parameterization of Stillinger-Weber potential. Thermoelectric figure of merit, ZT, is calculated using these electronic and phonon transmission spectra. In general, a thermoelectric generator is composed of thermocouples made of both n-type and p-type legs. Based on our calculations, monolayer MoS2 in armchair orientation is found to have the highest ZT value for both p-type and n-type legs compared to all other armchair and zigzag structures. We have proposed a thermoelectric generator based on monolayer MoS2 in armchair orientation. Moreover, we have studied the effect of various dopant species on thermoelectric current of our proposed generator. Further, we have compared output current of our proposed generator with those of Silicon thin films. Results indicate that thermoelectric current of MoS2 armchair monolayer is several orders of magnitude higher than that of Silicon thin films. PMID:26333948

Anisotropic thermoelectric behavior in armchair and zigzag mono- and fewlayer MoS2 in thermoelectric generator applications.

PubMed

Arab, Abbas; Li, Qiliang

2015-09-03

In this work, we have studied thermoelectric properties of monolayer and fewlayer MoS2 in both armchair and zigzag orientations. Density functional theory (DFT) using non-equilibrium Green's function (NEGF) method has been implemented to calculate the transmission spectra of mono- and fewlayer MoS2 in armchair and zigzag directions. Phonon transmission spectra are calculated based on parameterization of Stillinger-Weber potential. Thermoelectric figure of merit, ZT, is calculated using these electronic and phonon transmission spectra. In general, a thermoelectric generator is composed of thermocouples made of both n-type and p-type legs. Based on our calculations, monolayer MoS2 in armchair orientation is found to have the highest ZT value for both p-type and n-type legs compared to all other armchair and zigzag structures. We have proposed a thermoelectric generator based on monolayer MoS2 in armchair orientation. Moreover, we have studied the effect of various dopant species on thermoelectric current of our proposed generator. Further, we have compared output current of our proposed generator with those of Silicon thin films. Results indicate that thermoelectric current of MoS2 armchair monolayer is several orders of magnitude higher than that of Silicon thin films.

Adiabatic quantum pump in a zigzag graphene nanoribbon junction

NASA Astrophysics Data System (ADS)

Zhang, Lin

2015-11-01

The adiabatic electron transport is theoretically studied in a zigzag graphene nanoribbon (ZGNR) junction with two time-dependent pumping electric fields. By modeling a ZGNR p-n junction and applying the Keldysh Green’s function method, we find that a pumped charge current is flowing in the device at a zero external bias, which mainly comes from the photon-assisted tunneling process and the valley selection rule in an even-chain ZGNR junction. The pumped charge current and its ON and OFF states can be efficiently modulated by changing the system parameters such as the pumping frequency, the pumping phase difference, and the Fermi level. A ferromagnetic ZGNR device is also studied to generate a pure spin current and a fully polarized spin current due to the combined spin pump effect and the valley valve effect. Our finding might pave the way to manipulate the degree of freedom of electrons in a graphene-based electronic device. Project supported by the National Natural Science Foundation of China (Grant No. 110704033), the Natural Science Foundation of Jiangsu Province, China (Grant No. BK2010416), and the Natural Science Foundation for Colleges and Universities in Jiangsu Province, China (Grant No. 13KJB140005).

Thermally induced spin-dependent current based on Zigzag Germanene Nanoribbons

NASA Astrophysics Data System (ADS)

Majidi, Danial; Faez, Rahim

2017-02-01

In this paper, using first principle calculation and non-equilibrium Green's function, the thermally induced spin current in Hydrogen terminated Zigzag-edge Germanene Nanoribbon (ZGeNR-H) is investigated. In this model, because of the difference between the source and the drain temperature of ZGeNR device, the spin up and spin down currents flow in the opposite direction with two different threshold temperatures (Tth). Hence, a pure spin polarized current which belongs to spin down is obtained. It is shown that, for temperatures above the threshold temperature spin down current increases with the increasing temperature up to 75 K and then decreases. But spin up current rises steadily and in the high temperature we can obtain polarized spin up current. In addition, we show an acceptable spin current around the room temperature for ZGeNR. The transmission peaks in ZGeNR which are closer to the Fermi level rather than Zigzag Graphene Nanoribbon (ZGNRS) which causes ZGeNR to have spin current at higher temperatures. Finally, it is indicated that by tuning the back gate voltage, the spin current can be completely modulated and polarized. Simulation results verify the Zigzag Germanene Nanoribbon as a promising candidate for spin caloritronics devices, which can be applied in future low power consumption technology.

Application of the Refined Zigzag Theory to the Modeling of Delaminations in Laminated Composites

NASA Technical Reports Server (NTRS)

Groh, Rainer M. J.; Weaver, Paul M.; Tessler, Alexander

2015-01-01

The Refined Zigzag Theory is applied to the modeling of delaminations in laminated composites. The commonly used cohesive zone approach is adapted for use within a continuum mechanics model, and then used to predict the onset and propagation of delamination in five cross-ply composite beams. The resin-rich area between individual composite plies is modeled explicitly using thin, discrete layers with isotropic material properties. A damage model is applied to these resin-rich layers to enable tracking of delamination propagation. The displacement jump across the damaged interfacial resin layer is captured using the zigzag function of the Refined Zigzag Theory. The overall model predicts the initiation of delamination to within 8% compared to experimental results and the load drop after propagation is represented accurately.

Negative differential resistance and bias-modulated metal-to-insulator transition in zigzag C2N-h2D nanoribbon

NASA Astrophysics Data System (ADS)

He, Jing-Jing; Guo, Yan-Dong; Yan, Xiao-Hong

2017-04-01

Motivated by the fabrication of layered two-dimensional material C2N-h2D [Nat. Commun. 6, 6486 (2015)], we cut the single-layer C2N-h2D into a zigzag nanoribbon and perform a theoretical study. The results indicate that the band structure changes from semiconducting to metallic and a negative differential resistance effect occurs in the I-V curve. Interestingly, the current can be reduced to zero and this insulator-like state can be maintained as the bias increases. We find this unique property is originated from a peculiar band morphology, with only two subbands appearing around the Fermi level while others being far away. Furthermore the width and symmetry of the zigzag C2N-h2D nanoribbon can be used to tune the transport properties, such as cut-off bias and the maximum current. We also explore the electron transport property of an aperiodic model composed of two nanoribbons with different widths and obtain the same conclusion. This mechanism can be extended to other systems, e.g., hybrid BCN nanoribbons. Our discoveries suggest that the zigzag C2N-h2D nanoribbon has great potential in nanoelectronics applications.

Dual-channel current valve in a three terminal zigzag graphene nanoribbon junction

NASA Astrophysics Data System (ADS)

Zhang, L.

2017-02-01

We theoretically propose a dual-channel current valve based on a three terminal zigzag graphene nanoribbon (ZGNR) junction driven by three asymmetric time-dependent pumping potentials. By means of the Keldysh Green’s function method, we show that two asymmetric charge currents can be pumped in the different left-right terminals of the device at a zero bias, which mainly stems from the single photon-assisted pumping approximation and the valley valve effect in a ZGNR p-n junction. The ON and OFF states of pumped charge currents are crucially dependent on the even-odd chain widths of the three electrodes, the pumping frequency, the lattice potential and the Fermi level. Two-tunneling spin valves are also considered to spatially separate and detect 100% polarized spin currents owing to the combined spin pump effect and the valley selective transport in a three terminal ZGNR ferromagnetic junction. Our investigations might be helpful to control the spatial and spin degrees of freedom of electrons in graphene pumping devices.

Direction-dependent waist-shift-difference of Gaussian beam in a multiple-pass zigzag slab amplifier and geometrical optics compensation method.

PubMed

Li, Zhaoyang; Kurita, Takashi; Miyanaga, Noriaki

2017-10-20

Zigzag and non-zigzag beam waist shifts in a multiple-pass zigzag slab amplifier are investigated based on the propagation of a Gaussian beam. Different incident angles in the zigzag and non-zigzag planes would introduce a direction-dependent waist-shift-difference, which distorts the beam quality in both the near- and far-fields. The theoretical model and analytical expressions of this phenomenon are presented, and intensity distributions in the two orthogonal planes are simulated and compared. A geometrical optics compensation method by a beam with 90° rotation is proposed, which not only could correct the direction-dependent waist-shift-difference but also possibly average the traditional thermally induced wavefront-distortion-difference between the horizontal and vertical beam directions.

Charge transport in doped zigzag phosphorene nanoribbons

NASA Astrophysics Data System (ADS)

Nourbakhsh, Zahra; Asgari, Reza

2018-06-01

The effects of lattice distortion and chemical disorder on charge transport properties of two-terminal zigzag phosphorene nanoribbons (zPNRs), which shows resonant tunneling behavior under an electrical applied bias, are studied. Our comprehensive study is based on ab initio quantum transport calculations on the basis of the Landauer theory. We use nitrogen and silicon substitutional dopant atoms, and employ different physical quantities such as the I -V curve, voltage drop behavior, transmission spectrum, transmission pathway, and atomic current to explore the transport mechanism of zPNR devices under a bias voltage. The calculated transmission pathways show the transition from a ballistic transport regime to a diffusive and in some particular cases to localized transport regimes. Current flowing via the chemical bonds and hopping are monitored; however, the conductance originates mainly from the charge traveling through the chemical bonds in the vicinity of the zigzag edges. Our results show that in the doped systems, the device conductance decreases and the negative differential resistance characteristic becomes weak or is eliminated. Besides, the conductance in a pure zPNR system is almost independent of the ribbon width.

Comparison of noncovalent interactions of zigzag and armchair carbon nanotubes with heterocyclic and aromatic compounds: Imidazole and benzene, imidazophenazines, and tetracene

NASA Astrophysics Data System (ADS)

Zarudnev, Eugene S.; Stepanian, Stepan G.; Adamowicz, Ludwik; Leontiev, Victor S.; Karachevtsev, Victor A.

2017-02-01

We study non-covalent functionalization of SWCNT by linear heterocyclic compounds such as imidazophenazine (F1) and its derivatives (F2-F4). MP2 and DFT/M05-2X quantum-chemical methods are used to determine the structures and the interaction energies of complexes formed by F1-F4 with the zigzag(10,10) and armchair(6,6) nanotubes. The calculations show that for small diameter nanotubes the binding energies with zigzag nanotubes are stronger than with armchair nanotubes. But above the diameter of 1.4 nm the interaction energies for the armchair nanotubes become larger than for the zigzag nanotubes. Experimental measurements demonstrates that the ratio of the integral intensity of the resonance Raman bands assigned to the RBM modes of semiconducting nanotubes to the integral intensity of the metallic nanotubes increases for supernatant of SWCNT:F4 (1,2,3-triazole-[4,5-d]-phenazine) hybrids solved in 1-Methyl-2-pyrrolidone as compared to this ratio in sediment samples. It demonstrates that the linear heterocyclic compounds can be used for separating SWCNTs with different electron-conduction types.

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

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

He, Tian; Yue, Ke-Fen, E-mail: ykflyy@nwu.edu.cn; Zhao, Yi-xing

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 withmore » 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

Study on the Electronic Transport Properties of Zigzag GaN Nanotubes

NASA Astrophysics Data System (ADS)

Li, Enling; Wang, Xiqiang; Hou, Liping; Zhao, Danna; Dai, Yuanbin; Wang, Xuewen

2011-02-01

The electronic transport properties of zigzag GaN nanotubes (n, 0) (4 <= n <= 9) have been calculated using the density functional theory and non-equilibrium Green's functions method. Firstly, the density functional theory (DFT) is used to optimize and calculate the electronic structure of GaNNTs (n, 0) (4<=n<=9). Secondly, DFT and non-equilibrium Green function (NEGF) method are also used to predict the electronic transport properties of GaNNTs two-probe system. The results showed: there is a corresponding relation between the electronic transport properties and the valley of state density of each GaNNT. In addition, the volt-ampere curve of GaNNT is approximately linear.

Armchair and zigzag nanoribbons of gold and silver: A DFT study

NASA Astrophysics Data System (ADS)

Kapoor, Pooja; Sharma, Munish; Kumar, Ashok; Ahluwalia, P. K.

2018-04-01

This paper presents the results from a DFT-based computational study of structural and electronic properties of zigzag and armchair edge shaped nanoribbons of gold and silver in hexagonal phase. The cohesive energy of the considered nanoribbons are found to be more than the corresponding 2D counterpart, thereby, suggesting Au and Ag nanoribbons to be more stable in 1D as compared to 2D. All nanoribbons are found to be metallic with a modulation in quantum ballistic conductance with length and edge type of the nanoribbon. Au nanoribbons are found to have higher conductance than Ag nanoribbon. There is increase in conductance with increase in length of nanoribbon.

Electro-optical properties of zigzag and armchair boron nitride nanotubes under a transverse electric field: Tight binding calculations

NASA Astrophysics Data System (ADS)

Chegel, Raad; Behzad, Somayeh

2012-02-01

The electro-optical properties of zigzag and armchair BNNTs in a uniform transverse electric field are investigated within tight binding approximation. It is found that the electric field modifies the band structure and splits band degeneracy where these effects reflect in the DOS and JDOS spectra. A decrease in the band gap, as a function of the electric field, is observed. This gap reduction increases with the diameter and it is independent of chirality. An analytic function to estimate the electric field needed for band gap closing is proposed which is in good agreement with DFT results. In additional, we show that the larger diameter tubes are more sensitive than small ones. Number and position of peaks in DOS and JDOS spectra for armchair and zigzag tubes with similar radius are dependent on electric field strength.

Cyanide-bridged Fe(III)-Mn(III) bimetallic complexes with dimeric and chain structures constructed from a newly made mer-Fe tricyanide: structures and magnetic properties.

PubMed

Kim, Jae Il; Kwak, Hyun Young; Yoon, Jung Hee; Ryu, Dae Won; Yoo, In Young; Yang, Namgeun; Cho, Beong Ki; Park, Je-Geun; Lee, Hyosug; Hong, Chang Seop

2009-04-06

Four cyanide-linked Fe(III)-Mn(III) complexes were prepared by reacting Mn Schiff bases with a new molecular precursor (PPh(4))[Fe(qcq)(CN)(3)] [1; qcq = 8-(2-quinolinecarboxamido)quinoline anion]. They include a dimeric molecule, [Fe(qcq)(CN)(3)][Mn(3-MeOsalen)(H(2)O)] x 2 H(2)O [2 x 2 H(2)O; 3-MeOsalen = N,N'-ethylenebis(3-methoxysalicylideneiminato) dianion], and three 1D zigzag chains, [Fe(qcq)(CN)(3)][Mn(5-Clsalen)] x 3 H(2)O [3 x 2 MeOH; 5-Clsalen = N,N'-ethylenebis(5-chlorosalicylideneiminato) dianion], [Fe(qcq)(CN)(3)][Mn(5-Brsalen)] x 2 MeOH [4 x 2 MeOH; 5-Brsalen = N,N'-ethylenebis(5-bromosalicylideneiminato) dianion], and Fe(qcq)(CN)(3)][Mn(salen)].MeCN x H(2)O [5 x MeCN; salen = N,N'-ethylenebis(salicylideneiminato) dianion]. The complexes consist of extensive hydrogen bonding and pi-pi stacking interactions, generating multidimensional structures. Magnetic studies demonstrate that antiferromagnetic couplings are operative between Fe(III) and Mn(III) centers bridged by cyanide ligands. On the basis of an infinite chain model, magnetic coupling parameters of 2-5 range from -9.3 to -14.1 cm(-1). A long-range order is observed at 2.3 K for 3 and 2.2 K for 4, while compound 5 shows spin glass behavior possibly coupled with magnetic ordering.

Structure and energetic basis of overrepresented λ light chain in systemic light chain amyloidosis patients.

PubMed

Zhao, Jun; Zhang, Baohong; Zhu, Jianwei; Nussinov, Ruth; Ma, Buyong

2018-06-01

Amyloid formation and deposition of immunoglobulin light-chain proteins in systemic amyloidosis (AL) cause major organ failures. While the κ light-chain is dominant (λ/κ=1:2) in healthy individuals, λ is highly overrepresented (λ/κ=3:1) in AL patients. The structural basis of the amyloid formation and the sequence preference are unknown. We examined the correlation between sequence and structural stability of dimeric variable domains of immunoglobulin light chains using molecular dynamics simulations of 24 representative dimer interfaces, followed by energy evaluation of conformational ensembles for 20 AL patients' light chain sequences. We identified a stable interface with displaced N-terminal residues, provides the structural basis for AL protein fibrils formation. Proline isomerization may cause the N-terminus to adopt amyloid-prone conformations. We found that λ light-chains prefer misfolded dimer conformation, while κ chain structures are stabilized by a natively folded dimer. Our study may facilitate structure-based small molecule and antibody design to inhibit AL. This article is part of a Special Issue entitled: Accelerating Precision Medicine through Genetic and Genomic Big Data Analysis edited by Yudong Cai & Tao Huang. Copyright © 2017 Elsevier B.V. All rights reserved.

Zigzag laser with reduced optical distortion

DOEpatents

Albrecht, G.F.; Comaskey, B.; Sutton, S.B.

1994-04-19

The architecture of the present invention has been driven by the need to solve the beam quality problems inherent in Brewster's angle tipped slab lasers. The entrance and exit faces of a solid state slab laser are cut perpendicular with respect to the pump face, thus intrinsically eliminating distortion caused by the unpumped Brewster's angled faces. For a given zigzag angle, the residual distortions inherent in the remaining unpumped or lightly pumped ends may be reduced further by tailoring the pump intensity at these ends. 11 figures.

Zigzag laser with reduced optical distortion

DOEpatents

Albrecht, Georg F.; Comaskey, Brian; Sutton, Steven B.

1994-01-01

The architecture of the present invention has been driven by the need to solve the beam quality problems inherent in Brewster's angle tipped slab lasers. The entrance and exit faces of a solid state slab laser are cut perpendicular with respect to the pump face, thus intrinsically eliminating distortion caused by the unpumped Brewster's angled faces. For a given zigzag angle, the residual distortions inherent in the remaining unpumped or lightly pumped ends may be reduced further by tailoring the pump intensity at these ends.

Zigzagging Across Pluto

NASA Image and Video Library

2015-12-16

This high-resolution swat of Pluto sweeps over the cratered plains at the west of the New Horizons' encounter hemisphere and across numerous prominent faults, skimming the eastern margin of the dark, forbidding region informally known as Cthulhu Regio, and finally passing over the mysterious, possibly cryovolcanic edifice Wright Mons, before reaching the terminator or day-night line. Among the many notable details shown are the overlapping and infilling relationships between units of the relatively smooth, bright volatile ices from Sputnik Planum (at the edge of the mosaic) and the dark edge or "shore" of Cthulhu. The pictures in this mosaic were taken by the Long Range Reconnaissance Imager (LORRI) in "ride-along" mode with the LEISA spectrometer, which accounts for the 'zigzag' or step pattern. Taken shortly before New Horizons' July 14 closest approach to Pluto, details as small as 500 yards (500 meters) can be seen. http://photojournal.jpl.nasa.gov/catalog/PIA20286

Sensory Organ Like Response of Zigzag Edge Graphene Nanoribbons

NASA Astrophysics Data System (ADS)

Shenoy, Vijay; Bhowmick, Somnath

2011-03-01

Using a continuum Dirac theory, we study the density and spin response of zigzag edge terminated graphene ribbons subjected to edge potentials and Zeeman fields. Our analytical calculations of the density and spin responses of the closed system (fixed particle number) to the static edge fields, show a highly nonlinear Weber-Fechner type behavior where the response depends logarithmically on the edge potential. The dependence of the response on the size of the system (e.g.~width of a nanoribbon) is also uncovered. Zigzag edge graphene nanoribbons, therefore, provide a realization of response of organs such as the eye and ear that obey Weber-Fechner law. We validate our analytical results with tight binding calculations. These results are crucial in understanding important effects of electron-electron interactions in graphene nanoribbons such as edge magnetism etc., and also suggest possibilities for device applications of graphene nanoribbons. Work supported by DST, India through MONAMI and Ramanujan grants.

Spin density waves predicted in zigzag puckered phosphorene, arsenene and antimonene nanoribbons

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

Wu, Xiaohua; Zhang, Xiaoli; Wang, Xianlong

2016-04-15

The pursuit of controlled magnetism in semiconductors has been a persisting goal in condensed matter physics. Recently, Vene (phosphorene, arsenene and antimonene) has been predicted as a new class of 2D-semiconductor with suitable band gap and high carrier mobility. In this work, we investigate the edge magnetism in zigzag puckered Vene nanoribbons (ZVNRs) based on the density functional theory. The band structures of ZVNRs show half-filled bands crossing the Fermi level at the midpoint of reciprocal lattice vectors, indicating a strong Peierls instability. To remove this instability, we consider two different mechanisms, namely, spin density wave (SDW) caused by electron-electronmore » interaction and charge density wave (CDW) caused by electron-phonon coupling. We have found that an antiferromagnetic Mott-insulating state defined by SDW is the ground state of ZVNRs. In particular, SDW in ZVNRs displays several surprising characteristics:1) comparing with other nanoribbon systems, their magnetic moments are antiparallelly arranged at each zigzag edge and almost independent on the width of nanoribbons; 2) comparing with other SDW systems, its magnetic moments and band gap of SDW are unexpectedly large, indicating a higher SDW transition temperature in ZVNRs; 3) SDW can be effectively modified by strains and charge doping, which indicates that ZVNRs have bright prospects in nanoelectronic device.« less

A new security solution to JPEG using hyper-chaotic system and modified zigzag scan coding

NASA Astrophysics Data System (ADS)

Ji, Xiao-yong; Bai, Sen; Guo, Yu; Guo, Hui

2015-05-01

Though JPEG is an excellent compression standard of images, it does not provide any security performance. Thus, a security solution to JPEG was proposed in Zhang et al. (2014). But there are some flaws in Zhang's scheme and in this paper we propose a new scheme based on discrete hyper-chaotic system and modified zigzag scan coding. By shuffling the identifiers of zigzag scan encoded sequence with hyper-chaotic sequence and accurately encrypting the certain coefficients which have little relationship with the correlation of the plain image in zigzag scan encoded domain, we achieve high compression performance and robust security simultaneously. Meanwhile we present and analyze the flaws in Zhang's scheme through theoretical analysis and experimental verification, and give the comparisons between our scheme and Zhang's. Simulation results verify that our method has better performance in security and efficiency.

Ab-initio study of structural, electronic, and transport properties of zigzag GaP nanotubes.

PubMed

Srivastava, Anurag; Jain, Sumit Kumar; Khare, Purnima Swarup

2014-03-01

Stability and electronic properties of zigzag (3 ≤ n ≤ 16) gallium phosphide nanotubes (GaP NTs) have been analyzed by employing a systematic ab-intio approach based on density functional theory using generalized gradient approximation with revised Perdew Burke Ernzerhoff type parameterization. Diameter dependence of bond length, buckling, binding energy, and band gap has been investigated and the analysis shows that the bond length and buckling decreases with increasing diameter of the tube, highest binding energy of (16, 0) confirms this as the most stable amongst all the NTs taken into consideration. The present GaP NTs shows direct band gap and it increases with diameter of the tubes. Using a two probe model for (4, 0) NT the I-V relationship shows an exponential increase in current on applying bias voltage beyond 1.73 volt.

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

Wu, Jing-Yun, E-mail: jyunwu@ncnu.edu.tw; Tsai, Chi-Jou; Chang, Ching-Yun

A Zn(II)−salicylaldimine complex [Zn(L{sup salpyca})(H{sub 2}O)]{sub n} (1, where H{sub 2}L{sup salpyca}=4-hydroxy-3-(((pyridin-2-yl)methylimino)methyl)benzoic acid), with a one-dimensional (1D) chain structure, has been successfully converted to a discrete Ni(II)−salicylaldimine complex [Ni(L{sup salpyca})(H{sub 2}O){sub 3}] (2) and an infinite Cu(II)−salicylaldimine complex ([Cu(L{sup salpyca})]·3H{sub 2}O){sub n} (3) through a metal-ion exchange induced structural transformation process. However, such processes do not worked by Mn(II) and Co(II) ions. Solid-state structure analyses reveal that complexes 1–3 form comparable coordinative or supramolecular zigzag chains running along the crystallographic [201] direction. In addition, replacing Zn(II) ion by Ni(II) and Cu(II) ions caused changes in coordination environment and sphere ofmore » metal centers, from a 5-coordinate intermediate geometry of square pyramidal and trigonal bipyramidal in 1 to a 6-coordinate octahedral geometry in 2, and to a 4-coordiante square planar geometry in 3. This study shows that metal-ion exchange serves as a very efficient way of forming new coordination complexes that may not be obtained through direct synthesis. - Graphical abstract: A Zn(II)−salicylaldimine zigzag chain has been successfully converted to a Ni(II)−salicylaldimine supramolecular zigzag chain and a Cu(II)−salicylaldimine coordinative zigzag chain through metal-ion exchange induced structural transformations, which is not achieved by Mn(II) and Co(II) ions.« less

Zigzagging causility model of EPR correlations and on the interpretation of quantum mechanics

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

de Beauregard, O.C.

1988-09-01

Being formalized inside the S-matrix scheme, the zigzagging causility model of EPR correlations has full Lorentz and CPT invariance. EPR correlations, proper or reversed, and Wheeler's smoky dragon metaphor are respectively pictured in a spacetime or in the momentum-energy space, as V-shaped, anti LAMBDA-shaped, or C-shaped ABC zigzags, with a summation at B over virtual states absolute value B>=*. The reversibility = * implies that causality is CPT-invariant, or arrowless, at the microlevel. Arrowed causality is a macroscopic emergence, corollary to wave retardation and probability increase. Factlike irreversibility states repression, not suppression, of blind statistical retrodiction- that is, of finalmore » cause.« less

The Effect of Acceleration Sprint and Zig-zag Drill Combination to Increase Students’ Speed and Agility

NASA Astrophysics Data System (ADS)

Bana, O.; Mintarto, E.; Kusnanik, N. W.

2018-01-01

The purpose of this research is to analyze the following factors: (1) how far the effect of exercise acceleration sprint on the speed and agility (2) how much influence the zig-zag drill combination to the speed and agility (3) and is there any difference between the effects of exercise acceleration sprint and practice zig-zag drill combination of the speed and agility. This research is quantitative with quasi-experimental approach. The design of this study is matching only design.This study was conducted on 33 male students who take part in extracurricular and divided into 3 groups with 11 students in each group. Group 1 was given training of acceleration sprint, group 2 was given zig-zag training combination drills of conventional and exercises for group 3, for 8 weeks. The data collection was using sprint 30 meter to test the speed and agility t-test to test agility. Data were analyzed using t-test and analysis of variance. The conclusion of the research is (1) there is a significant effect of exercise acceleration sprint for the speed and agility, (2) there is a significant influence combination zig-zag drills, on speed and agility (3) and exercise acceleration sprint have more effect on the speed and agility.

Effect of chain stiffness on the structure of single-chain polymer nanoparticles

NASA Astrophysics Data System (ADS)

Moreno, Angel J.; Bacova, Petra; Lo Verso, Federica; Arbe, Arantxa; Colmenero, Juan; Pomposo, José A.

2018-01-01

Polymeric single-chain nanoparticles (SCNPs) are soft nano-objects synthesized by purely intramolecular cross-linking of single polymer chains. By means of computer simulations, we investigate the conformational properties of SCNPs as a function of the bending stiffness of their linear polymer precursors. We investigate a broad range of characteristic ratios from the fully flexible case to those typical of bulky synthetic polymers. Increasing stiffness hinders bonding of groups separated by short contour distances and increases looping over longer distances, leading to more compact nanoparticles with a structure of highly interconnected loops. This feature is reflected in a crossover in the scaling behaviour of several structural observables. The scaling exponents change from those characteristic for Gaussian chains or rings in θ-solvents in the fully flexible limit, to values resembling fractal or ‘crumpled’ globular behaviour for very stiff SCNPs. We characterize domains in the SCNPs. These are weakly deformable regions that can be seen as disordered analogues of domains in disordered proteins. Increasing stiffness leads to bigger and less deformable domains. Surprisingly, the scaling behaviour of the domains is in all cases similar to that of Gaussian chains or rings, irrespective of the stiffness and degree of cross-linking. It is the spatial arrangement of the domains which determines the global structure of the SCNP (sparse Gaussian-like object or crumpled globule). Since intramolecular stiffness can be varied through the specific chemistry of the precursor or by introducing bulky side groups in its backbone, our results propose a new strategy to tune the global structure of SCNPs.

Delicate crystal structure changes govern the magnetic properties of 1D coordination polymers based on 3d metal carboxylates.

PubMed

Gavrilenko, Konstantin S; Cador, Olivier; Bernot, Kevin; Rosa, Patrick; Sessoli, Roberta; Golhen, Stéphane; Pavlishchuk, Vitaly V; Ouahab, Lahcène

2008-01-01

Homo- and heterometallic 1D coordination polymers of transition metals (Co II, Mn II, Zn II) have been synthesized by an in-situ ligand generation route. Carboxylato-based complexes [Co(PhCOO)2]n (1 a, 1 b), [Co(p-MePhCOO)2]n (2), [ZnMn(PhCOO)4]n (3), and [CoZn(PhCOO)4]n (4) (PhCOOH=benzoic acid, p-MePhCOOH=p-methylbenzoic acid) have been characterized by chemical analysis, single-crystal X-ray diffraction, and magnetization measurements. The new complexes 2 and 3 crystallize in orthorhombic space groups Pnab and Pcab respectively. Their crystal structures consist of zigzag chains, with alternating M(II) centers in octahedral and tetrahedral positions, which are similar to those of 1 a and 1 b. Compound 4 crystallizes in monoclinic space group P2 1/c and comprises zigzag chains of M II ions in a tetrahedral coordination environment. Magnetic investigations reveal the existence of antiferromagnetic interactions between magnetic centers in the heterometallic complexes 3 and 4, while ferromagnetic interactions operate in homometallic compounds (1 a, 1 b, and 2). Compound 1 b orders ferromagnetically at TC=3.7 K whereas 1 a does not show any magnetic ordering down to 330 mK and displays typical single-chain magnet (SCM) behavior with slowing down of magnetization relaxation below 0.6 K. Single-crystal measurements reveal that the system is easily magnetized in the chain direction for 1 a whereas the chain direction coincides with the hard magnetic axis in 1 b. Despite important similarities, small differences in the molecular and crystal structures of these two compounds lead to this dramatic change in properties.

New members of the A{sub 2}M′M{sub 2}{sup ″} structure family (A=Ca, Sr, Yb, La; M′=In,Sn,Pb; M″=Si,Ge)

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

Jehle, Michael; Dürr, Ines; Fink, Saskia

The new mixed tetrelides Sr{sub 2}PbGe{sub 2} and Yb{sub 2}SnGe{sub 2}, several mixed Ca/Sr (A{sup II}) germanides A{sub 2}{sup II}(Sn,Pb)Ge{sub 2} and two polymorphs of La{sub 2}InSi{sub 2} represent new members of the general structure family of ternary alkaline-earth/lanthanoid main group silicides/germanides A{sub 2}M′M{sub 2}{sup ″}(M′=In,Sn,Pb;M″=Si,Ge). All compounds were synthesized from melts of the elements and their crystal structures have been determined by means of single crystal X-ray diffraction. Sr{sub 2}PbGe{sub 2} (Cmmm, a=402.36(11), b=1542.3(4), c=463.27(10) pm) crystallizes with the Mn{sub 2}AlB{sub 2}-type structure. In exhibiting infinite planar Ge zig-zag chains, it represents one border of the compound series. Themore » other borderline case, where only [Ge{sub 2}] dumbbells are left as Ge building units, is represented by the Ca/Yb tin germanides Ca{sub 2}SnGe{sub 2} and Yb{sub 2}SnGe{sub 2} (Mo{sub 2}FeB{sub 2}-type; P4/mbm, a=748.58(13)/740.27(7), c=445.59(8)/435.26(5) pm). In between these two border structures compounds with variable Si/Ge chain lengths could be obtained by varying the averaged size of the A{sup II} cations: Ca{sub 0.45}Sr{sub 1.55}PbGe{sub 2} (new structure type; Pbam, a=791.64(5), b=2311.2(2), c=458.53(3) pm) contains planar six-membered chain segments [Ge{sub 6}]. Tetrameric pieces [Ge{sub 4}] are the conspicuous structure elements in Ca{sub 1.16}Sr{sub 0.84}SnGe{sub 2} and La{sub 2}InSi{sub 2} (La{sub 2}InNi{sub 2}-type; Pbam, a=781.01(2)/762.01(13), b=1477.95(3)/1494.38(6), c=457.004(9)/442.1(3) pm). The tetragonal form of ’La{sub 2}InSi{sub 2}{sup ′} (exact composition: La{sub 2}In{sub 1.07}Si{sub 1.93}, P4/mbm, a=1309.11(12), c=443.32(4) pm) also crystallizes in a new structure type, containing only [Si{sub 3}] trimers as cutouts of the planar chains. In all structures the Si/Ge zig-zag chains/chain segments are connected by In/Sn/Pb atoms to form planar M layers, which are separated by pure A

Optical absorption of zigzag single walled boron nitride nanotubes

NASA Astrophysics Data System (ADS)

Moradian, Rostam; Chegel, Raad; Behzad, Somayeh

2010-11-01

In a realistic three-dimensional model, optical matrix element and linear optical absorption of zigzag single walled boron nitride nanotubes (BNNTs) in the tight binding approximation are studied. In terms of absolute value of dipole matrix elements of the first three direct transitions at kz=0, we divided the zigzag BNNTs into three groups and investigated their optical absorption spectrum in energy ranges E<5, 77.5 eV. We found that in lower energies, E<5 eV, all groups show different behaviors while in the higher energies, 77.5 eV, their behaviors depend on their even or odd nanotube index. We also found that in the energy range 7

Which nanowire couples better electrically to a metal contact: Armchair or zigzag nanotube?

NASA Technical Reports Server (NTRS)

Anantram, M. P.; Biegel, Bryan (Technical Monitor)

2001-01-01

The fundamental question of how chirality affects tile electronic coupling of a nanotube to metal contacts is important for tile application of nanotubes as nanowires. We show that metallic-zigzag nanotubes are superior to armchair nanotubes as nanowires, by modeling the metal-nanotube interface. More specifically, we show that as a function of coupling strength, the total electron transmission of armchair nanotubes increases and tends to be pinned close to unity for a metal with Fermi wave vector close to that of gold. In contrast, the transmission probability of zigzag nanotubes increases to the maximum possible value of two. The origin of these effects lies in the details of the wave function, which is explained.

Pillared graphene on the basis of zigzag carbon nanotubes for adsorption in medicine: mechanical properties

NASA Astrophysics Data System (ADS)

Kolesnikova, Anna S.; Mazepa, Margarita M.

2018-02-01

In nowadays the nanoscale materials are actively used in medicine, based on the properties of adsorption. One of the main problems of this field of medicine is the increase in specific surface of sorbent. We proposed to use carbon composites consisting of an extended in its directions graphene sheet with attached to it by chemical bonds zigzag carbon nanotubes (CNT). This paper presents the results of a theoretical study of the mechanical properties of graphene based on the CNT zigzag depending on the geometric dimensions of the composite (length and diameter of CNTs).

Systematic study of aggregation structure and thermal behavior of a series of unique H-shape alkane molecules.

PubMed

Yamamoto, Hiroko; Tashiro, Kohji; Nemoto, Norio; Motoyama, Yukihiro; Takahashi, Yoshiaki

2011-08-11

The H-shape alkanes of various arm lengths have been synthesized successfully through the Grignard reaction. The detailed investigation of these novel compounds may allow us to widen the topological chemistry field furthermore. The molecular form and molecular packing structure in the crystal lattice have been revealed successfully on the basis of X-ray structure analysis as well as the analysis of Raman longitudinal acoustic modes (LAM) sensitive to the alkyl zigzag chain segments. The molecular conformation in the crystal lattice is deformed markedly from the originally imagined H-shape. In the cases of C3HOH to C6HOH, for example, the molecules are packed in a complicated manner and the OH···O hydrogen bonds govern the whole intermolecular interactions mainly. Since the alkyl segmental length is not very long, the conformational change is not very drastic, i.e., the small configurational entropy. Synergic effect of the hydrogen bonds and the small configurational entropy gives the higher melting point as known from the thermal data. On the other hand, in the cases of C10HOH and C12HOH, one of the long alkyl chain arms is found to be bent by 90° so that all of the alky chain segments of planar-zigzag conformation can be packed as closely as possible, and the intermolecular OH···O hydrogen bonds are also formed effectively without any mistake. As a result, the contribution of nonbonded intra- and intermolecular van der Waals interactions between the trans-zigzag alkyl chain segments become major, and the coupling of this enthalpy effect with the larger configurational entropy effect of the molecular shape results in the decrement of the melting point which approaches gradually that of longer n-alkane compound. In this way a sensitive balance between the nonbonded van der Waals interactions, the OH···O hydrogen bonds, as well as the configurational entropy effect gives the characteristic thermal behavior of the H-shape compounds. The thus

Surface-micromachined chain for use in microelectromechanical structures

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

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 beingmore » connected between the drive sprocket and one or more driven sprockets.« less

Application of silicon zig-zag wall arrays for anodes of Li-ion batteries

NASA Astrophysics Data System (ADS)

Li, G. V.; Rumyantsev, A. M.; Levitskii, V. S.; Beregulin, E. V.; Zhdanov, V. V.; Terukov, E. I.; Astrova, E. V.

2016-01-01

Cyclic tests of anodes based on zigzag wall arrays fabricated by the electrochemical etching and post-anodization treatment of silicon have been performed. Compared with anodes based on nanowires and planar thin films, these structures have several advantages. An ex situ analysis of the morphology and structural transformations in a material subjected to cyclic lithiation was conducted by electron microscopy and micro-Raman spectroscopy. The effect of geometrical parameters and a cycling mode on the degradation rate was studied. It is shown that a significant rise in the cycle life of the anode can be obtained by the restriction of the inserted amount of lithium. The anode, subjected to galvanostatic cycling at a rate C/2.8 at a limited charge capacity of 1000 mA · h g-1, demonstrates no degradation after 1200 cycles.

Quantifying side-chain conformational variations in protein structure

PubMed Central

Miao, Zhichao; Cao, Yang

2016-01-01

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. PMID:27845406

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.

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.

All-carbon sp-sp2 hybrid structures: Geometrical properties, current rectification, and current amplification

PubMed Central

Zhang, Zhenhua; Zhang, Junjun; Kwong, Gordon; Li, Ji; Fan, Zhiqiang; Deng, Xiaoqing; Tang, Guiping

2013-01-01

All-carbon sp-sp2 hybrid structures comprised of a zigzag-edged trigonal graphene (ZTG)and carbon chains are proposed and constructed as nanojunctions. It has been found that such simple hybrid structures possess very intriguing propertiesapp:addword:intriguing. The high-performance rectifying behaviors similar to macroscopic p-n junction diodes, such as a nearly linear positive-bias I-V curve (metallic behavior), a very small leakage current under negative bias (insulating behavior), a rather low threshold voltage, and a large bias region contributed to a rectification, can be predicted. And also, a transistor can be built by such a hybrid structure, which can show an extremely high current amplification. This is because a sp-hybrid carbon chain has a special electronic structure which can limit the electronic resonant tunneling of the ZTG to a unique and favorable situation. These results suggest that these hybrid structures might promise importantly potential applications for developing nano-scale integrated circuits. PMID:23999318

Magneto-structural correlation in a series of bimetallic alternating chain complexes of [CrIIIL(CN)4]n[MnIII(salpn)]n.nsolvents (L=2,2'-bipy or 9,10-phen, salpn=substituted salicyldehyde, solvents=water and methanol).

PubMed

Pan, Feng; Wang, Zhe-Ming; Gao, Song

2007-11-26

Five chain compounds based on the building block of [Cr(L)(CN)4]- (L=2,2'-bipy, 1-4; L=9,10-phen, 5) and [Mn(salpn)]+ (salpn=substituted salicyldehyde-type Schiff base in Scheme 1) have been prepared and characterized structurally and magnetically. The four compounds (1-4) consisting of [Cr(bipy)(CN)4]- units possess straight bimetallic chains as the [Cr(bpy)(CN)4]- unit links the two neighbor [Mn(salpn)]+ units with the two trans-cyanide ligands, while in 5 the chain is zigzag because the [Cr(phen)(CN)4]- unit connects the [Mn(salpn)]+ units with its two cis-cyanide ligands. The bond angles of Mn-N-C-Cr are adjusted by different coligands of salpn and bipy/phen. The chains are stacking via mainly the aromatic pi-pi-type interactions. All compounds show 3D antiferromagnetic ordering with Néel temperatures ranging from 3.7 to 8.1 K, and they are metamagnets displaying antiferromagnetic to ferrimagnetic transition at critical fields of 4.0-13.1 kOe at 1.9 K. This is due to weak interchain antiferromagnetic interactions between the ferrimagnetic bimetallic chains in the materials. The intrachain couplings (J, in cm(-1)) in the materials, between cyanide-bridged CrIII and MnIII ions, from -1.84 to -5.35 cm(-1), follow a linear relationship (J=-33+0.18alpha) to the Mn-N-C angles (alpha, in deg). In addition, the weak interchain antiferromagnetic interactions and critical fields for antiferromagnetic-ferrimagnetic transition are closely related to some of their structural factors, which were studied very superficially only referring to the separations of nearest chains in each material.

Electronic and magnetic properties of zigzag silicene nanoribbons with Stone–Wales defects

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

Dong, Haixia; Institute of Solid State Physics, Shanxi Datong University, Datong 037009; Fang, Dangqi

2015-02-14

The structural, electronic, and magnetic properties of zigzag silicene nanoribbons (ZSiNRs) with Stone–Wales (SW) defects were investigated using first-principles calculations. We found that two types of SW defects (named SW-Ι and SW-ΙΙ) exist in ZSiNRs. The SW defect was found to be the most stable at the edge of the ZSiNR, independently of the defect orientation, even more stable than it is in an infinite silicene sheet. In addition, the ZSiNRs can transition from semiconductor to metal or half-metal by modifying the SW defect location and concentration. For the same defect concentration, the band structures influenced by the SW-Ι defectmore » are more distinct than those influenced by the SW-ΙΙ when the SW defect is at the edge. The present study suggests the possibility of tuning the electronic properties of ZSiNRs using the SW defects and might motivate their potential application in nanoelectronics and spintronics.« less

Drawing dependent structures, mechanical properties and cyclization behaviors of polyacrylonitrile and polyacrylonitrile/carbon nanotube composite fibers prepared by plasticized spinning.

PubMed

Li, Xiang; Qin, Aiwen; Zhao, Xinzhen; Liu, Dapeng; Wang, Haiye; He, Chunju

2015-09-14

Drawing to change the structural properties and cyclization behaviors of the polyacrylonitrile (PAN) chains in crystalline and amorphous regions is carried out on PAN and PAN/carbon nanotube (CNT) composite fibers. Various characterization methods including Fourier transform infrared spectroscopy, differential scanning calorimetry, X-ray diffraction and thermal gravimetric analysis are used to monitor the structural evolution and cyclization behaviors of the fibers. With an increase of the draw ratio during the plasticized spinning process, the structural parameters of the fibers, i.e. crystallinity and planar zigzag conformation, are decreased at first, and then increased, which are associated with the heat exchange rate and the oriented-crystallization rate. A possible mechanism for plasticized spinning is proposed to explain the changing trends of crystallinity and planar zigzag conformation. PAN and PAN/CNT fibers exhibit various cyclization behaviors induced by drawing, e.g., the initiation temperature for the cyclization (Ti) of PAN fibers is increased with increasing draw ratio, while Ti of PAN/CNT fibers is decreased. Drawing also facilitates cyclization and lowers the percentage of β-amino nitrile for PAN/CNT fibers during the stabilization.

Protein-linked Ubiquitin Chain Structure Restricts Activity of Deubiquitinating Enzymes*

PubMed Central

Schaefer, Jonathan B.; Morgan, David O.

2011-01-01

The attachment of lysine 48 (Lys48)-linked polyubiquitin chains to proteins is a universal signal for degradation by the proteasome. Here, we report that long Lys48-linked chains are resistant to many deubiquitinating enzymes (DUBs). Representative enzymes from this group, Ubp15 from yeast and its human ortholog USP7, rapidly remove mono- and diubiquitin from substrates but are slow to remove longer Lys48-linked chains. This resistance is lost if the structure of Lys48-linked chains is disrupted by mutation of ubiquitin or if chains are linked through Lys63. In contrast to Ubp15 and USP7, Ubp12 readily cleaves the ends of long chains, regardless of chain structure. We propose that the resistance to many DUBs of long, substrate-attached Lys48-linked chains helps ensure that proteins are maintained free from ubiquitin until a threshold of ubiquitin ligase activity enables degradation. PMID:22072716

Chain and mirophase-separated structures of ultrathin polyurethane films

NASA Astrophysics Data System (ADS)

Kojio, Ken; Uchiba, Yusuke; Yamamoto, Yasunori; Motokucho, Suguru; Furukawa, Mutsuhisa

2009-08-01

Measurements are presented how chain and microphase-separated structures of ultrathin polyurethane (PU) films are controlled by the thickness. The film thickness is varied by a solution concentration for spin coating. The systems are PUs prepared from commercial raw materials. Fourier-transform infrared spectroscopic measurement revealed that the degree of hydrogen bonding among hard segment chains decreased and increased with decreasing film thickness for strong and weak microphase separation systems, respectively. The microphase-separated structure, which is formed from hard segment domains and a surrounding soft segment matrix, were observed by atomic force microscopy. The size of hard segment domains decreased with decreasing film thickness, and possibility of specific orientation of the hard segment chains was exhibited for both systems. These results are due to decreasing space for the formation of the microphase-separated structure.

Enhancement of thermoelectric figure of merit in zigzag graphene nanoribbons with periodic edge vacancies

NASA Astrophysics Data System (ADS)

Kolesnikov, D. V.; Sadykova, O. G.; Osipov, V. A.

2017-06-01

The influence of periodic edge vacancies and antidot arrays on the thermoelectric properties of zigzag graphene nanoribbons (ZGNRs) are investigated. Using Green’s function method, the tight-binding approximation for the electron Hamiltonian and the 4th nearest neighbor approximation for the phonon dynamical matrix, we calculate the Seebeck coefficient and the thermoelectric figure of merit. It is found that, at a certain periodic arrangement of vacancies on both edges of zigzag nanoribbon, a finite band gap opens and almost twofold degenerate energy levels appear. As a result, a marked increase in the Seebeck coefficient takes place. It is shown that an additional enhancement of the thermoelectric figure of merit can be achieved by a combination of periodic edge defects with an antidot array.

Crystal structure of catena-poly[N,N,N′,N′-tetra­methyl­guanidinium [(chlorido­cadmate)-di-μ-chlorido

PubMed Central

Ndiaye, Mamadou; Samb, Abdoulaye; Diop, Libasse; Maris, Thierry

2016-01-01

In the structure of the title salt, {(C5H14N3)[CdCl3]}n, the CdII atom of the complex anion is five-coordinated by one terminal and four bridging Cl atoms. The corresponding coordination polyhedron is a distorted trigonal bipyramid, with Cd—Cl distances in the range 2.4829 (4)–2.6402 (4) Å. The bipyramids are condensed into a polyanionic zigzag chain extending parallel to [101]. The tetra­methyl­guanidinium cations are situated between the polyanionic chains and are linked to them through N—H⋯Cl hydrogen bonds, forming a layered network parallel to (010). PMID:26870572

Crystal structure of 3-({[(morpholin-4-yl)carbono-thio-yl]sulfan-yl}acet-yl)phenyl benzoate.

PubMed

Ambekar, Sachin P; Mahesh Kumar, K; Shirahatti, Arun Kumar M; Kotresh, O; Anil Kumar, G N

2014-11-01

In the title compound, C20H19NO4S2, the morpholine ring adopts the expected chair conformation. The central phenyl ring makes dihedral angles of 67.97 (4) and 7.74 (3)°, respectively, with the benzoate phenyl ring and the morpholine mean plane. In the crystal, mol-ecules are linked by C-H⋯O hydrogen bonds, forming zigzag chains along the b-axis direction. C-H⋯π inter-actions link centrosymmetrically related mol-ecules, reinforcing the three-dimensional structure.

Superconductivity of Ca2 InN with a layered structure embedding an anionic indium chain array

NASA Astrophysics Data System (ADS)

Jeong, Sehoon; Matsuishi, Satoru; Lee, Kimoon; Toda, Yoshitake; Wng Kim, Sung; Hosono, Hideo

2014-05-01

We report the emergence of superconductivity in Ca2InN consisting of a two-dimensional (2D) array of zigzag indium chains embedded between Ca2N layers. A sudden drop of resistivity and a specific heat (Cp) jump attributed to the superconducting transition were observed at 0.6 K. The Sommerfeld coefficient γ = 4.24 mJ mol-1K-2 and Debye temperature ΘD = 322 K were determined from the Cp of the normal conducting state and the superconducting volume fraction was estimated to be ˜80% from the Cp jump, assuming a BCS-type weak coupling. Density functional theory calculations demonstrated that the electronic bands near the Fermi level (EF) are mainly derived from In 5p orbitals with π and σ bonding states and the Fermi surface is composed of cylindrical parts, corresponding to the quasi-2D electronic state of the In-chain array. By integrating the projected density of states of the In-p component up to EF, a valence electron population of ˜1.6 electrons/In was calculated, indicating that partially anionic state of In. The In 3d binding energies observed in Ca2InN by x-ray photoemission spectroscopy were negatively shifted from that in In metal. The superconductivity of Ca2InN is associated with the p-p bonding states of the anionic In layer.

Energetics and electronic structures of chemically decorated C60 chains

NASA Astrophysics Data System (ADS)

Furutani, Sho; Okada, Susumu

2018-06-01

We studied the energetics and electronic structures of one-dimensional molecular chains of [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) using the density functional theory (DFT). Our DFT calculations show that the binding energies of PCBM range from 90 to 300 meV, depending on not only the intermolecular spacing but also the intermolecular arrangements owing to the interaction between functional groups and C60. The electronic structure of PCBM chains are also sensitive to the mutual arrangements of PCBM in their chain structure. The calculated effective masses of the conduction band range from 0.58 to 634.97m e, giving rise to anisotropic transport properties in their condensed phase.

An Implementation of RC4+ Algorithm and Zig-zag Algorithm in a Super Encryption Scheme for Text Security

NASA Astrophysics Data System (ADS)

Budiman, M. A.; Amalia; Chayanie, N. I.

2018-03-01

Cryptography is the art and science of using mathematical methods to preserve message security. There are two types of cryptography, namely classical and modern cryptography. Nowadays, most people would rather use modern cryptography than classical cryptography because it is harder to break than the classical one. One of classical algorithm is the Zig-zag algorithm that uses the transposition technique: the original message is unreadable unless the person has the key to decrypt the message. To improve the security, the Zig-zag Cipher is combined with RC4+ Cipher which is one of the symmetric key algorithms in the form of stream cipher. The two algorithms are combined to make a super-encryption. By combining these two algorithms, the message will be harder to break by a cryptanalyst. The result showed that complexity of the combined algorithm is θ(n2 ), while the complexity of Zig-zag Cipher and RC4+ Cipher are θ(n2 ) and θ(n), respectively.

Studies of mixed-chain diacyl phosphatidylcholines with highly asymmetric acyl chains: a Fourier transform infrared spectroscopic study of interfacial hydration and hydrocarbon chain packing in the mixed interdigitated gel phase.

PubMed Central

Lewis, R N; McElhaney, R N

1993-01-01

The mixed interdigitated gel phases of unlabeled, specifically 13C = O-labeled, and specifically chain-perdeuterated samples of 1-O-eicosanoyl, 2-O-lauroyl phosphatidylcholine and 1-O-decanoyl, 2-O-docosanoyl phosphatidylcholine were studied by infrared spectroscopy. Our results suggest that at the liquid-crystalline/gel phase transition temperatures of these lipids, there is a greater redistribution in the populations of free and hydrogen-bonded ester carbonyl groups than is commonly observed with symmetric chain n-saturated diacyl phosphatidylcholines. The formation of the mixed interdigitated gel phase coincides with the appearance of a marked asymmetry in the contours of the C = O stretching band, a process which becomes more pronounced as the temperature is reduced. This asymmetry is ascribed to the emergence of a predominant lipid population consisting of free sn1- and hydrogen-bonded (hydrated) sn2-ester carbonyl groups. This suggests that the region of the mixed interdigitated bilayer polar/apolar interface near to the sn1-ester carbonyl group is less hydrated than is the case with the noninterdigitated gel-phase bilayers formed by normal symmetric chain phosphatidylcholines. In the methylene deformation region of the spectrum, the unlabeled lipids exhibit a pronounced splitting of the CH2 scissoring bands. This splitting is significantly attenuated when the short chains are perdeuterated and collapses completely upon perdeuteration of the long chains, irrespective of whether the long (or short) chains are esterified to the sn1 or sn2 positions of the glycerol backbone. These results are consistent with a global hydrocarbon chain packing motif in which the zigzag planes of the hydrocarbon chains are perpendicular to each other and the sites occupied by long chains are twice as numerous as those occupied by short chains. The experimental support for this chain-packing motif enabled more detailed considerations of the possible ways in which these lipid

Structure-directing weak phosphoryl XH...O=P (X = C, N) hydrogen bonds in cyclic oxazaphospholidines and oxazaphosphinanes.

PubMed

van der Lee, A; Rolland, M; Marat, X; Virieux, D; Volle, J N; Pirat, J L

2008-04-01

The structures of six cyclic oxazaphospholidines and three cyclic oxazaphosphinanes have been determined and their supramolecular structures have been compared. The molecules differ with respect to the functional groups attached to the central five- or six-membered rings, but have one phosphoryl group in common. The predominant feature in the supramolecular structures is the existence of relatively weak intermolecular phosphoryl XH...O=P (X = C, N) hydrogen bonds, creating in nearly all cases linear zigzag or double molecular chains. The molecular chains are in general linked to each other via very weak CH...pi or usual hydrogen-bond interactions. A survey of the Cambridge Structural Database on similar XH...O=P interactions shows a very large flexibility of the XH...O angle, which is in agreement with the DFT calculation reported elsewhere. The strength of the XH...O=P interaction can therefore be considered as relatively weak to moderately strong, and is expected to play at least a role in the formation of secondary substructures.

Platinum atomic wire encapsulated in gold nanotubes: A first principle study

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

Nigam, Sandeep, E-mail: snigam@barc.gov.in; Majumder, Chiranjib; Sahoo, Suman K.

2014-04-24

The nanotubes of gold incorporated with platinum atomic wire have been investigated by means of firstprinciples density functional theory with plane wave pseudopotential approximation. The structure with zig-zag chain of Pt atoms in side gold is found to be 0.73 eV lower in energy in comparison to straight chain of platinum atoms. The Fermi level of the composite tube was consisting of d-orbitals of Pt atoms. Further interaction of oxygen with these tubes reveals that while tube with zig-zag Pt prefers dissociative adsorption of oxygen molecule, the gold tube with linear Pt wire favors molecular adsorption.

Thermal Lens Measurement in Diode-Pumped Nd:YAG Zig-Zag Slab

NASA Technical Reports Server (NTRS)

Smoak, M. C.; Kay, R. B.; Coyle, D. B.; Hopf, D.

1998-01-01

A major advantage that solid state zig-zag slab lasers have over conventional rod-based designs is that a much weaker thermal lens is produced in the slab when side-pumped with Quasi-CW laser diode arrays, particularly if the pump radiation is kept well away from the Brewster-cut ends. This paper reports on a rather strong thermal lens produced when diode pump radiation is collimated into a narrow portion of the zig-zag slab. The collimation of multi-bar pump packages to increase brightness and improve overlap is a direct consequence of designs which seek to maximize performance and efficiency. Our slab design employed a 8.1 cm x 2.5 mm x 5 mm slab with opposing Brewster end faces. It was pumped through the 2.5 mm direction by seven laser diode array packages, each housing four 6OW diode bars, 1 cm in width. The pump face, anti-reflection (AR) coated at 809 nm, was 6.8 cm in width and the 8.1 cm opposing side, high-reflection (HR) coated at 809 nm, reflected the unabsorbed pump beam for a second pass through the slab.

Functionalization and migration of bromine adatoms on zigzag graphene nanoribbons: A first-principles study

NASA Astrophysics Data System (ADS)

Jaiswal, Neeraj K.; Kumar, Amit; Patel, Chandrabhan

2018-05-01

Tailoring the electronic band gap of graphene nanoribbons (GNR) through edge functionalization and understanding the adsorption of guest adatoms on GNR is crucial for realization of upcoming organic devices. In the present work, we have investigated the structural stability and electronic property of bromine (Br) termination at the edges of zigzag GNR (ZGNR). The migration pathways of Br adatom on ZGNR have also been discussed along four different diffusion paths. It is revealed that Br termination induces metallicity in ZGNR and caused upward shifting of Fermi level. Further, the migration is predicted to take place preferable along the ribbon edges whereas across the ribbon width, migration is least probable to take place due to sufficiently higher migration barrier of ˜160 meV.

Dispersion relations for circular single and double dusty plasma chains

NASA Astrophysics Data System (ADS)

Tkachenko, D. V.; Sheridan, T. E.; Misko, V. R.

2011-10-01

We derive dispersion relations for a system of identical particles confined in a two-dimensional annular harmonic well and which interact through a Yukawa potential, e.g., a dusty plasma ring. When the particles are in a single chain (i.e., a one-dimensional ring), we find a longitudinal acoustic mode and a transverse optical mode which show approximate agreement with the dispersion relation for a straight configuration for large radii of the ring. When the radius decreases, the dispersion relations modify: there appears an anticrossing of the modes near the crossing point resulting in a frequency gap between the lower and upper branches of the modified dispersion relations. For the double chain (i.e., a two-dimensional zigzag configuration), the dispersion relation has four branches: longitudinal acoustic and optical and transverse acoustic and optical.

Redetermination of the borax structure from laboratory X-ray data at 145 K

PubMed Central

Gainsford, Graeme J.; Kemmitt, Tim; Higham, Caleb

2008-01-01

The title compound, sodium tetraborate decahydrate (mineral name: borax), Na2[B4O5(OH)4]·8H2O, has been studied previously using X-ray [Morimoto (1956). Miner. J. 2, 1–18] and neutron [Levy & Lisensky (1978). Acta Cryst. B34, 3502–3510] diffraction data. The structure contains tetra­borate anions [B4O5(OH)4]2− with twofold rotation symmetry, which form hydrogen-bonded chains, and [Na(H2O)6] octa­hedra that form zigzag chains [Na(H2O)4/2(H2O)2/1]. The O—H bond distances obtained from the present redetermination at 145 K are shorter than those in the neutron study by an average of 0.127 (19) Å. PMID:21202161

A New, Simple and Versatile Strategy for the Synthesis of Short Segments of Zigzag-Type Carbon Nanotubes.

PubMed

André, Etienne; Boutonnet, Baptiste; Charles, Pauline; Martini, Cyril; Aguiar-Hualde, Juan-Manuel; Latil, Sylvain; Guérineau, Vincent; Hammad, Karim; Ray, Priyanka; Guillot, Régis; Huc, Vincent

2016-02-24

Short segments of zigzag single-walled carbon nanotubes (SWCNTs) were obtained from a calixarene scaffold by using a completely new, simple and expedited strategy that allowed fine-tuning of their diameters. This new approach also allows for functionalised short segments of zigzag SWCNTs to be obtained; a prerequisite towards their lengthening. These new SWCNT short segments/calixarene composites show interesting behaviour in solution. DFT analysis of these new compounds also suggests interesting photophysical behaviour. Along with the synthesis of various SWCNTs segments, this approach also constitutes a powerful tool for the construction of new, radially oriented π systems. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Unique Zigzag-Shaped Buckling Zn2C Monolayer with Strain-Tunable Band Gap and Negative Poisson Ratio.

PubMed

Meng, Lingbiao; Zhang, Yingjuan; Zhou, Minjie; Zhang, Jicheng; Zhou, Xiuwen; Ni, Shuang; Wu, Weidong

2018-02-19

Designing new materials with reduced dimensionality and distinguished properties has continuously attracted intense interest for materials innovation. Here we report a novel two-dimensional (2D) Zn 2 C monolayer nanomaterial with exceptional structure and properties by means of first-principles calculations. This new Zn 2 C monolayer is composed of quasi-tetrahedral tetracoordinate carbon and quasi-linear bicoordinate zinc, featuring a peculiar zigzag-shaped buckling configuration. The unique coordinate topology endows this natural 2D semiconducting monolayer with strongly strain tunable band gap and unusual negative Poisson ratios. The monolayer has good dynamic and thermal stabilities and is also the lowest-energy structure of 2D space indicated by the particle-swarm optimization (PSO) method, implying its synthetic feasibility. With these intriguing properties the material may find applications in nanoelectronics and micromechanics.

The complex metal-rich boride Ti1+xRh2-x+yIr3-yB3 (x=0.68, y=1.06) with a new structure type containing B4 zigzag fragments: Synthesis, crystal chemistry and theoretical calculations

NASA Astrophysics Data System (ADS)

Goerens, Christian; Fokwa, Boniface P. T.

2012-08-01

Polycrystalline samples and single crystals of the new complex boride Ti1+xRh2-x+yIr3-yB3 (x=0.68; y=1.06) were synthesized by arc-melting the elements in a water-cooled copper crucible under an argon atmosphere and characterized by X-Ray diffraction as well as EDX measurements. The crystal structure was refined on the basis of single crystal data. The new phase, which represents a new structure type containing trans zigzag B4 fragments as well as isolated boron atoms crystallizes in the orthorhombic space group Pbam (Nr. 55) with the lattice parameters a=8.620(1) Å, b=14.995(2) Å and c=3.234(1) Å. First-principles density functional theory calculations using the Vienna ab-initio simulation package (VASP) were performed on an appropriate structural model (using a supercell approach) and the experimental crystallographic data could be reproduced accurately. Based on this model, the density of states and crystal orbital Hamilton population (for bonding analysis) were calculated, using the linear muffin-tin orbital atomic sphere approximation (LMTO-ASA) method. According to these calculations, this metal-rich compound should be metallic, as expected. Furthermore, very strong boron-boron interactions are observed in the trans zigzag B4 fragment, which induce a clear differentiation of two types of metal-boron contacts with different strength. The observed three-dimensional metal-metal interaction is in good agreement with the predicted metallic behavior.

Enzymatic preparation of structured oils containing short-chain fatty acids.

PubMed

Kanda, Ayato; Namiki, Fusako; Hara, Setsuko

2010-01-01

Structured oils prepared by enzymatic transacylation with triacylglycerols (TAGs) and various fatty acids (FAs) were characterized. Transacylation with trilaurin and saturated FAs (C4:0-C16:0) was performed using Lipozyme RM-IM under standard reaction conditions. The structured oils thus produced had transacylation ratios of 25-37%, as medium-chain FAs > long-chain FAs > short-chain FAs. This result confirmed that short-chain FAs have little reactivity in enzymatic transacylation. All prepared oils shared the same composition of TAG molecular species, as demonstrated by HPLC analysis, and contained a mixture of mono-substituted, di-substituted, and non-substituted TAGs. The reaction conditions for transacylation with TAGs and short-chain FAs were optimized to improve transacylation ratios. The introduction ratios of C4:0, C5:0, and C6:0 into trilaurin were increased to 52.4, 42.5, and 34.1%, respectively, by extending the reaction time. Transacylation between TAGs and short-chain FAs was further examined by using Lipase PL. C4:0 was introduced at 51.1%, the same ratio as for Lipozyme RM-IM. When C5:0 and C6:0 were used as the FA substrate, the transacylation ratios obtained were 47.7 and 43.4%, respectively, higher than those for Lipase RM-IM. Lipase PL is therefore useful for introducing short-chain FAs into TAGs.

Dispersion relations for circular single and double dusty plasma chains

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

Tkachenko, D. V.; Misko, V. R.; Sheridan, T. E.

2011-10-15

We derive dispersion relations for a system of identical particles confined in a two-dimensional annular harmonic well and which interact through a Yukawa potential, e.g., a dusty plasma ring. When the particles are in a single chain (i.e., a one-dimensional ring), we find a longitudinal acoustic mode and a transverse optical mode which show approximate agreement with the dispersion relation for a straight configuration for large radii of the ring. When the radius decreases, the dispersion relations modify: there appears an anticrossing of the modes near the crossing point resulting in a frequency gap between the lower and upper branchesmore » of the modified dispersion relations. For the double chain (i.e., a two-dimensional zigzag configuration), the dispersion relation has four branches: longitudinal acoustic and optical and transverse acoustic and optical.« less

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.

Low resistivity of graphene nanoribbons with zigzag-dominated edge fabricated by hydrogen plasma etching combined with Zn/HCl pretreatment

NASA Astrophysics Data System (ADS)

Liu, Fengkui; Li, Qi; Wang, Rubing; Xu, Jianbao; Hu, Junxiong; Li, Weiwei; Guo, Yufen; Qian, Yuting; Deng, Wei; Ullah, Zaka; Zeng, Zhongming; Sun, Mengtao; Liu, Liwei

2017-11-01

Graphene nanoribbons (GNRs) have attracted intensive research interest owing to their potential applications in high performance graphene-based electronics. However, the deterioration of electrical performance caused by edge disorder is still an important obstacle to the applications. Here, we report the fabrication of low resistivity GNRs with a zigzag-dominated edge through hydrogen plasma etching combined with the Zn/HCl pretreatment method. This method is based on the anisotropic etching properties of hydrogen plasma in the vicinity of defects created by sputtering zinc (Zn) onto planar graphene. The polarized Raman spectra measurement of GNRs exhibits highly polarization dependence, which reveals the appearance of the zigzag-dominated edge. The as-prepared GNRs exhibit high carrier mobility (˜1332.4 cm2 v-1 s-1) and low resistivity (˜0.7 kΩ) at room temperature. Particularly, the GNRs can carry large current density (5.02 × 108 A cm-2) at high voltage (20.0 V) in the air atmosphere. Our study develops a controllable method to fabricate zigzag edge dominated GNRs for promising applications in transistors, sensors, nanoelectronics, and interconnects.

Crystal structure of 3-({[(morpholin-4-yl)carbono­thio­yl]sulfan­yl}acet­yl)phenyl benzoate

PubMed Central

Ambekar, Sachin P.; Mahesh Kumar, K.; Shirahatti, Arun Kumar M.; Kotresh, O.; Anil Kumar, G. N.

2014-01-01

In the title compound, C20H19NO4S2, the morpholine ring adopts the expected chair conformation. The central phenyl ring makes dihedral angles of 67.97 (4) and 7.74 (3)°, respectively, with the benzoate phenyl ring and the morpholine mean plane. In the crystal, mol­ecules are linked by C—H⋯O hydrogen bonds, forming zigzag chains along the b-axis direction. C—H⋯π inter­actions link centrosymmetrically related mol­ecules, reinforcing the three-dimensional structure. PMID:25484757

Tertiary structure of human {Lambda}6 light chains.

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

Pokkuluri, P. R.; Solomon, A.; Weiss, D. T.

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 thatmore » 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

Metal aminocarboxylate coordination polymers with chain and layered structures.

PubMed

Dan, Meenakshi; Rao, C N R

2005-11-18

The synthesis and structures of metal aminocarboxylates prepared in acidic, neutral, or alkaline media have been explored with the purpose of isolating coordination polymers with linear chain and two-dimensional layered structures. Metal glycinates of the formulae [CoCl2(H2O)2(CO2CH2NH3)] (I), [MnCl2(CO2CH2NH3)2] (II), and [Cd3Cl6(CO2CH2NH3)4] (III) with one-dimensional chain structures have been obtained by the reaction of the metal salts with glycine in an acidic medium under hydro/solvothermal conditions. These chain compounds contain glycine in the zwitterionic form. 4-Aminobutyric acid transforms to a cyclic amide under such reaction conditions, and the amide forms a chain compound of the formula [CdBr2(C4H7NO)2] (IV). Glycine in the zwitterionic form also forms a two-dimensional layered compound of the formula [Mn(H2O)2(CO2CH2NH3)2]Br2 (V). 6-Aminocaproic acid under alkaline conditions forms layered compounds with metals at room temperature, the metal being coordinated both by the amino nitrogen and the carboxyl oxygen atoms. Of the two layered compounds [Cd{CO2(CH2)5NH2}2]2 H2O (VI) and [Cu{CO2(CH2)5NH2}2]2 H2O (VII), the latter has voids in which water molecules reside.

Synthesis, characterization and crystal structure of a 1D thiocyanato bridged [Cu(en)2Zn(NCS)4]ṡH2O. Comparison of the three structures with the same [Cu(en)2Zn(NCS)4] unit - different in structural terms

NASA Astrophysics Data System (ADS)

Wrzeszcz, Grzegorz; Muzioł, Tadeusz M.; Tereba, Natalia

2015-03-01

In this paper we report the synthesis method and the structure of a one-dimensional thiocyanato bridged heterometallic compound, [Cu(en)2Zn(NCS)4]ṡH2O (1). Moreover, we compare the structure of (1) with the previously described structures of [Cu(en)2Zn(NCS)4]ṡ0.5H2O (2) and [Cu(en)2Zn(NCS)4]ṡCH3CN (3) Pryma et al. (2003) [7]. The compound (1) has been characterized by thermal decomposition, IR, Vis and EPR spectra, and magnetic studies. Structure has been determined by X-ray analysis. Described coordination polymer crystallizes in the orthorhombic Cmcm space group with a = 12.414(2), b = 10.3276(14), c = 14.967(2) Å, α = β = γ = 90°, V = 1918.8(5) Å3 and Z = 4. Each distorted tetrahedral zinc(II) centre (with N-bonded NCS-) links two tetragonally distorted octahedral copper(II) centres by two end-to-end thiocyanato bridges and vice versa forming a zigzag type of CuZn chain. The structures of (1), (2) and (3) differ in crystallographic system, space group and/or CuZn chain type as well as in details. Variable temperature magnetic susceptibility measurements show very weak antiferromagnetic interactions between the paramagnetic copper(II) ions for compound (1).

Spin Transport in Electric-Barrier-Modulated Ferromagnetic/Normal/Ferromagnetic Monolayer Zigzag MoS2 Nanoribbon Junction

NASA Astrophysics Data System (ADS)

Xia, Y.-Y.; Yuan, R.-Y.; Yang, Q.-J.; Sun, Q.; Zheng, J.; Guo, Y.

In this paper, with the three-band tight-binding model and non-equilibrium Green’s function technique, we investigate spin transport in electric-barrier-modulated Ferromagnetic/Normal/Ferromagnetic (F/N/F) monolayer (ML) zigzag MoS2 nanoribbon junction. The results demonstrate that once the double electric barriers structure emerges, the oscillations of spin conductances become violent, especially for spin-down conductance, the numbers of resonant peaks increase obviously, thus we can obtain 100% spin polarization in the low energy region. It is also found that with the intensity of the exchange field enhancement, the resonant peaks of spin-up and spin-down conductances move in the opposite direction in a certain energy region. As a consequence, the spin-down conductance can be filtered out completely. The findings here indicate that the present structure may be considered as a good candidate for spin filter.

Modeling Bi-induced changes in the electronic structure of GaAs1-xBix alloys

NASA Astrophysics Data System (ADS)

Virkkala, Ville; Havu, Ville; Tuomisto, Filip; Puska, Martti J.

2013-12-01

We suggested recently [V. Virkkala , Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.88.035204 88, 035204 (2013)] that the band-gap narrowing in dilute GaAs1-xNx alloys can be explained to result from the broadening of the localized N states due to the N-N interaction along the zigzag chains in the <110> directions. In that study our tight-binding modeling based on first-principles density-functional calculations took into account the random distribution of N atoms in a natural way. In this work we extend our modeling to GaAs1-xBix alloys. Our results indicate that Bi states mix with host material states. However, the states near the valence-band edge agglomerate along the zigzag chains originating from individual Bi atoms. This leads to Bi-Bi interactions in a random alloy broadening these states in energy and causing the band-gap narrowing.

Discovery of the beta-form crystal structure in electrospun nanofibers of bio-based poly[(R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate] and its implication on properties

NASA Astrophysics Data System (ADS)

Gong, Liang

Bacterially produced poly[(R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate] (PHBHx) is a new type of bioplastic which not only inherits the excellent biodegradability and biocompatibility of its parent homopolymer, polyhydroxybutyrate (PHB), but also overcomes PHB’s brittleness and stiffness with the incorporation of 3-hydroxyhexanoate (Hx) comonomer units with medium-chain-length (mcl) side chains. The tough and ductile PHBHx, with a much lower crystallinity and melting temperature, is well-suited for many practical applications. Efforts have been made to broaden the application range of PHBHx by introducing the beta-form crystalline structure, where the molecular chains adopt a planar zig-zag conformation. However, it is extremely difficult to produce this beta-form in PHBHx due to its much lower crystallinity and much more flexible molecular chains. In this study, we report an approach using the technique of electrospinning. The strain-induced metastable β-form crystalline structure was successfully introduced in PHBHx by collecting the macroscopically aligned electrospun PHBHx nanofibers across the air gap on a piece of aluminum foil and on the tapered edge of a high-speed rotary disk. The presence of the β-form crystal structure in electrospun fiber mats was confirmed by wide-angle X-ray diffraction (WAXD) and Fourier transform infrared spectroscopy (FTIR), with molecular orientation of the polymer chains along the fiber axis revealed by polarized FTIR. Selected area electron diffraction (SAED) and AFM-IR were utilized to investigate the morphological and structural details of individual PHBHx nanofibers. The results demonstrated a coexistence of the thermodynamically stable α-form crystalline structure, where molecular chains adopt a left-handed 21 helical conformation, and the β-form in single fibers. The molecular orientation level and the relative amounts of the two crystalline polymorphs were found to be highly dependent on fiber collection methods

Inhibition of telomerase by linear-chain fatty acids: a structural analysis.

PubMed Central

Oda, Masako; Ueno, Takamasa; Kasai, Nobuyuki; Takahashi, Hirotada; Yoshida, Hiromi; Sugawara, Fumio; Sakaguchi, Kengo; Hayashi, Hideya; Mizushina, Yoshiyuki

2002-01-01

In the present study, we have found that mono-unsaturated linear-chain fatty acids in the cis configuration with C(18) hydrocarbon chains (i.e. oleic acid) strongly inhibited the activity of human telomerase in a cell-free enzymic assay, with an IC(50) value of 8.6 microM. Interestingly, fatty acids with hydrocarbon chain lengths below 16 or above 20 carbons substantially decreased the potency of inhibition of telomerase. Moreover, the cis-mono-unsaturated C(18) linear-chain fatty acid oleic acid was the strongest inhibitor of all the fatty acids tested. A kinetic study revealed that oleic acid competitively inhibited the activity of telomerase ( K (i)=3.06 microM) with respect to the telomerase substrate primer. The energy-minimized three-dimensional structure of the linear-chain fatty acid was calculated and modelled. A molecule width of 11.53-14.26 A (where 1 A=0.1 nm) in the C(16) to C(20) fatty acid structure was suggested to be important for telomerase inhibition. The three-dimensional structure of the telomerase active site (i.e. the substrate primer-binding site) appears to have a pocket that could bind oleic acid, with the pocket being 8.50 A long and 12.80 A wide. PMID:12121150

Crystal Structures of Lys-63-linked tri- and di-ubiquitin Reveal a Highly Extended Chain Architecture

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

Weeks, S.; Grasty, K; Hernandez-Cuebas, L

2009-01-01

The covalent attachment of different types of poly-ubiquitin chains signal different outcomes for the proteins so targeted. For example, a protein modified with Lys-48-linked poly-ubiquitin chains is targeted for proteasomal degradation, whereas Lys-63-linked chains encode nondegradative signals. The structural features that enable these different types of chains to encode different signals have not yet been fully elucidated. We report here the X-ray crystal structures of Lys-63-linked tri- and di-ubiquitin at resolutions of 2.3 and 1.9 {angstrom}, respectively. The tri- and di-ubiquitin species adopt essentially identical structures. In both instances, the ubiquitin chain assumes a highly extended conformation with a left-handedmore » helical twist; the helical chain contains four ubiquitin monomers per turn and has a repeat length of {approx}110 {angstrom}. Interestingly, Lys-48 ubiquitin chains also adopt a left-handed helical structure with a similar repeat length. However, the Lys-63 architecture is much more open than that of Lys-48 chains and exposes much more of the ubiquitin surface for potential recognition events. These new crystal structures are consistent with the results of solution studies of Lys-63 chain conformation, and reveal the structural basis for differential recognition of Lys-63 versus Lys-48 chains.« less

Aspects of electron transport in zigzag graphene nanoribbons

NASA Astrophysics Data System (ADS)

Bhalla, Pankaj; Pratap, Surender

2018-05-01

In this paper, we investigate the aspects of electron transport in the zigzag graphene nanoribbons (ZGNRs) using the nonequilibrium Green’s function (NEGF) formalism. The latter is an esoteric tool in mesoscopic physics. It is used to perform an analysis of ZGNRs by considering potential well. Within this potential, the dependence of transmission coefficient, local density of states (LDOS) and electron transport properties on number of atoms per unit cell is discussed. It is observed that there is an increment in electron and thermal conductance with increasing number of atoms. In addition to these properties, the dependence of same is also studied in figure of merit. The results infer that the contribution of electrons to enhance the figure of merit is important above the crossover temperature.

Eccentric mastectomy and zigzag periareolar incision for gynecomastia.

PubMed

Tu, Lung-Chen; Tung, Kwang-Yi; Chen, Heng-Chang; Huang, Wen-Chen; Hsiao, Hung-Tao

2009-07-01

Gynecomastia is enlargement of the male breast caused by gland proliferation. Surgery is performed for symptom relief or for cosmetic reasons. The authors used a modified operative procedure, then evaluated the results and safety. Between 2001 and 2005, 22 men (median age, 26 years; range, 13-63 years) with gynecomastia underwent surgery. The operative procedure included a zigzag periareolar skin incision, eccentric subcutaneous mastectomy, and liposuction, with postoperative compression. All the patients were satisfied with the results of the surgery, which produced a chest contour resembling a normal male chest rather than simply a smaller breast. The only complication was a hematoma. One patient was found to have breast cancer. The normal male chest contour can be restored by the described method of eccentric subcutaneous mastectomy.

Quantum superintegrable system with a novel chain structure of quadratic algebras

NASA Astrophysics Data System (ADS)

Liao, Yidong; Marquette, Ian; Zhang, Yao-Zhong

2018-06-01

We analyse the n-dimensional superintegrable Kepler–Coulomb system with non-central terms. We find a novel underlying chain structure of quadratic algebras formed by the integrals of motion. We identify the elements for each sub-structure and obtain the algebra relations satisfied by them and the corresponding Casimir operators. These quadratic sub-algebras are realized in terms of a chain of deformed oscillators with factorized structure functions. We construct the finite-dimensional unitary representations of the deformed oscillators, and give an algebraic derivation of the energy spectrum of the superintegrable system.

Inner edge magnetisms in carbon honeycombs

NASA Astrophysics Data System (ADS)

Liu, Xiaofei; Guo, Wanlin

2018-04-01

We show by comprehensive ab initio calculations that sp2 carbon honeycombs recently synthesised by Krainyukova et al. [Phys. Rev. Lett. 116, 055501 (2016)] exhibit antiferromagnetism, not only at the inner edge of the zigzag ribbon component but also at the chain of sp2 carbon that joins three zigzag ribbons. The π antiferromagnetism at the joint chain has spin orientations that alternatively change along the axis and stems from a super-exchange mechanism. Along with the spin-polarization, the joint chain conduction channel opens an energy gap. The spin-polarization of the zigzag edge due to the magnetic instability of the localized edge states is less stable in energy. Through hole doping, the zigzag edge antiferromagnetism is enhanced and stabilized as the magnetic ground state, along with the re-opening of the joint chain conduction channel. When the carbon honeycombs are reconstructed into sp3-sp2 hybrid honeycombs, the π states of the joint are diminished, but the zigzag edge magnetism is preserved. Our results propose carbon honeycombs as novel magnetic carbon with competing polarization configurations.

Effect of short-chain branching on interfacial polymer structure and dynamics under shear flow.

PubMed

Jeong, Sohdam; Kim, Jun Mo; Cho, Soowon; Baig, Chunggi

2017-11-22

We present a detailed analysis on the effect of short-chain branches on the structure and dynamics of interfacial chains using atomistic nonequilibrium molecular dynamics simulations of confined polyethylene melts in a wide range of shear rates. The intrinsically fast random motions of the short branches constantly disturb the overall chain conformation, leading to a more compact and less deformed chain structure of the short-chain branched (SCB) polymer against the imposed flow field in comparison with the corresponding linear polymer. Moreover, such highly mobile short branches along the backbone of the SCB polymer lead to relatively weaker out-of-plane wagging dynamics of interfacial chains, with highly curvy backbone structures in the intermediate flow regime. In conjunction with the contribution of short branches (as opposed to that of the backbone) to the total interfacial friction between the chains and the wall, the SCB polymer shows a nearly constant behavior in the degree of slip (d s ) with respect to shear rate in the weak-to-intermediate flow regimes. On the contrary, in the strong flow regime where irregular chain rotation and tumbling dynamics occur via intensive dynamical collisions between interfacial chains and the wall, an enhancement effect on the chain detachment from the wall, caused by short branches, leads to a steeper increase in d s for the SCB polymer than for the linear polymer. Remarkably, the SCB chains at the interface exhibit two distinct types of rolling mechanisms along the backbone, with a half-dumbbell mesoscopic structure at strong flow fields, in addition to the typical hairpin-like tumbling behavior displayed by the linear chains.

Crystal structure of (E)-2-hy-droxy-4'-meth-oxy-aza-stilbene.

PubMed

Chantrapromma, Suchada; Kaewmanee, Narissara; Boonnak, Nawong; Chantrapromma, Kan; Ghabbour, Hazem A; Fun, Hoong-Kun

2015-06-01

The title aza-stilbene derivative, C14H13NO2 {systematic name: (E)-2-[(4-meth-oxy-benzyl-idene)amino]-phenol}, is a product of the condensation reaction between 4-meth-oxy-benzaldehyde and 2-amino-phenol. The mol-ecule adopts an E conformation with respect to the azomethine C=N bond and is almost planar, the dihedral angle between the two substituted benzene rings being 3.29 (4)°. The meth-oxy group is coplanar with the benzene ring to which it is attached, the Cmeth-yl-O-C-C torsion angle being -1.14 (12)°. There is an intra-molecular O-H⋯N hydrogen bond generating an S(5) ring motif. In the crystal, mol-ecules are linked via C-H⋯O hydrogen bonds, forming zigzag chains along [10-1]. The chains are linked via C-H⋯π inter-actions, forming a three-dimensional structure.

Phonon stiffen and soften at zigzag- and armchair-dominated edges of exfoliated bilayer graphene ribbon presented by Raman spectra

NASA Astrophysics Data System (ADS)

Xia, Minggang; Zhou, Xiaohua; Xin, Duqiang; Xu, Qiang

2018-01-01

The Raman spectra at the edge of the exfoliated bilayer graphene ribbon (GR) were investigated in detail. Results show that both G and 2D phonons stiffen (wave number increases) at zigzag-dominated edge, while they soften at armchair-dominated edge compared with those at the middle position in the GR. Furthermore, the full widths at half maximum intensity of both G and 2D Raman peaks narrow at the zigzag-dominated edge, while they broaden at the armchair-dominated edge. The stiffness and softness are attributed to the C-C bonds at the edge. For zigzag-dominated edge, the stiffness may originate in the increase of the force constant induced by the shrinking of C-C bond. For armchair-dominated edge, the softness may be due to the decrease of the force constant induced by the unsaturated hanging bonds at edge, which is different from Kohn anomaly and charge doping. The analysis is in agreement well with others calculation results about C-C bonds and the edge energy. These results may be useful to understand physical properties at the bilayer graphene edge and for applications in the device by taking advantage of the edge states in bilayer graphene.

STM/STS investigation of edge structure in epitaxial graphene

NASA Astrophysics Data System (ADS)

Ridene, M.; Girard, J. C.; Travers, L.; David, C.; Ouerghi, A.

2012-08-01

In this paper, we have used low temperature scanning tunneling microscopy and spectroscopy (LT-STM/STS) to study zigzag or armchair edges of epitaxial graphene on 6H-SiC (0001). The monolayer carbon structures exhibit occasionally one-dimensional ridge (1D) in close vicinity to step edge. This ridge exhibits different edges orientations in armchair-zigzag transition which give rise to different local density of states (LDOS) along this 1D structure. This ridge formation is likely explained by residual compressive in-plane stresses.

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

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

Li,H.; van Vranken, S.; Zhao, Y.

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, conformationalmore » 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.« less

Modulating the spin transport behaviors in ZBNCNRs by edge hydrogenation and position of BN chain

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

Ouyang, Jun; Long, Mengqiu, E-mail: mqlong@csu.edu.cn, E-mail: ygao@csu.edu.cn; Zhang, Dan

2016-03-15

Using the density functional theory and the nonequilibrium Green’s function method, we study the spin transport behaviors in zigzag boron-nitrogen-carbon nanoribbons (ZBNCNRs) by modulating the edge hydrogenation and the position of B-N nanoribbons (BNNRs) chain. The different edge hydrogenations of the ZBNCNRs and the different position relationships of the BNNRs have been considered systematically. Our results show that the metallic, semimetallic and semiconductive properties of the ZBNCNRs can be modulated by the different edge hydrogenations and different position relationships of BN chains. And our proposaled ZBNCNRs devices act as perfect spin-filters with nearly 100% spin polarization. These effects would havemore » potential applications for boron-nitrogen-carbon-based nanomaterials in spintronics nano-devices.« less

Effect of gamma-irradiation of bovine serum albumin solution on the formation of zigzag film textures

NASA Astrophysics Data System (ADS)

Glibitskiy, Dmitriy M.; Gorobchenko, Olga A.; Nikolov, Oleg T.; Cheipesh, Tatiana A.; Roshal, Alexander D.; Zibarov, Artem M.; Shestopalova, Anna V.; Semenov, Mikhail A.; Glibitskiy, Gennadiy M.

2018-03-01

Formation of patterns on the surface of dried films of saline biopolymer solutions is influenced by many factors, including particle size and structure. Proteins may be modified under the influence of ionizing radiation. By irradiating protein solutions with gamma rays, it is possible to affect the formation of zigzag (Z) structures on the film surface. In our study, the films were obtained by desiccation of bovine serum albumin (BSA) solutions, which were irradiated by a 60Co gamma-source at doses ranging from 1 Gy to 12 kGy. The analysis of the resulting textures on the surface of the films was carried out by calculating the specific length of Z-structures. The results are compared against the absorption and fluorescence spectroscopy and dynamic light scattering (DLS) data. Gamma-irradiation of BSA solutions in the 1-200 Gy range practically does not influence the amount of Z-structures on the film surface. The decrease in fluorescence intensity and increase in absorbance intensity point to the destruction of BSA structure at 2 and 12 kGy, and DLS shows a more than 160% increase in particle size as a result of BSA aggregation at 2 kGy. This prevents the formation of Z-structures, which is reflected in the decrease of their specific length.

Electrical controllable spin pump based on a zigzag silicene nanoribbon junction.

PubMed

Zhang, Lin; Tong, Peiqing

2017-12-13

We propose a possible electrical controllable spin pump based on a zigzag silicene nanoribbon ferromagnetic junction by applying two time-dependent perpendicular electric fields. By using the Keldysh Green's function method, we derive the analytic expression of the spin-resolved current at the adiabatic approximation and demonstrate that two asymmetric spin up and spin down currents can be pumped out in the device without an external bias. The pumped currents mainly come from the interplay between the photon-assisted spin pump effect and the electrically-modulated energy band structure of the tunneling junction. The spin valve phenomena are not only related to the energy gap opened by two perpendicular staggered potentials, but also dependent on the system parameters such as the pumping frequency, the pumping phase difference, the spin-orbit coupling and the Fermi level, which can be tuned by the electrical methods. The proposed device can also be used to produce a pure spin current and a 100% polarized spin current through the photon-assisted pumping process. Our investigations may provide an electrical manipulation of spin-polarized electrons in graphene-like pumping devices.

Optimal design of wavy microchannel and comparison of heat transfer characteristics with zigzag and straight geometries

NASA Astrophysics Data System (ADS)

Parlak, Zekeriya

2018-05-01

Design concept of microchannel heat exchangers is going to plan with new flow microchannel configuration to reduce the pressure drop and improve heat transfer performance. The study aims to find optimum microchannel design providing the best performance of flow and heat transfer characterization in a heat sink. Therefore, three different types of microchannels in which water is used, straight, wavy and zigzag have been studied. The optimization operation has been performed to find optimum geometry with ANSYS's Response Surface Optimization Tool. Primarily, CFD analysis has been performed by parameterizing a wavy microchannel geometry. Optimum wavy microchannel design has been obtained by the response surface created for the range of velocity from 0.5 to 5, the range of amplitude from 0.06 to 0.3, the range of microchannel height from 0.1 to 0.2, the range of microchannel width from 0.1 to 0.2 and range of sinusoidal wave length from 0.25 to 2.0. All simulations have been performed in the laminar regime for Reynolds number ranging from 100 to 900. Results showed that the Reynolds number range corresponding to the industrial pressure drop limits is between 100 and 400. Nu values obtained in this range for optimum wavy geometry were found at a rate of 10% higher than those of the zigzag channel and 40% higher than those of the straight channels. In addition, when the pressure values of the straight channel did not exceed 10 kPa, the inlet pressure data calculated for zigzag and wavy channel data almost coincided with each other.

Effect of Chain Conformation on the Single-Molecule Melting Force in Polymer Single Crystals: Steered Molecular Dynamics Simulations Study.

PubMed

Feng, Wei; Wang, Zhigang; Zhang, Wenke

2017-02-28

Understanding the relationship between polymer chain conformation as well as the chain composition within the single crystal and the mechanical properties of the corresponding single polymer chain will facilitate the rational design of high performance polymer materials. Here three model systems of polymer single crystals, namely poly(ethylene oxide) (PEO), polyethylene (PE), and nylon-66 (PA66) have been chosen to study the effects of chain conformation, helical (PEO) versus planar zigzag conformation (PE, PA66), and chain composition (PE versus PA66) on the mechanical properties of a single polymer chain. To do that, steered molecular dynamics simulations were performed on those polymer single crystals by pulling individual polymer chains out of the crystals. Our results show that the patterns of force-extension curve as well as the chain moving mode are closely related to the conformation of the polymer chain in the single crystal. In addition, hydrogen bonds can enhance greatly the force required to stretch the polymer chain out of the single crystal. The dynamic breaking and reformation of multivalent hydrogen bonds have been observed for the first time in PA66 at the single molecule level.

Electronic structure and electric polarity of edge-functionalized graphene nanoribbons

NASA Astrophysics Data System (ADS)

Taira, Remi; Yamanaka, Ayaka; Okada, Susumu

2017-08-01

On the basis of the density functional theory combined with the effective screening medium method, we studied the electronic structure of graphene nanoribbons with zigzag edges, which are terminated by functional groups. The work function of the nanoribbons is sensitive to the functional groups. The edge state inherent in the zigzag edges is robust against edge functionalization. OH termination causes the injection of electrons into the nearly free electron states situated alongside the nanoribbons, resulting in the formation of free electron channels outside the nanoribbons. We also demonstrated that the polarity of zigzag graphene nanoribbons is controllable by the asymmetrical functionalization of their edges.

Solvent induced synthesis, structure and properties of coordination polymers based on 5-hydroxyisophthalic acid as linker and 1,10-phenanthroline as auxiliary ligand

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

Kariem, Mukaddus; Yawer, Mohd; Sheikh, Haq Nawaz, E-mail: hnsheikh@rediffmail.com

2015-11-15

Three new coordination polymers [Mn(hip)(phen) (H{sub 2}O)]{sub n} (1), [Co(hip)(phen) (H{sub 2}O)]{sub n} (2), and [Cd(hip) (phen) (H{sub 2}O)]{sub n} (3) (H{sub 2}hip=5-hydroxyisophthalic acid; phen=1,10-phenanthroline) have been synthesized by solvo-hydrothermal method using diethyl formamide-water (DEF-H{sub 2}O) as solvent system. Single-crystal X-ray diffraction analysis reveals that all three coordination polymers 1, 2 and 3 crystallize in monoclinic space group P2/n. Metal ions are inter-connected by hydroxyisophthalate anions forming zig-zag 1D chain. 1D chains are further inter-connected by hydrogen bonding and π–π stacking interactions leading to 3D supramolecular architecture. Hydrogen-bonding and π–π stacking provide thermal stability to polymers. Compounds 1 and 2more » are paramagnetic at room temperature and variable temperature magnetic moment measurements revealed weak ferromagnetic interactions between metal ions at low temperature. Compound 3 exhibits excellent photoluminescence with large Stokes shift. - Graphical abstract: 1D helical chains of coordination polymers were synthesized by solvo-hydrothermal reaction of 5-hydroxyisopthalic acid and 1,10-phenanthroline with MnCl{sub 2}·4H{sub 2}O / CoCl{sub 2}·6H{sub 2}O / Cd(NO{sub 3}){sub 2}·6H{sub 2}O. - Highlights: • Solvent induced synthesis of three coordination polymers with 1D zig-zag structure. • Crystal structures of coordination polymers are reported and discussed. • 1,10-Phenanthroline influences magnetic and luminescent properties of polymers. • Coordination polymer of Cd is luminescent exhibiting large Stokes shift.« less

Primary structure of the hemoglobin alpha-chain of rose-ringed parakeet (Psittacula krameri).

PubMed

Islam, A; Beg, O U; Persson, B; Zaidi, Z H; Jörnvall, H

1988-10-01

The structure of the hemoglobin alpha-chain of Rose-ringed Parakeet was determined by sequence degradations of the intact subunit, the CNBr fragments, and peptides obtained by digestion with staphylococcal Glu-specific protease and trypsin. Using this analysis, the complete alpha-chain structure of 21 avian species is known, permitting comparisons of the protein structure and of avian relationships. The structure exhibits differences from previously established avian alpha-chains at a total of 61 positions, five of which have residues unique to those of the parakeet (Ser-12, Gly-65, Ser-67, Ala-121, and Leu-134). The analysis defines hemoglobin variation within an additional avian order (Psittaciformes), demonstrates distant patterns for evaluation of relationships within other avian orders, and lends support to taxonomic conclusions from molecular data.

Formation and structural phase transition in Co atomic chains on a Cu(775) surface

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

Syromyatnikov, A. G.; Kabanov, N. S.; Saletsky, A. M.

The formation of Co atomic chains on a Cu(775) surface is investigated by the kinetic Monte Carlo method. It is found that the length of Co atomic chains formed as a result of self-organization during epitaxial growth is a random quantity and its mean value depends on the parameters of the experiment. The existence of two structural phases in atomic chains is detected using the density functional theory. In the first phase, the separations between an atom and its two nearest neighbors in a chain are 0.230 and 0.280 nm. In the second phase, an atomic chain has identical atomicmore » spacings of 0.255 nm. It is shown that the temperature of the structural phase transition depends on the length of the atomic chain.« less

Crystal Structure of 17α-Dihydroequilin, C18H22O2, from Synchrotron Powder Diffraction Data and Density Functional Theory

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

Kaduk, James; Gindhart, Amy; Blanton, Thomas

The crystal structure of 17α-dihydroequilin has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. 17α-dihydroequilin crystallizes in space group P212121 (#19) with a = 6.76849(1) Å, b = 8.96849(1) Å, c = 23.39031(5) Å, V = 1419.915(3) Å3, and Z = 4. Both hydroxyl groups form hydrogen bonds to each other, resulting in zig-zag chains along the b-axis. The powder diffraction pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ as the entry 00-066-1608.

In Situ Nondestructive Analysis of Kalanchoe pinnata Leaf Surface Structure by Polarization-Modulation Infrared Reflection-Absorption Spectroscopy.

PubMed

Hama, Tetsuya; Kouchi, Akira; Watanabe, Naoki; Enami, Shinichi; Shimoaka, Takafumi; Hasegawa, Takeshi

2017-12-14

The outermost surface of the leaves of land plants is covered with a lipid membrane called the cuticle that protects against various stress factors. Probing the molecular-level structure of the intact cuticle is highly desirable for understanding its multifunctional properties. We report the in situ characterization of the surface structure of Kalanchoe pinnata leaves using polarization-modulation infrared reflection-absorption spectroscopy (PM-IRRAS). Without sample pretreatment, PM-IRRAS measures the IR spectra of the leaf cuticle of a potted K. pinnata plant. The peak position of the CH 2 -related modes shows that the cuticular waxes on the leaf surface are mainly crystalline, and the alkyl chains are highly packed in an all-trans zigzag conformation. The surface selection rule of PM-IRRAS revealed the average orientation of the cuticular molecules, as indicated by the positive and negative signals of the IR peaks. This unique property of PM-IRRAS revealed that the alkyl chains of the waxes and the main chains of polysaccharides are oriented almost perpendicular to the leaf surface. The nondestructive, background-free, and environmental gas-free nature of PM-IRRAS allows the structure and chemistry of the leaf cuticle to be studied directly in its native environment.

Primary structure of the hemoglobin beta-chain of rose-ringed parakeet (Psittacula krameri).

PubMed

Islam, A; Persson, B; Zaidi, Z H; Jörnvall, H

1989-08-01

The primary structure of Rose-ringed Parakeet hemoglobin beta-chain was established, completing the analysis of this hemoglobin. Comparison with other avian beta-chains show variations smaller than those for the corresponding alpha-chains. There are 11 amino acid exchanges in relationship to the only other characterized psittaciform beta-chain, and a total of 35 positions are affected by differences among all avian beta-chains analyzed (versus 61 for the alpha-chains). At three positions, the Psittacula beta-chain has residues unique to this species. Three alpha 1 beta 1 contacts are modified, by substitutions at positions beta 51, beta 116, and beta 125.

A first-principles study of electronic properties of H and F-terminated zigzag BNC nanoribbons

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

Alaal, Naresh; Department of Physics, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.; Department of Materials Engineering, Monash University, Clayton, Victoria -3800, Australia.

2016-05-06

Nanoribbons are quasi one-dimensional structures which have interesting electronic properties on the basis of their edge geometries, and width. We studied the electronic properties of hydrogen and fluorine-terminated zigzag BNC nanoribbons (BNCNRs) using a first-principles based density functional theory approach. We considered BNCNRs that were composed of an equal number of C-C and B-N dimers; one of the edges ends with an N atom and opposite edge ends with a C atom. These two edge atoms are passivated by H or F atoms. Our results suggest that hydrogen-terminated BNCNRs (H-BNCNRs) and flourine-terminated BNCNRs (F-BNCNRs) have different electronic properties. H-BNCNRs exhibitmore » intrinsic half-metallic behavior while F-BNCNRs are indirect band gap semiconductors. Chemical functionalization of BNCNRs with H and F atoms show that BNCNRs have a diverse range of electronic properties.« less

Six uranyl-organic frameworks with naphthalene-dicarboxylic acid and bipyridyl-based spacers: syntheses, structures, and properties.

PubMed

Xu, Wei; Ren, Ya-Nan; Xie, Miao; Zhou, Lin-Xia; Zheng, Yue-Qing

2018-03-28

A new series of uranium coordination polymers have been hydrothermally synthesized by using 1,4-naphthalene dicarboxylic acid (H 2 NDC), namely, (H 3 O) 2 [(UO 2 ) 2 (NDC) 3 ]·H 2 O (1), (H 2 -bpp)[(UO 2 ) 2 (NDC) 3 ]·EtOH·5H 2 O (2), (H 2 -bpe) 2/2 [(UO 2 ) 2 (NDC) 3 ]·EtOH (3), (H 2 -bpp)[(UO 2 ) 2 (NDC) 3 ]·5H 2 O (4), (H 2 -bpp)[(UO 2 )(HNDC)(NDC)] 2 ·2H 2 O (5), and (H 2 -bpy)[(UO 2 )(NDC) 2 ] (6) [bpp = 1,3-di(4-pyridyl) propane, bpe = 4,4'-vinylenedipyridine, bpy = 4,4'-bipyridine]. Single-crystal X-ray diffraction demonstrates that complex 1 represents the uranyl-organic polycatenated framework derived from a simple two-dimensional honeycomb grid network structure via a H 2 NDC linker. Complexes 2-4 contain the dinuclear motifs of the two UO 7 pentagonal and one UO 8 hexagonal bipyramids which are linked by NDC 2- anions creating a (UO 2 ) 4 (NDC) 2 unit, and further extend to a 2D layer through NDC 2- anions. Complex 5 displays a 1D zigzag double chain structure, in which the carboxylate groups of the NDC 2- anions adopt a chelate mode and further extends to a 2D framework via hydrogen bonds. The 1D structure of complex 6 is similar to the zigzag chain of complex 5. In addition, powder X-ray diffraction, elemental analysis, IR, thermal stability and luminescence properties of all complexes have also been investigated in this paper. The photocatalytic properties of the six complexes for the degradation of tetracycline hydrochloride (TC) under UV irradiation have been examined. Moreover, density functional theory (DFT) calculations were carried out to explore the electronic structural and bonding properties of the uranyl complexes 1-6.

Solution structure of a small protein containing a fluorinated side chain in the core

PubMed Central

Cornilescu, Gabriel; Hadley, Erik B.; Woll, Matthew G.; Markley, John L.; Gellman, Samuel H.; Cornilescu, Claudia C.

2007-01-01

We report the first high-resolution structure for a protein containing a fluorinated side chain. Recently we carried out a systematic evaluation of phenylalanine to pentafluorophenylalanine (Phe → F5-Phe) mutants for the 35-residue chicken villin headpiece subdomain (c-VHP), the hydrophobic core of which features a cluster of three Phe side chains (residues 6, 10, and 17). Phe → F5-Phe mutations are interesting because aryl–perfluoroaryl interactions of optimal geometry are intrinsically more favorable than either aryl–aryl or perfluoroaryl–perfluoroaryl interactions, and because perfluoroaryl units are more hydrophobic than are analogous aryl units. Only one mutation, Phe10 → F5-Phe, was found to provide enhanced tertiary structural stability relative to the native core (by ∼1 kcal/mol, according to guanidinium chloride denaturation studies). The NMR structure of this mutant, described here, reveals very little variation in backbone conformation or side chain packing relative to the wild type. Thus, although Phe → F5-Phe mutations offer the possibility of greater tertiary structural stability from side chain–side chain attraction and/or side chain desolvation, the constraints associated with the native c-VHP fold apparently prevent the modified polypeptide from taking advantage of this possibility. Our findings are important because they complement several studies that have shown that fluorination of saturated side chain carbon atoms can provide enhanced conformational stability. PMID:17123960

Ab initio study of gold-doped zigzag graphene nanoribbons

NASA Astrophysics Data System (ADS)

Srivastava, Pankaj; Dhar, Subhra; Jaiswal, Neeraj K.

2014-12-01

The electronic transport properties of zigzag graphene nanoribbons (ZGNRs) through covalent functionalization of gold (Au) atoms is investigated by using non-equilibrium Green's function combined with density functional theory. It is revealed that the electronic properties of Au-doped ZGNRs vary significantly due to spin and its non-inclusion. We find that the DOS profiles of Au-adsorbed ZGNR due to spin reveal very less number of states available for conduction, whereas non-inclusion of spin results in higher DOS across the Fermi level. Edge Au-doped ribbons exhibit stable structure and are energetically more favorable than the center Au-doped ZGNRs. Though the chemical interaction at the ZGNR-Au interface modifies the Fermi level, Au-adsorbed ZGNR reveals semimetallic properties. A prominent qualitative change of the I-V curve from linear to nonlinear is observed as the Au atom shifts from center toward the edges of the ribbon. Number of peaks present near the Fermi level ensures conductance channels available for charge transport in case of Au-center-substituted ZGNR. We predict semimetallic nature of the Au-adsorbed ZGNR with a high DOS peak distributed over a narrow energy region at the Fermi level and fewer conductance channels. Our calculations for the magnetic properties predict that Au functionalization leads to semiconducting nature with different band gaps for spin up and spin down. The outcomes are compared with the experimental and theoretical results available for other materials.

Unconventional quantum antiferromagnetism with a fourfold symmetry breaking in a spin-1/2 Ising-Heisenberg pentagonal chain

NASA Astrophysics Data System (ADS)

Karľová, Katarína; Strečka, Jozef; Lyra, Marcelo L.

2018-03-01

The spin-1/2 Ising-Heisenberg pentagonal chain is investigated with use of the star-triangle transformation, which establishes a rigorous mapping equivalence with the effective spin-1/2 Ising zigzag ladder. The investigated model has a rich ground-state phase diagram including two spectacular quantum antiferromagnetic ground states with a fourfold broken symmetry. It is demonstrated that these long-period quantum ground states arise due to a competition between the effective next-nearest-neighbor and nearest-neighbor interactions of the corresponding spin-1/2 Ising zigzag ladder. The concurrence is used to quantify the bipartite entanglement between the nearest-neighbor Heisenberg spin pairs, which are quantum-mechanically entangled in two quantum ground states with or without spontaneously broken symmetry. The pair correlation functions between the nearest-neighbor Heisenberg spins as well as the next-nearest-neighbor and nearest-neighbor Ising spins were investigated with the aim to bring insight into how a relevant short-range order manifests itself at low enough temperatures. It is shown that the specific heat displays temperature dependencies with either one or two separate round maxima.

Bridging cobalt-calixarene subunits into a Co8 entity or a chain with 4,4‧-bipyridyl

NASA Astrophysics Data System (ADS)

Liu, Wei; Liu, Mei; Du, Shangchao; Li, Yafeng; Liao, Wuping

2014-02-01

Two novel calixarene-based compounds, {[Co4Cl(TC4A)(HCOO)3]2(4,4‧-bpy)2} (CIAC-206) and {[Co3(H2O)(SC4A-SO2)(HCOO)2]2(4,4‧-bpy)}n (CIAC-207) (H4TC4A = p-tert-butylthiacalix[4]arene, SC4A-SO2 = p-tert-butylsulfonylcalix[4]arene, 4,4‧-bpy = 4,4‧-bipyridyl) were synthesized under solvothermal conditions, and characterized by single crystal X-ray diffraction analysis, TG-DSC analysis, elemental analysis and IR spectroscopy. These two structures are featured with isolated Z-shaped Co8 entities containing two Co4-TC4A subunits bridged by two parallel 4,4‧-bpy (CIAC-206) and some zigzag chains with [Co3-SC4A-SO2]2 dimers bridged by single 4,4‧-bpy (CIAC-207), respectively. In order to evaluate their properties, the N2 sorption behavior and magnetic property were examined.

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

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

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

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 connectingmore » 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.« less

Effects of electric and magnetic fields on the electronic properties of zigzag carbon and boron nitride nanotubes

NASA Astrophysics Data System (ADS)

Chegel, Raad; Behzad, Somayeh; Ahmadi, Eghbal

2012-04-01

We have investigated the electronic properties of zigzag CNTs and BNNTs under the external transverse electric field and axial magnetic field, using tight binding approximation. It was found that after switching on the electric and magnetic fields, the band modification such as distortion of the degeneracy, change in energy dispersion, subband spacing and band gap size reduction occurs. The band gap of zigzag BNNTs decreases linearly with increasing the electric field strength but the band gap variation for CNTs increases first and later decreases (Metallic) or first hold constant and then decreases (semiconductor). For type (II) CNTs, at a weak magnetic field, by increasing the electric field strength, the band gap remains constant first and then decreases and in a stronger magnetic field the band gap reduction becomes parabolic. For type (III) CNTs, in any magnetic field, the band gap increases slowly until reaches a maximum value and then decreases linearly. Unlike to CNTs, the magnetic field has less effects on the BNNTs band gap variation.

Absence of long range order in SrDy2O4 frustrated magnet due to trapped defects from a dimensionality crossover

NASA Astrophysics Data System (ADS)

Gauthier, Nicolas; Fennell, Amy; Uldry, Anne-Christine; Delley, Bernard; Sibille, Romain; White, Jonathan; Niedermayer, Christof; Pomjakushin, Vladimir; Kenzelmann, Michel; Prevost, Bobby; Desilets-Benoit, Alexandre; Bianchi, Andrea D.; Dabkowska, Hanna A.; Nilsen, Goran; Regnault, Louis-Pierre

The simultaneous occurence of geometrical frustration and low dimensionality can lead to strongly correlated fluctuating ground states. In the SrLn2O4 compounds, the Ln magnetic ions form one-dimensional (1D) zig-zag chains that have both of these characteristics, offering a playground to study novel states of matter. In SrDy2O4, the two inequivalent Dy3+ sites are Ising-like with perpendicular easy-axes, favouring the decoupling of neighbouring zig-zag chains. No long range order is observed down to T = 60 mK in zero field but diffuse neutron scattering indicates short range correlations that are consistent with those of the 1D Ising zig-zag chain model. AC susceptibility measurements indicate a slowing down of the fluctuations at low temperatures. We attribute this behaviour to the domain walls in the zig-zag chains. Experimental evidence of a dimensionality crossover at low temperatures in SrDy2O4 suggest that the domains walls are trapped because of interchain interactions, precluding long-range order to the lowest temperatures.

Experimental study and modeling of atomic-scale friction in zigzag and armchair lattice orientations of MoS2

PubMed Central

Li, Meng; Shi, Jialin; Liu, Lianqing; Yu, Peng; Xi, Ning; Wang, Yuechao

2016-01-01

Abstract Physical properties of two-dimensional materials, such as graphene, black phosphorus, molybdenum disulfide (MoS2) and tungsten disulfide, exhibit significant dependence on their lattice orientations, especially for zigzag and armchair lattice orientations. Understanding of the atomic probe motion on surfaces with different orientations helps in the study of anisotropic materials. Unfortunately, there is no comprehensive model that can describe the probe motion mechanism. In this paper, we report a tribological study of MoS2 in zigzag and armchair orientations. We observed a characteristic power spectrum and friction force values. To explain our results, we developed a modified, two-dimensional, stick-slip Tomlinson model that allows simulation of the probe motion on MoS2 surfaces by combining the motion in the Mo layer and S layer. Our model fits well with the experimental data and provides a theoretical basis for tribological studies of two-dimensional materials. PMID:27877869

Experimental study and modeling of atomic-scale friction in zigzag and armchair lattice orientations of MoS2.

PubMed

Li, Meng; Shi, Jialin; Liu, Lianqing; Yu, Peng; Xi, Ning; Wang, Yuechao

2016-01-01

Physical properties of two-dimensional materials, such as graphene, black phosphorus, molybdenum disulfide (MoS 2 ) and tungsten disulfide, exhibit significant dependence on their lattice orientations, especially for zigzag and armchair lattice orientations. Understanding of the atomic probe motion on surfaces with different orientations helps in the study of anisotropic materials. Unfortunately, there is no comprehensive model that can describe the probe motion mechanism. In this paper, we report a tribological study of MoS 2 in zigzag and armchair orientations. We observed a characteristic power spectrum and friction force values. To explain our results, we developed a modified, two-dimensional, stick-slip Tomlinson model that allows simulation of the probe motion on MoS 2 surfaces by combining the motion in the Mo layer and S layer. Our model fits well with the experimental data and provides a theoretical basis for tribological studies of two-dimensional materials.

Effects of an electric field on the electronic and optical properties of zigzag boron nitride nanotubes

NASA Astrophysics Data System (ADS)

Chegel, Raad; Behzad, Somayeh

2011-02-01

We have investigated the electro-optical properties of zigzag BNNTs, under an external electric field, using the tight binding approximation. It is found that an electric field modifies the band structure and splits the band degeneracy. Also the large electric strength leads to coupling the neighbor subbands which these effects reflect in the DOS and JDOS spectrum. It has been shown that, unlike CNTs, the band gap of BNNTs can be reduced linearly by applying a transverse external electric field. Also we show that the larger diameter tubes are more sensitive than small ones. The semiconducting metallic transition can be achieved through increasing the applied fields. The number and position of peaks in the JDOS spectrum are dependent on electric field strength. It is found that at a high electric field, the two lowest subbands are oscillatory with multiple nodes at the Fermi level.

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/.

Stick-slip nanofriction in cold-ion traps

NASA Astrophysics Data System (ADS)

Mandelli, Davide; Vanossi, Andrea; Tosatti, Erio

2013-03-01

Trapped cold ions are known to form linear or planar zigzag chains, helices or clusters depending on trapping conditions. They may be forced to slide over a laser induced corrugated potential, a mimick of sliding friction. We present MD simulations of an incommensurate 101 ions chain sliding subject to an external electric field. As expected with increasing corrugation, we observe the transition from a smooth-sliding, highly lubric regime to a strongly dissipative stick-slip regime. Owing to inhomogeneity the dynamics shows features reminiscent of macroscopic frictional behaviors. While the chain extremities are pinned, the incommensurate central part is initially free to slide. The onset of global sliding is preceded by precursor events consisting of partial slips of chain portions further from the center. We also look for frictional anomalies expected for the chain sliding across the linear-zigzag structural phase transition. Although the chain is too short for a proper critical behavior, the sliding friction displays a frank rise near the transition, due to opening of a new dissipative channel via excitations of transverse modes. Research partly sponsored by Sinergia Project CRSII2 136287/1.

Hydrothermal synthesis, crystal structure, and magnetic properties of a new inorganic vanadium(III) phosphate with a chain structure.

PubMed

Ferdov, Stanislav; Reis, Mario S; Lin, Zhi; Ferreira, Rute A Sá

2008-11-03

A new vanadium(III) phosphate, Na3V(OH)(HPO4)(PO4), has been synthesized by using mild hydrothermal conditions under autogeneous pressure. This material represents a very rare example of sodium vanadium(III) phosphate with a chain structure. The crystal structure has been determined by refinement of powder X-ray diffraction data, starting from the atomic coordinates of an isotypic compound, Na3Al(OH)(HPO4)(PO4), which was obtained under high temperature and high pressure. The phase crystallizes in monoclinic space group C2/m (No. 12) with lattice parameters a = 15.423(9) A, b = 7.280(0) A, c = 7.070(9) A, beta = 96.79(7) degrees, V = 788.3(9) A(3), and Z = 4. The structure consists of one-dimensional chains composed of corner-sharing VO5(OH) octahedra running along the b direction. They are decorated by isolated PO4 and HPO4 tetrahedra sharing two of their corners with the ones of the vanadium octahedra. The interconnection between the chains is assured by three crystallographically distinct Na(+) cations. Magnetic investigation confirms the 3+ oxidation state of the vanadium ions and reveals an antiferromagnetic arrangement between those ions through the chain.

Optimization of the Synthesis of Structured Phosphatidylcholine with Medium Chain Fatty Acid.

PubMed

Ochoa-Flores, Angélica A; Hernández-Becerra, Josafat A; Cavazos-Garduño, Adriana; Vernon-Carter, Eduardo J; García, Hugo S

2017-11-01

Structured phosphatidylcholine was successfully produced by acidolysis between phosphatidylcholine and free medium chain fatty acid, using phospholipase A 1 immobilized on Duolite A568. Response surface methodology was applied to optimize the reaction system using three process parameters: molar ratio of substrates (phosphatidylcholine to free medium chain fatty acid), enzyme loading, and reaction temperature. All parameters evaluated showed linear and quadratic significant effects on the production of modified phosphatidylcholine; molar ratio of substrates contributed positively, but temperature influenced negatively. Increased enzyme loading also led to increased production of modified phosphatidylcholine but only during the first 9 hours of the acidolysis reaction. Optimal conditions obtained from the model were a ratio of phosphatidylcholine to free medium chain fatty acid of 1:15, an enzyme loading of 12%, and a temperature of 45°C. Under these conditions a production of modified phosphatidylcholine of 52.98 % were obtained after 24 h of reaction. The prediction was confirmed from the verification experiments; the production of modified phosphatidylcholine was 53.02%, the total yield of phosphatidylcholine 64.28% and the molar incorporation of medium chain fatty acid was 42.31%. The acidolysis reaction was scaled-up in a batch reactor with a similar production of modified phosphatidylcholine, total yield of phosphatidylcholine and molar incorporation of medium chain fatty acid. Purification by column chromatography of the structured phosphatidylcholine yielded 62.53% of phosphatidylcholine enriched with 42.52% of medium chain fatty acid.

Landscaping the structures of GAVI country vaccine supply chains and testing the effects of radical redesign.

PubMed

Lee, Bruce Y; Connor, Diana L; Wateska, Angela R; Norman, Bryan A; Rajgopal, Jayant; Cakouros, Brigid E; Chen, Sheng-I; Claypool, Erin G; Haidari, Leila A; Karir, Veena; Leonard, Jim; Mueller, Leslie E; Paul, Proma; Schmitz, Michelle M; Welling, Joel S; Weng, Yu-Ting; Brown, Shawn T

2015-08-26

Many of the world's vaccine supply chains do not adequately provide vaccines, prompting several questions: how are vaccine supply chains currently structured, are these structures closely tailored to individual countries, and should these supply chains be radically redesigned? We segmented the 57 GAVI-eligible countries' vaccine supply chains based on their structure/morphology, analyzed whether these segments correlated with differences in country characteristics, and then utilized HERMES to develop a detailed simulation model of three sample countries' supply chains and explore the cost and impact of various alternative structures. The majority of supply chains (34 of 57) consist of four levels, despite serving a wide diversity of geographical areas and population sizes. These four-level supply chains loosely fall into three clusters [(1) 18 countries relatively more bottom-heavy, i.e., many more storage locations lower in the supply chain, (2) seven with relatively more storage locations in both top and lower levels, and (3) nine comparatively more top-heavy] which do not correlate closely with any of the country characteristics considered. For all three cluster types, our HERMES modeling found that simplified systems (a central location shipping directly to immunization locations with a limited number of Hubs in between) resulted in lower operating costs. A standard four-tier design template may have been followed for most countries and raises the possibility that simpler and more tailored designs may be warranted. Copyright © 2015 Elsevier Ltd. All rights reserved.

Correlation between protein secondary structure, backbone bond angles, and side-chain orientations.

PubMed

Lundgren, Martin; Niemi, Antti J

2012-08-01

We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central C(α) carbon of a protein backbone, and for this we develop new visualization techniques to analyze high-resolution x-ray structures in the Protein Data Bank. We observe that there is a correlation between the deformations of the ideal tetrahedral symmetry and the local secondary structure of the protein. We propose a universal coarse-grained energy function to describe the ensuing side-chain geometry in terms of the C(β) carbon orientations. The energy function can model the side-chain geometry with a subatomic precision. As an example we construct the C(α)-C(β) structure of HP35 chicken villin headpiece. We obtain a configuration that deviates less than 0.4 Å in root-mean-square distance from the experimental x-ray structure.

The Crystal Structure and Conformations of an Unbranched Mixed Tri-Ubiquitin Chain Containing K48 and K63 Linkages.

PubMed

Padala, Prasanth; Soudah, Nadine; Giladi, Moshe; Haitin, Yoni; Isupov, Michail N; Wiener, Reuven

2017-12-08

The ability of ubiquitin to function in a wide range of cellular processes is ascribed to its capacity to cause a diverse spectrum of modifications. While a target protein can be modified with monoubiquitin, it can also be modified with ubiquitin chains. The latter include seven types of homotypic chains as well as mixed ubiquitin chains. In a mixed chain, not all the isopeptide bonds are restricted to a specific lysine of ubiquitin, resulting in a chain possessing more than one type of linkage. While structural characterization of homotypic chains has been well elucidated, less is known about mixed chains. Here we present the crystal structure of a mixed tri-ubiquitin chain at 3.1-Å resolution. In the structure, the proximal ubiquitin is connected to the middle ubiquitin via K48 and these two ubiquitins adopt a compact structure as observed in K48 di-ubiquitin. The middle ubiquitin links to the distal ubiquitin via its K63 and these ubiquitins adopt two conformations, suggesting a flexible structure. Using small-angle X-ray scattering, we unexpectedly found differences between the conformational ensembles of the above tri-ubiquitin chains and chains possessing the same linkages but in the reverse order. In addition, cleavage of the K48 linkage by DUB is faster if this linkage is at the distal end. Taken together, our results suggest that in mixed chains, not only the type of the linkages but also their sequence determine the structural and functional properties of the chain. Copyright © 2017 Elsevier Ltd. All rights reserved.

New members of the A2 M ‧ M2″ structure family (A=Ca, Sr, Yb, La; M ‧ = In , Sn , Pb; M ″ = Si , Ge)

NASA Astrophysics Data System (ADS)

Jehle, Michael; Dürr, Ines; Fink, Saskia; Lang, Britta; Langenmaier, Michael; Steckhan, Julia; Röhr, Caroline

2015-01-01

The new mixed tetrelides Sr2PbGe2 and Yb2SnGe2, several mixed Ca/Sr (AII) germanides A2II (Sn, Pb)Ge2 and two polymorphs of La2 InSi2 represent new members of the general structure family of ternary alkaline-earth/lanthanoid main group silicides/germanides A2 M ‧ M2″ (M ‧ = In , Sn , Pb ; M ″ = Si , Ge). All compounds were synthesized from melts of the elements and their crystal structures have been determined by means of single crystal X-ray diffraction. Sr2PbGe2 (Cmmm, a=402.36(11), b=1542.3(4), c=463.27(10) pm) crystallizes with the Mn2AlB2 -type structure. In exhibiting infinite planar Ge zig-zag chains, it represents one border of the compound series. The other borderline case, where only [Ge2 ] dumbbells are left as Ge building units, is represented by the Ca/Yb tin germanides Ca2SnGe2 and Yb2SnGe2 (Mo2FeB2 -type; P4/mbm, a=748.58(13)/740.27(7), c=445.59(8)/435.26(5) pm). In between these two border structures compounds with variable Si/Ge chain lengths could be obtained by varying the averaged size of the AII cations: Ca0.45Sr1.55PbGe2 (new structure type; Pbam, a=791.64(5), b=2311.2(2), c=458.53(3) pm) contains planar six-membered chain segments [Ge6 ]. Tetrameric pieces [Ge4 ] are the conspicuous structure elements in Ca1.16Sr0.84SnGe2 and La2 InSi2 (La2InNi2 -type; Pbam, a=781.01(2)/762.01(13), b=1477.95(3)/1494.38(6), c=457.004(9)/442.1(3) pm). The tetragonal form of 'La2 In Si2‧ (exact composition: La2In1.07Si1.93, P4/mbm, a=1309.11(12), c=443.32(4) pm) also crystallizes in a new structure type, containing only [Si3 ] trimers as cutouts of the planar chains. In all structures the Si/Ge zig-zag chains/chain segments are connected by In/Sn/Pb atoms to form planar M layers, which are separated by pure A layers. Band structure calculations within the FP-LAPW DFT approach together with the Zintl formalism, extended by the presence of hypervalent bonding of the heavier M ‧ elements, give insight into the chemical bonding of this series of p

Raman spectroscopic study of the conformation of dicarboxylic acid salts in aqueous solutions

NASA Astrophysics Data System (ADS)

Fukushima, Kunio; Watanabe, Toshiaki; Umemura, Matome

1986-08-01

It is already known that the molecules of long chain monocarboxylic acid salts have a tendency to form micelles in aqueous solutions, the molecular chain taking the all- trans zigzag structure. However it is considered difficult for dicarboxylic acid salts to adopt the same structure as the monocarboxylic acid salts as they have two carboxyl groups, one on each end of the molecular chain. Therefore, a special structure is expected to exist for dicarboxylic acid salts in aqueous solution. In order to examine this, Raman spectra of suberic acid salt and azelaic acid salt in aqueous solution were measured and the normal vibrational calculation carried out, showing that dicarboxylic acid salts have a helical structure in aqueous solution.

Raman scattering and X-ray powder diffraction studies of hydrate layered perovskites: dirubidium aquapentafluoromanganate(III) and dipotassium aquapentafluoroferrate(III)

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

Galicka, Karolina; Slodczyk, Aneta; Ratuszna, Alicja

2004-06-08

The structural and vibrational properties of above mentioned crystals were determined using X-ray powder diffraction and Raman scattering experiments. At room temperature hydrate layered perovskites: Rb{sub 2}MnF{sub 5}{center_dot}H{sub 2}O and K{sub 2}FeF{sub 5}{center_dot}H{sub 2}O exhibit orthorhombic--Cmcm (D{sub 2h}{sup 17}) and monoclinic--C2/c (C{sub 2h}{sup 6}) symmetry. Their structure is built up of MnF{sub 6} or FeF{sub 5}{center_dot}H{sub 2}O octahedra forming trans-linked zig-zag chains or hydrogen bonded zig-zag chains along the major crystallographic direction [0 0 1], respectively. To confirm crystal structures and to describe lattice dynamics of these compounds the vibrational normal modes (in {gamma} point of first Brillouin zone) weremore » calculated on the base of the group theory analysis and compared with the spectra obtained from Raman scattering experiments. A relatively good reliability was obtained for both X-ray powder diffraction and Raman scattering.« less

Structure of resonances and formation of stationary points in symmetrical chains of bilinear oscillators

NASA Astrophysics Data System (ADS)

Dyskin, Arcady V.; Pasternak, Elena; Shufrin, Igor

2014-12-01

Dynamics of strongly nonlinear systems can in many cases be modelled by bilinear oscillators, which are the oscillators whose springs have different stiffnesses in compression and tension. This underpins the analysis of a wide range of phenomena, from oscillations of fragmented structures, connections and mooring lines to deformation of geological media. Single bilinear oscillators were studied previously and the presence of multiple resonances both super- and sub-harmonic was found. Less attention was paid to systems of multiple bilinear oscillators that describe many natural and engineering processes such as for example the behaviour of fragmented solids. Here we fill this gap concentrating on the simplest case - 1D symmetrical chains of bilinear oscillators. We show that the presence and structure of resonances in a symmetric chain of bilinear oscillators with fixed ends depends upon the number of oscillating masses. Two elementary chains act as the basic ones: a single mass bilinear chain (a mass connected to the fixed points by two bilinear springs) that behaves as a linear oscillator with a single resonance and a two mass chain that is a coupled bilinear oscillator (two masses connected by three bilinear springs). The latter has multiple resonances. We demonstrate that longer chains either do not have resonances or get decomposed, in the resonance, into either the single mass or two mass elementary chains with stationary masses in between. The resonance frequencies are inherited from the basic chains of decomposition. We show that if the number of masses is odd the chain can be decomposed into the single mass bilinear chains separated by stationary masses. It then inherits the resonances of the single mass bilinear chain. The chains with the number of masses minus 2 divisible by 3 can be decomposed into the two mass bilinear chains separated by stationary masses and inherit the resonances of the two mass chains. The chains whose lengths satisfy both criteria

Canonical Structure and Orthogonality of Forces and Currents in Irreversible Markov Chains

NASA Astrophysics Data System (ADS)

Kaiser, Marcus; Jack, Robert L.; Zimmer, Johannes

2018-03-01

We discuss a canonical structure that provides a unifying description of dynamical large deviations for irreversible finite state Markov chains (continuous time), Onsager theory, and Macroscopic Fluctuation Theory (MFT). For Markov chains, this theory involves a non-linear relation between probability currents and their conjugate forces. Within this framework, we show how the forces can be split into two components, which are orthogonal to each other, in a generalised sense. This splitting allows a decomposition of the pathwise rate function into three terms, which have physical interpretations in terms of dissipation and convergence to equilibrium. Similar decompositions hold for rate functions at level 2 and level 2.5. These results clarify how bounds on entropy production and fluctuation theorems emerge from the underlying dynamical rules. We discuss how these results for Markov chains are related to similar structures within MFT, which describes hydrodynamic limits of such microscopic models.

Baryonic popcorn

NASA Astrophysics Data System (ADS)

Kaplunovsky, Vadim; Melnikov, Dmitry; Sonnenschein, Jacob

2012-11-01

In the large N c limit cold dense nuclear matter must be in a lattice phase. This applies also to holographic models of hadron physics. In a class of such models, like the generalized Sakai-Sugimoto model, baryons take the form of instantons of the effective flavor gauge theory that resides on probe flavor branes. In this paper we study the phase structure of baryonic crystals by analyzing discrete periodic configurations of such instantons. We find that instanton configurations exhibit a series of "popcorn" transitions upon increasing the density. Through these transitions normal (3D) lattices expand into the transverse dimension, eventually becoming a higher dimensional (4D) multi-layer lattice at large densities. We consider 3D lattices of zero size instantons as well as 1D periodic chains of finite size instantons, which serve as toy models of the full holographic systems. In particular, for the finite-size case we determine solutions of the corresponding ADHM equations for both a straight chain and for a 2D zigzag configuration where instantons pop up into the holographic dimension. At low density the system takes the form of an "abelian anti- ferromagnetic" straight periodic chain. Above a critical density there is a second order phase transition into a zigzag structure. An even higher density yields a rich phase space characterized by the formation of multi-layer zigzag structures. The finite size of the lattices in the transverse dimension is a signal of an emerging Fermi sea of quarks. We thus propose that the popcorn transitions indicate the onset of the "quarkyonic" phase of the cold dense nuclear matter.

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

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

Dave, Mudra R., E-mail: mdave-phy@yahoo.co.in; 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.

Effect of edge modification on the zigzag BC2N nanoribbons

NASA Astrophysics Data System (ADS)

Xiao, Xiang; Li, Hong; Tie, Jun; Lu, Jing

2016-08-01

We use first principles calculations to investigate the effects of edge modification with nonmetal species on zigzag-edged BC2N nanoribbons (ZBC2NNRs). These ZBC2NNRs show either semiconducting or metallic behaviors depending on the edge modifications and ribbon widths. We find that the O-modification induces a ferromagnetic ground state with a metallic behavior for all the ribbon widths investigated. And when the ribbon width is more than 3.32 nm (NZ ⩾ 16), an antiferromagnetic ground state with a half-metallic behavior is realized in the H-passivated ZBC2NNRs. These versatile electronic properties render the ZBC2NNRs a promising candidate material in nanoelectronics and nanospintronics.

Geometric effects on mixing performance in a novel passive micromixer with trapezoidal-zigzag channels

NASA Astrophysics Data System (ADS)

Le The, Hai; Ta, Bao Quoc; Le Thanh, Hoa; Dong, Tao; Nguyen Thoi, Trung; Karlsen, Frank

2015-09-01

A novel passive micromixer, called a trapezoidal-zigzag micromixer (TZM), is reported. A TZM is composed of trapezoidal channels in a zigzag and split-recombine arrangement that enables multiple mixing mechanisms, including splitting-recombining, twisting, transversal flows, vortices, and chaotic advection. The effects of geometric parameters of the TZM on mixing performance are systematically investigated by the Taguchi method and numerical simulations in COMSOL Multiphysics. The number of mixing units, the slope angle of the trapezoidal channel, the height of the constriction element, and the width ratio between the middle-trapezoidal channel and the side-trapezoidal channel are the four parameters under study. The mixing performance of the TZM is investigated at three different Reynolds number (Re) values of 0.5, 5, and 50. The results showed that a TZM with six mixing units, a trapezoidal slope angle of 75°, a constricting height of 100 µm, and a width ratio of 0.5 has the highest mixing efficiency. This optimal TZM has a mixing efficiency greater than 85% for Re values from 0.1 to 80. In particular, for Re  ⩽  0.9 and Re  ⩾  20, the mixing efficiency of the optimal TZM is greater than 90%. The proposed TZM has a higher mixing efficiency and a smaller footprint than previously reported micromixers.

Negative differential resistance and magnetoresistance in zigzag borophene nanoribbons

NASA Astrophysics Data System (ADS)

Liu, Jiayi; Wu, Jiaxin; Chen, Changpeng; Han, Lu; Zhu, Ziqing; Wu, Jinping

2018-02-01

Since borophene has been grown experimentally, its extraordinary characteristics have attracted more and more attentions. In this paper, we construct pristine zigzag-edged borophene nanoribbons (ZBNRs) of different widths to study the transport properties, using the first-principles calculations. The differences of the quantum transport properties are discussed, where even-N ZBNRs and odd-N ZBNRs have different current-voltage relationships. Especially, the negative differential resistance (NDR) can be observed within certain bias range in 5-ZBNR and 7-ZBNR, while 6-ZBNR behaves like a metal whose current rises with the increase of the voltage. Moreover, borophene nanoribbon shows interesting magnetic transport properties. The spin-filtering effect can be revealed when the two electrodes have opposite magnetization directions. Besides, the magnetoresistance effect appears to exist in even-N ZBNRs and the maximum value can reach 70%. The mechanisms of these phenomena are proposed in detail.

High performance current and spin diode of atomic carbon chain between transversely symmetric ribbon electrodes.

PubMed

Dong, Yao-Jun; Wang, Xue-Feng; Yang, Shuo-Wang; Wu, Xue-Mei

2014-08-21

We demonstrate that giant current and high spin rectification ratios can be achieved in atomic carbon chain devices connected between two symmetric ferromagnetic zigzag-graphene-nanoribbon electrodes. The spin dependent transport simulation is carried out by density functional theory combined with the non-equilibrium Green's function method. It is found that the transverse symmetries of the electronic wave functions in the nanoribbons and the carbon chain are critical to the spin transport modes. In the parallel magnetization configuration of two electrodes, pure spin current is observed in both linear and nonlinear regions. However, in the antiparallel configuration, the spin-up (down) current is prohibited under the positive (negative) voltage bias, which results in a spin rectification ratio of order 10(4). When edge carbon atoms are substituted with boron atoms to suppress the edge magnetization in one of the electrodes, we obtain a diode with current rectification ratio over 10(6).

High performance current and spin diode of atomic carbon chain between transversely symmetric ribbon electrodes

PubMed Central

Dong, Yao-Jun; Wang, Xue-Feng; Yang, Shuo-Wang; Wu, Xue-Mei

2014-01-01

We demonstrate that giant current and high spin rectification ratios can be achieved in atomic carbon chain devices connected between two symmetric ferromagnetic zigzag-graphene-nanoribbon electrodes. The spin dependent transport simulation is carried out by density functional theory combined with the non-equilibrium Green's function method. It is found that the transverse symmetries of the electronic wave functions in the nanoribbons and the carbon chain are critical to the spin transport modes. In the parallel magnetization configuration of two electrodes, pure spin current is observed in both linear and nonlinear regions. However, in the antiparallel configuration, the spin-up (down) current is prohibited under the positive (negative) voltage bias, which results in a spin rectification ratio of order 104. When edge carbon atoms are substituted with boron atoms to suppress the edge magnetization in one of the electrodes, we obtain a diode with current rectification ratio over 106. PMID:25142376

Structural Basis for Substrate Fatty Acyl Chain Specificity

PubMed Central

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

2008-01-01

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-Å resolution. The overall fold of the N-terminal ∼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 α-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 12Å and permitting substrate acyl chain lengths as long as 24 carbons to bind. VLCAD deficiency is among the more common defects of mitochondrial β-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. PMID:18227065

An Analysis of Conceptual Flow Patterns and Structures in the Physics Classroom

NASA Astrophysics Data System (ADS)

Eshach, Haim

2010-03-01

The aim of the current research is to characterize the conceptual flow processes occurring in whole-class dialogic discussions with a high level of interanimation; in the present case, of a high-school class learning about image creation on plane mirrors. Using detailed chains of interaction and conceptual flow discourse maps-both developed for the purpose of this research-the classroom discourse, audio-taped and transcribed verbatim, was analyzed and three discussion structures were revealed: accumulation around budding foci concepts, zigzag between foci concepts, and concept tower. These structures as well as two additional factors, suggest the Two-Space Model of the whole class discussion proposed in the present article. The two additional factors are: (1) the teacher intervention; and (2) the conceptual barriers observed among the students, namely, materialistic thinking, and the tendency to attribute "unique characteristics" to optical devices. This model might help teachers to prepare and conduct efficient whole-class discussions which accord with the social constructivist perspective of learning.

M(II)-dipyridylamide-based coordination frameworks (M=Mn, Co, Ni): Structural transformation

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

Tzeng, Biing-Chiau; Selvam, TamilSelvi; Tsai, Miao-Hsin

2016-11-15

A series of 1-D double-zigzag (([M(papx){sub 2}(H{sub 2}O){sub 2}](ClO{sub 4}){sub 2}){sub n}; M=Mn, x=s (1), x=o (3); M=Co, x=s (4), x=o (5); M=Ni, x=s (6), x=o (7)) and 2-D polyrotaxane ([Mn(paps){sub 2}(ClO{sub 4}){sub 2}]{sub n} (2)) frameworks were synthesized by reactions of M(ClO{sub 4}){sub 2} (M=Mn, Co, and Ni) with papx (paps, N,N’-bis(pyridylcarbonyl)-4,4’-diaminodiphenylthioether; papo, N,N’-bis(pyridylcarbonyl)-4,4’-diaminodiphenyl ether), which have been isolated and structurally characterized by X-ray diffraction. Based on powder X-ray diffraction (PXRD) experiments, heating the double-zigzag frameworks underwent structural transformation to give the respective polyrotaxane ones. Moreover, grinding the solid samples of the respective polyrotaxanes in the presence of moisturemore » also resulted in the total conversion to the original double-zigzag frameworks. In this study, we have successfully extended studies to Mn{sup II}, Co{sup II}, and Ni{sup II} frameworks from the previous Zn{sup II}, Cd{sup II}, and Cu{sup II} ones, and interestingly such structural transformation is able to be proven experimentally by powder and single-crystal X-ray diffraction studies as well. - Graphical abstract: 1-D double-zigzag and 2-D polyrotaxane frameworks of M(II)-papx (x=s, o; M=Mn, Co, Ni) frameworks can be interconverted by heating and grinding in the presence of moiture, and such structural transformation has be proven experimentally by powder and single-crystal X-ray diffraction studies.« less

Using spiral chain models for study of nanoscroll structures

NASA Astrophysics Data System (ADS)

Savin, Alexander V.; Sakovich, Ruslan A.; Mazo, Mikhail A.

2018-04-01

Molecular nanoribbons with different chemical structures can form scrolled packings possessing outstanding properties and application perspectives due to their morphology. Here, we propose a simplified two-dimensional model of the molecular chain that allows us to describe the molecular nanoribbon's scrolled packings of various structures as a spiral packaging chain. The model allows us to obtain the possible stationary states of single-layer nanoribbon scrolls of graphene, graphane, fluorographene, fluorographane (graphene hydrogenated on one side and fluorinated on the other side), graphone C4H (graphene partially hydrogenated on one side), and fluorographone C4F . The obtained states and the states of the scrolls found through all-atomic models coincide with good accuracy. We show the stability of scrolled packings and calculate the dependence of energy, the number of coils, and the inner and outer radius of the scrolled packing on the nanoribbon length. It is shown that a scrolled packing is the most energetically favorable conformation for nanoribbons of graphene, graphane, fluorographene, and fluorographane at large lengths. A double-scrolled packing when the nanoribbon is symmetrically rolled into a scroll from opposite ends is more advantageous for longer length nanoribbons of graphone and fluorographone. We show the possibility of the existence of scrolled packings for nanoribbons of fluorographene and the existence of two different types of scrolls for nanoribbons of fluorographane, which correspond to the left and right Archimedean spirals of the chain model. The simplicity of the proposed model allows us to consider the dynamics of molecular nanoribbon scrolls of sufficiently large lengths and at sufficiently large time intervals.

Zigzag-Elongated Fused π-Electronic Core: A Molecular Design Strategy to Maximize Charge-Carrier Mobility.

PubMed

Yamamoto, Akito; Murata, Yoshinori; Mitsui, Chikahiko; Ishii, Hiroyuki; Yamagishi, Masakazu; Yano, Masafumi; Sato, Hiroyasu; Yamano, Akihito; Takeya, Jun; Okamoto, Toshihiro

2018-01-01

Printed and flexible electronics requires solution-processable organic semiconductors with a carrier mobility (μ) of ≈10 cm 2 V -1 s -1 as well as high chemical and thermal durability. In this study, chryseno[2,1- b :8,7- b ']dithiophene (ChDT) and its derivatives, which have a zigzag-elongated fused π-electronic core (π-core) and a peculiar highest occupied molecular orbital (HOMO) configuration, are reported as materials with conceptually new semiconducting π-cores. ChDT and its derivatives are prepared by a versatile synthetic procedure. A comprehensive investigation reveals that the ChDT π-core exhibits increasing structural stability in the bulk crystal phase, and that it is unaffected by a variation of the transfer integral, induced by the perpetual molecular motion of organic materials owing to the combination of its molecular shape and its particular HOMO configuration. Notably, ChDT derivatives exhibit excellent chemical and thermal stability, high charge-carrier mobility under ambient conditions (μ ≤ 10 cm 2 V -1 s -1 ), and a crystal phase that is highly stable, even at temperatures above 250 °C.

Preparation of Desirable Porous Cell Structure Polylactide/Wood Flour Composite Foams Assisted by Chain Extender

PubMed Central

Wang, Youyong; Song, Yongming; Du, Jun; Xi, Zhenhao; Wang, Qingwen

2017-01-01

Polylactide (PLA)/wood flour composite foam were prepared through a batch foaming process. The effect of the chain extender on the crystallization behavior and dynamic rheological properties of the PLA/wood flour composites were investigated as well as the crystal structure and cell morphology of the composite foams. The incorporation of the chain extender enhanced the complex viscosity and storage modulus of PLA/wood flour composites, indicating the improved melt elasticity. The chain extender also led to a decreased crystallization rate and final crystallinity of PLA/wood flour composites. With an increasing chain extender content, a finer and more uniform cell structure was formed, and the expansion ratio of PLA/wood flour composite foams was much higher than without the chain extender. Compared to the unfoamed composites, the crystallinity of the foamed PLA/wood flour composites was improved and the crystal was loosely packed. However, the new crystalline form was not evident. PMID:28846604

Width-Tuned Magnetic Order Oscillation on Zigzag Edges of Honeycomb Nanoribbons.

PubMed

Chen, Wen-Chao; Zhou, Yuan; Yu, Shun-Li; Yin, Wei-Guo; Gong, Chang-De

2017-07-12

Quantum confinement and interference often generate exotic properties in nanostructures. One recent highlight is the experimental indication of a magnetic phase transition in zigzag-edged graphene nanoribbons at the critical ribbon width of about 7 nm [ Magda , G. Z. et al. Nature 2014 , 514 , 608 ]. Here we show theoretically that with further increase in the ribbon width, the magnetic correlation of the two edges can exhibit an intriguing oscillatory behavior between antiferromagnetic and ferromagnetic, driven by acquiring the positive coherence between the two edges to lower the free energy. The oscillation effect is readily tunable in applied magnetic fields. These novel properties suggest new experimental manifestation of the edge magnetic orders in graphene nanoribbons and enhance the hopes of graphene-like spintronic nanodevices functioning at room temperature.

Four structural risk factors identify most fibril-forming kappa light chains.

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

Stevens, F. J.; Biosciences Division

2000-09-01

Antibody light chains (LCs) comprise the most structurally diverse family of proteins involved in amyloidosis. Many antibody LCs incorporate structural features that impair their stability and solubility, leading to their assembly into fibrils and to their subsequent pathological deposition when produced in excess during multiple myeloma and primary amyloidosis. The particular amino acid variations in antibody LCs that account for fibril formation and amyloidogenesis have not been identified. This study focuses on amyloidogenesis within the Kl family of human LCs. Reanalysis of the current database of primary structures of proteins from more than 100 patients who produced Kl LCS, 37more » of which were amyloidogenic, reveals apparent structural features that may contribute to amyloidosis. These features include loss of conserved residues or the gain of particular residues through mutation at sites involving a repertoire of approximately 20% of the amino acid positions in the light chain variable domain (V{sub L}). Moreover, 80% of all K1 amyloidogenic V{sub L}s are identifiable by the presence of at least one of three single-site substitutions or the acquisition of an N-linked glycosylation site through mutations. These findings suggest that it is feasible to predict fibril propensity by analysis of primary structure.« less

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…

Structure and thermodynamic properties of (C5H12N)CuBr3: a new weakly coupled antiferromagnetic spin-1/2 chain complex lying in the 1D-3D dimensional cross-over regime.

PubMed

Pan, Bingying; Wang, Yang; Zhang, Lijuan; Li, Shiyan

2014-04-07

Single crystals of a metal organic complex (C5H12N)CuBr3 (C5H12N = piperidinium, pipH for short) have been synthesized, and the structure was determined by single-crystal X-ray diffraction. (pipH)CuBr3 crystallizes in the monoclinic group C2/c. Edging-sharing CuBr5 units link to form zigzag chains along the c axis, and the neighboring Cu(II) ions with spin-1/2 are bridged by bibromide ions. Magnetic susceptibility data down to 1.8 K can be well fitted by the Bonner-Fisher formula for the antiferromagnetic spin-1/2 chain, giving the intrachain magnetic coupling constant J ≈ -17 K. At zero field, (pipH)CuBr3 shows three-dimensional (3D) order below TN = 1.68 K. Calculated by the mean-field theory, the interchain coupling constant J' = -0.91 K is obtained and the ordered magnetic moment m0 is about 0.23 μB. This value of m0 makes (pipH)CuBr3 a rare compound suitable to study the 1D-3D dimensional cross-over problem in magnetism, since both 3D order and one-dimensional (1D) quantum fluctuations are prominent. In addition, specific heat measurements reveal two successive magnetic transitions with lowering temperature when external field μ0H ≥ 3 T is applied along the a' axis. The μ0H-T phase diagram of (pipH)CuBr3 is roughly constructed.

Dynamical quadrupole structure factor of frustrated ferromagnetic chain

NASA Astrophysics Data System (ADS)

Onishi, Hiroaki

2018-05-01

We investigate the dynamical quadrupole structure factor of a spin-1/2 J1-J2 Heisenberg chain with competing ferromagnetic J1 and antiferromagnetic J2 in a magnetic field by exploiting density-matrix renormalization group techniques. In a field-induced spin nematic regime, we observe gapless excitations at q = π according to quasi-long-range antiferro-quadrupole correlations. The gapless excitation mode has a quadratic form at the saturation, while it changes into a linear dispersion as the magnetization decreases.

A Multi-scale Refined Zigzag Theory for Multilayered Composite and Sandwich Plates with Improved Transverse Shear Stresses

NASA Technical Reports Server (NTRS)

Iurlaro, Luigi; Gherlone, Marco; Di Sciuva, Marco; Tessler, Alexander

2013-01-01

The Refined Zigzag Theory (RZT) enables accurate predictions of the in-plane displacements, strains, and stresses. The transverse shear stresses obtained from constitutive equations are layer-wise constant. Although these transverse shear stresses are generally accurate in the average, layer-wise sense, they are nevertheless discontinuous at layer interfaces, and thus they violate the requisite interlaminar continuity of transverse stresses. Recently, Tessler applied Reissner's mixed variational theorem and RZT kinematic assumptions to derive an accurate and efficient shear-deformation theory for homogeneous, laminated composite, and sandwich beams, called RZT(m), where "m" stands for "mixed". Herein, the RZT(m) for beams is extended to plate analysis, where two alternative assumptions for the transverse shear stresses field are examined: the first follows Tessler's formulation, whereas the second is based on Murakami's polynomial approach. Results for elasto-static simply supported and cantilever plates demonstrate that Tessler's formulation results in a powerful and efficient structural theory that is well-suited for the analysis of multilayered composite and sandwich panels.

Oxygen vacancy effect on dielectric and hysteretic properties of zigzag ferroelectric iron dioxide nanoribbon

NASA Astrophysics Data System (ADS)

Zriouel, S.; Taychour, B.; Yahyaoui, F. El; Drissi, L. B.

2017-07-01

Zigzag FeO2 nanoribbon defected by the removal of oxygen atoms is simulated using Monte Carlo simulations. All possible arrangements of positions and number of oxygen vacancy are investigated. Temperature dependence of polarization, dielectric susceptibility, internal energy, specific heat and dielectric hysteresis loops are all studied. Results show the presence of second order phase transition and Q - type behavior. Dielectric properties dependence on ribbon's edge, positions and number of oxygen vacancy are discussed in detail. Moreover, single and square hysteresis loops are observed whatever the number of oxygen vacancy in the system.

Structural study of gold clusters.

PubMed

Xiao, Li; Tollberg, Bethany; Hu, Xiankui; Wang, Lichang

2006-03-21

Density functional theory (DFT) calculations were carried out to study gold clusters of up to 55 atoms. Between the linear and zigzag monoatomic Au nanowires, the zigzag nanowires were found to be more stable. Furthermore, the linear Au nanowires of up to 2 nm are formed by slightly stretched Au dimers. These suggest that a substantial Peierls distortion exists in those structures. Planar geometries of Au clusters were found to be the global minima till the cluster size of 13. A quantitative correlation is provided between various properties of Au clusters and the structure and size. The relative stability of selected clusters was also estimated by the Sutton-Chen potential, and the result disagrees with that obtained from the DFT calculations. This suggests that a modification of the Sutton-Chen potential has to be made, such as obtaining new parameters, in order to use it to search the global minima for bigger Au clusters.

Structural domains and main-chain flexibility in prion proteins.

PubMed

Blinov, N; Berjanskii, M; Wishart, D S; Stepanova, M

2009-02-24

In this study we describe a novel approach to define structural domains and to characterize the local flexibility in both human and chicken prion proteins. The approach we use is based on a comprehensive theory of collective dynamics in proteins that was recently developed. This method determines the essential collective coordinates, which can be found from molecular dynamics trajectories via principal component analysis. Under this particular framework, we are able to identify the domains where atoms move coherently while at the same time to determine the local main-chain flexibility for each residue. We have verified this approach by comparing our results for the predicted dynamic domain systems with the computed main-chain flexibility profiles and the NMR-derived random coil indexes for human and chicken prion proteins. The three sets of data show excellent agreement. Additionally, we demonstrate that the dynamic domains calculated in this fashion provide a highly sensitive measure of protein collective structure and dynamics. Furthermore, such an analysis is capable of revealing structural and dynamic properties of proteins that are inaccessible to the conventional assessment of secondary structure. Using the collective dynamic simulation approach described here along with a high-temperature simulations of unfolding of human prion protein, we have explored whether locations of relatively low stability could be identified where the unfolding process could potentially be facilitated. According to our analysis, the locations of relatively low stability may be associated with the beta-sheet formed by strands S1 and S2 and the adjacent loops, whereas helix HC appears to be a relatively stable part of the protein. We suggest that this kind of structural analysis may provide a useful background for a more quantitative assessment of potential routes of spontaneous misfolding in prion proteins.

Polymorphism in 'L' shaped lipids: structure of N-, O-diacylethanolamines with mixed acyl chains.

PubMed

Tarafdar, Pradip K; Swamy, Musti J

2009-11-01

Although solid state polymorphism in lipids has been established by spectroscopic and calorimetric studies long ago, only in a few cases crystal structures of different polymorphs of the same compound have been reported, possibly due to difficulties in obtaining high quality single crystals of individual polymorphs. Recent studies show that N-, O-diacylethanolamines (DAEs) can be derived by the O-acylation of the stress-related lipids, the N-acylethanolamines under physiological conditions. In this study, two DAEs with mixed acyl chains, namely N-palmitoyl, O-octanoylethanolamine and N-palmitoyl, O-decanoylethanolamine have been synthesized and their three-dimensional structures were determined. Both the compounds were found to adopt 'L' shaped structures and exist in two polymorphic forms, alpha and beta. In the alpha form a mixed-type chain packing has been observed whereas in the beta form the chain packing is symmetric. Similar polymorphic forms are likely to exist in other 'L' shaped lipids such as 1,3-diacylglycerols and ceramides, where polymorphism has been detected earlier, but three-dimensional structures - which can give precise information about the packing at atomic resolution - have not been reported.

Chemical construction and structural permutation of neurotoxic natural product, antillatoxin: importance of the three-dimensional structure of the bulky side chain

PubMed Central

INOUE, Masayuki

2014-01-01

Antillatoxin 1 is a unique natural product that displays potent neurotoxic and neuritogenic activities through activation of voltage-gated sodium channels. The peptidic macrocycle of 1 was attached to a side chain with an exceptionally high degree of methylation. In this review, we discuss the total synthesis and biological evaluation of 1 and its analogues. First we describe an efficient synthetic route to 1. This strategy enabled the unified preparation of nine side chain analogues. Structure-activity relationship studies of these analogues revealed that subtle side chain modification leads to dramatic changes in activity, and detailed structural analyses indicated the importance of the overall size and three dimensional shape of the side chain. Based on these data, we designed and synthesized a photoresponsive analogue, proving that the activity of 1 was modulated via a photochemical reaction. The knowledge accumulated through these studies will be useful for the rational design of new tailor-made molecules to control the function and behavior of ion channels. PMID:24522155

Lanthanide coordination polymers: Synthesis, diverse structure and luminescence properties

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

Song, Xue-Qin, E-mail: songxq@mail.lzjtu.cn; Lei, Yao-Kun; Wang, Xiao-Run

2014-10-15

The new semirigid exo-bidentate ligand incorporating furfurysalicylamide terminal groups, namely, 1,4-bis([(2′-furfurylaminoformyl)phenoxyl]methyl)-2,5-bismethylbenzene (L) was synthesized and used as building blocks for constructing lanthanide coordination polymers with luminescent properties. The series of lanthanide nitrate complexes have been characterized by elemental analysis, IR spectroscopy, and X-ray diffraction analysis. The semirigid ligand L, as a bridging ligand, reacts with lanthanide nitrates forming three distinct structure types: chiral noninterpenetrated two-dimensional (2D) honeycomblike (6,3) (hcb, Schläfli symbol 6{sup 3}, vertex symbol 6 6 6) topological network as type I, 1D zigzag chain as type II and 1D trapezoid ladder-like chain as type III. The structural diversitiesmore » indicate that lanthanide contraction effect played significant roles in the structural self-assembled process. The luminescent properties of Eu{sup III}, Tb{sup III} and Dy{sup III} complexes are discussed in detail. Due to the good match between the lowest triplet state of the ligand and the resonant energy level of the lanthanide ion, the lanthanide ions in Eu{sup III}, Tb{sup III} and Dy{sup III} complexes can be efficiently sensitized by the ligand. - Graphical abstract: We present herein six lanthanide coordination polymers of a new semirigid exo-bidentate ligand which not only display diverse structures but also possess strong luminescence properties. - Highlights: • We present lanthanide coordination polymers of a new semirigid exo-bidentate ligand. • The lanthanide coordination polymers exhibit diverse structures. • The luminescent properties of Tb{sup III}, Eu{sup III} and Dy{sup III} complexes are discussed in detail.« less

Two-dimensional thermography image retrieval from zig-zag scanned data with TZ-SCAN

NASA Astrophysics Data System (ADS)

Okumura, Hiroshi; Yamasaki, Ryohei; Arai, Kohei

2008-10-01

TZ-SCAN is a simple and low cost thermal imaging device which consists of a single point radiation thermometer on a tripod with a pan-tilt rotator, a DC motor controller board with a USB interface, and a laptop computer for rotator control, data acquisition, and data processing. TZ-SCAN acquires a series of zig-zag scanned data and stores the data as CSV file. A 2-D thermal distribution image can be retrieved by using the second quefrency peak calculated from TZ-SCAN data. An experiment is conducted to confirm the validity of the thermal retrieval algorithm. The experimental result shows efficient accuracy for 2-D thermal distribution image retrieval.

Structure of a short-chain dehydrogenase/reductase from Bacillus anthracis

PubMed Central

Hou, Jing; Wojciechowska, Kamila; Zheng, Heping; Chruszcz, Maksymilian; Cooper, David R.; Cymborowski, Marcin; Skarina, Tatiana; Gordon, Elena; Luo, Haibin; Savchenko, Alexei; Minor, Wladek

2012-01-01

The crystal structure of a short-chain dehydrogenase/reductase from Bacillus anthracis strain ‘Ames Ancestor’ complexed with NADP has been determined and refined to 1.87 Å resolution. The structure of the enzyme consists of a Rossmann fold composed of seven parallel β-strands sandwiched by three α-­helices on each side. An NADP molecule from an endogenous source is bound in the conserved binding pocket in the syn conformation. The loop region responsible for binding another substrate forms two perpendicular short helices connected by a sharp turn. PMID:22684058

Electron doping effects on the electrical conductivity of zigzag carbon nanotubes and corresponding unzipped armchair graphene nanoribbons

NASA Astrophysics Data System (ADS)

Mousavi, Hamze; Jalilvand, Samira; Kurdestany, Jamshid Moradi; Grabowski, Marek

2017-10-01

The Kubo formula is used to extract the electrical conductivity (EC) of different diameters of doped zigzag carbon nanotubes and their corresponding unzipped armchair graphene nanoribbons, as a function of temperature and chemical potential, within the tight-binding Hamiltonian model and Green's functions approach. The results reveal more sensitivity to temperature for semiconducting systems in addition to a decrease in EC of all systems with increasing cross-sections.

Designing of spin-filtering devices in zigzag graphene nanoribbons heterojunctions by asymmetric hydrogenation and B-N doping

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

Zhang, Dan; Zhang, Xiaojiao; Ouyang, Fangping

2015-01-07

Using nonequilibrium Green's function in combination with the spin-polarized density functional theory, the spin-dependent transport properties of boron and nitrogen doped zigzag graphene nanoribbons (ZGNRs) heterojunctions with single or double edge-saturated hydrogen have been investigated. Our results show that the perfect spin-filtering effect (100%), rectifying behavior and negative differential resistance can be realized in the ZGNRs-based systems. And the corresponding physical analysis has been given.

Electronic and transport properties of 1D aluminum at atomic scale

NASA Astrophysics Data System (ADS)

Bhuyan, Prabal Dev; Gupta, Sanjeev K.; Sonvane, Yogesh; Kumar, Ashok

2018-04-01

In this paper, we have studied the structural, electronic and transport properties of 1D carbyne like chain and ribbon like zigzag structures of aluminum (Al) nanowire. The ribbon with width of 4.79Å (2R) and 7.01Å (3R) shows better room temperature conductivity i.e. 3.50×1019 (Ω m s)-1 and 3.91×1019 (Ω m s)-1 respectively. We have observed that Al chain conducts better than Al ribbon; however the conductivity for the ribbon can be enhanced by increasing the width. On the other hand, higher thermal conductivity has been found to possess Al ribbon (3R) structure.

Field characteristics of an alvarez-type linac structure having chain-like electrode array

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

Odera, M.; Goto, A.; Hemmi, M.

1985-10-01

A chain-like electrode configuration in an Alvarez-type linac cavity was studied by models. The structure has been devised to get a moderate shunt impedance together with simplicity of operation, in ion velocity region of more than a few percent of that of light by incorporating focusing scheme by high frequency quadrupolar fields into an TM-010 accelerating field of an Alvarez linac. It has a chain-like electrode array instead of drift tubes containing quadrupole lenses for ordinary linacs. The chain-like electrode structure generates along its central axis, high frequency acceleration and focusing fields alternately, separating the acceleration and focusing functions inmore » space. The separation discriminates this structure from spatially uniform acceleration and focusing scheme of the RFQs devised by Kapchinsky and Teplyakov. It gives beam acceleration effects different from those by conventional linacs and reveals possibility of getting a high acceleration efficiency. Resonant frequency spectrum was found relatively simple by measurements on high frequency models. Separation of unwanted modes from the TM-010 acceleration mode is large; a few 10 MHz, at least. Tilt of the acceleration field is not very sensitive to pertubation in gap capacitance for the TM-010 mode.« less

Effects of edge magnetism on the Kohn anomalies of zigzag graphene nanoribbons.

PubMed

Culchac, F J; Capaz, Rodrigo B

2016-02-12

The effects of edge magnetism on the Kohn anomaly (KA) of the G-band phonons of zigzag graphene nanoribbons (ZGNRs) are studied using a combination of the tight-binding and mean-field Hubbard models. We show that the opening of an energy gap, induced by magnetic ordering, significantly changes the KA effects, particularly for narrow ribbons in which the gap is larger than the phonon energy. Therefore, the G-band phonon frequency and lifetime are altered for a magnetically-ordered edge state with respect to an unpolarized edge state. The effects of temperature, ZGNR width, doping and transverse electric fields are systematically investigated. We propose using this effect to probe the magnetic order of edge states in graphene nanoribbons using Raman spectroscopy.

Cobalt(II) complexes with bis(N-imidazolyl/benzimidazolyl) pyridazine: Structures, photoluminescent and photocatalytic properties

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

Li, Jin-Ping; Fan, Jian-Zhong; Wang, Duo-Zhi, E-mail: wangdz@xju.edu.cn

2016-07-15

Six new Co{sup II} complexes [Co(L{sup 1}){sub 4}(OH){sub 2}] (1), {[Co(L"1)(H_2O)_4]·2ClO_4}{sub ∞} (2), {[Co(L"1)(H_2O)_4]·SiF_6}{sub ∞} (3), {[Co(L"1)_3]·2ClO_4}{sub ∞} (4), [Co(L{sup 2})Cl{sub 2}]{sub ∞} (5) and {[Co(L"2)_2]·SiF_6}{sub ∞} (6) [L{sup 1}=3,6-bis(N-imidazolyl) pyridazine, L{sup 2}=3,6-bis (N-benzimidazolyl) pyridazine] have been synthesized and characterized by elemental analysis, IR spectra and single crystal X-ray diffraction. Complex 1 has a mononuclear structure, while complexes 2 and 3 have 1-D chain structures. Considering the Co{sup II} centers were linked by the L{sup 1} ligands, the 3-D framework of complex 4 can be rationalized to be a {4^12.6^3} 6-c topological net with the stoichiometry uninodal net. 5 revealsmore » a coordination 1-D zigzag chain structure consisting of a neutral chain [Co(L{sup 2})Cl{sub 2}]{sub n} with the Co{sup II} centers. Complex 6 has a rhombohedral grid with a (4, 4) topology. The TGA property, fluorescent property and photocatalytic activity of complexes 1–6 have been investigated and discussed. - Graphical abstract: Six Co{sup II} complexes of bis(N-imidazolyl/benzimidazolyl)pyridazine were synthesized and structurally characterized. The fluorescence properties and photocatalytic activity for dye degradation under UV light of all complexes have been investigated and discussed. Display Omitted - Highlights: • Six new Co{sup II} complexes with bis(N-imidazolyl/benzimidazolyl) pyridazine. • Structural analysis of all complexes. • Fluorescent property of all complexes. • Photocatalytic activity for dye degradation under UV light of all complexes.« less

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

NASA Astrophysics Data System (ADS)

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

2016-07-01

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.

Determining Science Student Teachers' Cognitive Structure on the Concept of "Food Chain"

ERIC Educational Resources Information Center

Çinar, Derya

2015-01-01

The current study aims to determine science student teachers' cognitive structure on the concept of food chain. Qualitative research method was applied in this study. Fallacies detected in the pre-service teachers' conceptual structures are believed to result in students' developing misconceptions in their future classes and will adversely affect…

Chromatin conformation in living cells: support for a zig-zag model of the 30 nm chromatin fiber

NASA Technical Reports Server (NTRS)

Rydberg, B.; Holley, W. R.; Mian, I. S.; Chatterjee, A.

1998-01-01

A new method was used to probe the conformation of chromatin in living mammalian cells. The method employs ionizing radiation and is based on the concept that such radiation induces correlated breaks in DNA strands that are in spatial proximity. Human dermal fibroblasts in G0 phase of the cell cycle and Chinese hamster ovary cells in mitosis were irradiated by X-rays or accelerated ions. Following lysis of the cells, DNA fragments induced by correlated breaks were end-labeled and separated according to size on denaturing polyacrylamide gels. A characteristic peak was obtained for a fragment size of 78 bases, which is the size that corresponds to one turn of DNA around the nucleosome. Additional peaks between 175 and 450 bases reflect the relative position of nearest-neighbor nucleosomes. Theoretical calculations that simulate the indirect and direct effect of radiation on DNA demonstrate that the fragment size distributions are closely related to the chromatin structure model used. Comparison of the experimental data with theoretical results support a zig-zag model of the chromatin fiber rather than a simple helical model. Thus, radiation-induced damage analysis can provide information on chromatin structure in the living cell. Copyright 1998 Academic Press.

Focusing and directional beaming effects of airborne sound through a planar lens with zigzag slits

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

Tang, Kun; Qiu, Chunyin, E-mail: cyqiu@whu.edu.cn; Lu, Jiuyang

2015-01-14

Based on the Huygens-Fresnel principle, we design a planar lens to efficiently realize the interconversion between the point-like sound source and Gaussian beam in ambient air. The lens is constructed by a planar plate perforated elaborately with a nonuniform array of zigzag slits, where the slit exits act as subwavelength-sized secondary sources carrying desired sound responses. The experiments operated at audible regime agree well with the theoretical predictions. This compact device could be useful in daily life applications, such as for medical and detection purposes.

Width-Tuned Magnetic Order Oscillation on Zigzag Edges of Honeycomb Nanoribbons

DOE PAGES

Chen, Wen-Chao; Zhou, Yuan; Yu, Shun-Li; ...

2017-06-24

Quantum confinement and interference often generate exotic properties in nanostructures. One recent highlight is the experimental indication of a magnetic phase transition in zigzag-edged graphene nanoribbons at the critical ribbon width of about 7 nm [Magda, G. Z. et al. Nature 2014, 514, 608]. Here in this work, we show theoretically that with further increase in the ribbon width, the magnetic correlation of the two edges can exhibit an intriguing oscillatory behavior between antiferromagnetic and ferromagnetic, driven by acquiring the positive coherence between the two edges to lower the free energy. The oscillation effect is readily tunable in applied magneticmore » fields. In conclusion, these novel properties suggest new experimental manifestation of the edge magnetic orders in graphene nanoribbons and enhance the hopes of graphene-like spintronic nanodevices functioning at room temperature.« less

Atomic Chain Electronics

NASA Technical Reports Server (NTRS)

Yamada, Toshishige; Saini, Subhash (Technical Monitor)

1998-01-01

Adatom chains, precise structures artificially created on an atomically regulated surface, are the smallest possible candidates for future nanoelectronics. Since all the devices are created by combining adatom chains precisely prepared with atomic precision, device characteristics are predictable, and free from deviations due to accidental structural defects. In this atomic dimension, however, an analogy to the current semiconductor devices may not work. For example, Si structures are not always semiconducting. Adatom states do not always localize at the substrate surface when adatoms form chemical bonds to the substrate atoms. Transport properties are often determined for the entire system of the chain and electrodes, and not for chains only. These fundamental issues are discussed, which will be useful for future device considerations.

Encapsulation and Polymerization of White Phosphorus Inside Single-Wall Carbon Nanotubes.

PubMed

Hart, Martin; White, Edward R; Chen, Ji; McGilvery, Catriona M; Pickard, Chris J; Michaelides, Angelos; Sella, Andrea; Shaffer, Milo S P; Salzmann, Christoph G

2017-07-03

Elemental phosphorus displays an impressive number of allotropes with highly diverse chemical and physical properties. White phosphorus has now been filled into single-wall carbon nanotubes (SWCNTs) from the liquid and thereby stabilized against the highly exothermic reaction with atmospheric oxygen. The encapsulated tetraphosphorus molecules were visualized with transmission electron microscopy, but found to convert readily into chain structures inside the SWCNT "nanoreactors". The energies of the possible chain structures were determined computationally, highlighting a delicate balance between the extent of polymerization and the SWCNT diameter. Experimentally, a single-stranded zig-zag chain of phosphorus atoms was observed, which is the lowest energy structure at small confinement diameters. These one-dimensional chains provide a glimpse into the very first steps of the transformation from white to red phosphorus. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Idiosyncratic Findings in Trichoscopy of Tinea Capitis: Comma, Zigzag Hairs, Corkscrew, and Morse Code-like Hair.

PubMed

Elghblawi, Ebtisam

2016-01-01

Dermoscopy is a method of growing significance in the diagnoses of dermatological pigmented skin diseases. However, in my case, mycology culture was negative and successful treatment was given on the basis of trichoscopy and wood lamp examination. I hereby describe a young boy with tinea capitis, multiple "comma hairs" and "zigzag hair" and a subtle additional feature "Morse code-like hair" when intensification was applied. Dermatoscopic aspects found skin Type 2 in a child of as a distinctive dermoscopic finding.

Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations.

PubMed

Zhu, Tong; Zhang, John Z H; He, Xiao

2014-09-14

In this work, protein side chain (1)H chemical shifts are used as probes to detect and correct side-chain packing errors in protein's NMR structures through structural refinement. By applying the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) method for ab initio calculation of chemical shifts, incorrect side chain packing was detected in the NMR structures of the Pin1 WW domain. The NMR structure is then refined by using molecular dynamics simulation and the polarized protein-specific charge (PPC) model. The computationally refined structure of the Pin1 WW domain is in excellent agreement with the corresponding X-ray structure. In particular, the use of the PPC model yields a more accurate structure than that using the standard (nonpolarizable) force field. For comparison, some of the widely used empirical models for chemical shift calculations are unable to correctly describe the relationship between the particular proton chemical shift and protein structures. The AF-QM/MM method can be used as a powerful tool for protein NMR structure validation and structural flaw detection.

Tunable magnetic states on the zigzag edges of hydrogenated and halogenated group-IV nanoribbons

NASA Astrophysics Data System (ADS)

Wang, Tzu-Cheng; Hsu, Chia-Hsiu; Huang, Zhi-Quan; Chuang, Feng-Chuan; Su, Wan-Sheng; Guo, Guang-Yu

2016-12-01

The magnetic and electronic properties of hydrogenated and halogenated group-IV zigzag nanoribbons (ZNRs) are investigated by first-principles density functional calculations. Fascinatingly, we find that all the ZNRs have magnetic edges with a rich variety of electronic and magnetic properties tunable by selecting the parent and passivating elements as well as controlling the magnetization direction and external strain. In particular, the electric property of the edge band structure can be tuned from the conducting to insulating with a band gap up to 0.7 eV. The last controllability would allow us to develop magnetic on-off nano-switches. Furthermore, ZNRs such as SiI, Ge, GeI and SnH, have fully spin-polarized metallic edge states and thus are promising materials for spintronics. The calculated magnetocrystalline anisotropy energy can be as large as ~9 meV/edge-site, being 2×103 time greater than that of bulk Ni and Fe (~5 μeV/atom), and thus has great potential for high density magneto-electric data-storage devices. Finally, the calculated exchange coupling strength and thus magnetic transition temperature increases as the applied strain goes from -5% to 5%. Our findings thus show that these ZNRs would have exciting applications in next-generation electronic and spintronic nano-devices.

Structural analysis of N-linked carbohydrate chains of funnel web spider (Agelenopsis aperta) venom peptide isomerase.

PubMed

Shikata, Y; Ohe, H; Mano, N; Kuwada, M; Asakawa, N

1998-06-01

The structure of the N-linked carbohydrate chains of peptide isomerase from the venom of the funnel web spider (Agelenopsis aperta) has been analyzed. Carbohydrates were released from peptide isomerase by hydrazinolysis and reductively aminated with 2-aminopyridine. The fluorescent derivatives were purified by phenol/chloroform extraction, followed by size-exclusion HPLC. The structure of the purified pyridylamino (PA-) carbohydrate chains were analyzed by a combination of two-dimensional HPLC mapping, sugar composition analysis, sequential exoglycosidase digestions, and mass spectrometry. The peptide isomerase contains six kinds of N-linked carbohydrate chains of truncated high-mannose type, with a fucose alpha 1-6 linked to the reducing N-acetylglucosamine in approximately 80% of them.

Lymphatic recovery of exogenous oleic acid in rats on long chain or specific structured triacylglycerol diets.

PubMed

Vistisen, Bodil; Mu, Huiling; Høy, Carl-Erik

2006-09-01

Specific structured triacylglycerols, MLM (M = medium-chain fatty acid, L = long-chain fatty acid), rapidly deliver energy and long-chain fatty acids to the body and are used for longer periods in human enteral feeding. In the present study rats were fed diets of 10 wt% MLM or LLL (L = oleic acid [18:1 n-9], M = caprylic acid [8:01) for 2 wk. Then lymph was collected 24 h following administration of a single bolus of 13C-labeled MLM or LLL. The total lymphatic recovery of exogenous 18:1 n-9 24 h after administration of a single bolus of MLM or LLL was similar in rats on the LLL diet (43% and 45%, respectively). However, the recovery of exogenous 18:1 n-9 was higher after a single bolus of MLM compared with a bolus of LLL in rats on the MLM diet (40% and 24%, respectively, P = 0.009). The recovery of lymphatic 18:1 n-9 of the LLL bolus tended to depend on the diet triacylglycerol structure and composition (P= 0.07). This study demonstrated that with a diet containing specific structured triacylglycerol, the lymphatic recovery of 18:1 n-9 after a single bolus of fat was dependent on the triacylglycerol structure of the bolus. This indicates that the lymphatic recovery of long-chain fatty acids from a single meal depends on the overall long-chain fatty acid composition of the habitual diet. This could have implications for enteral feeding for longer periods.

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

A structural insight into mechanical strength of graphene-like carbon and carbon nitride networks

NASA Astrophysics Data System (ADS)

Rahaman, Obaidur; Mortazavi, Bohayra; Dianat, Arezoo; Cuniberti, Gianaurelio; Rabczuk, Timon

2017-02-01

Graphene, one of the strongest materials ever discovered, triggered the exploration of many 2D materials in the last decade. However, the successful synthesis of a stable nanomaterial requires a rudimentary understanding of the relationship between its structure and strength. In the present study, we investigate the mechanical properties of eight different carbon-based 2D nanomaterials by performing extensive density functional theory calculations. The considered structures were just recently either experimentally synthesized or theoretically predicted. The corresponding stress-strain curves and elastic moduli are reported. They can be useful in training force field parameters for large scale simulations. A comparative analysis of these results revealed a direct relationship between atomic density per area and elastic modulus. Furthermore, for the networks that have an armchair and a zigzag orientation, we observed that they were more stretchable in the zigzag direction than the armchair direction. A critical analysis of the angular distributions and radial distribution functions suggested that it could be due to the higher ability of the networks to suppress the elongations of the bonds in the zigzag direction by deforming the bond angles. The structural interpretations provided in this work not only improve the general understanding of a 2D material’s strength but also enables us to rationally design them for higher qualities.

Idiosyncratic Findings in Trichoscopy of Tinea Capitis: Comma, Zigzag Hairs, Corkscrew, and Morse Code-like Hair

PubMed Central

Elghblawi, Ebtisam

2016-01-01

Dermoscopy is a method of growing significance in the diagnoses of dermatological pigmented skin diseases. However, in my case, mycology culture was negative and successful treatment was given on the basis of trichoscopy and wood lamp examination. I hereby describe a young boy with tinea capitis, multiple “comma hairs” and “zigzag hair” and a subtle additional feature “Morse code-like hair” when intensification was applied. Dermatoscopic aspects found skin Type 2 in a child of as a distinctive dermoscopic finding. PMID:28442876

Improved properties of recycled polypropylene by introducing the long chain branched structure through reactive extrusion.

PubMed

Li, Yingchun; Jia, Shuai; Du, Shuanli; Wang, Yafei; Lv, Lida; Zhang, Jianbin

2018-06-01

An approach originated from preparing long chain branched polypropylene (PP) was applied to modify the properties of recycled PP that involved reactive extrusion to introduce a branched chain structure onto recycled PP under the assistance of chemical reaction between maleic anhydride (MAH) monomer and glycidyl methacrylate (GMA) grafts. The results from Fourier transformed infrared spectroscopy (FTIR) indicated the reaction took place during melt mixing, and the intensity of ester increased with increasing amount of MAH. Several rheological plots including complex viscosity, storage modulus, loss modulus, loss tangent and Cole-Cole plot were used to investigate the rheological properties of recycled PP and modified PP with MAH, which indicated an additional longer relaxation time that was not shown in recycled PP. The effects of branched structure on melting and crystallization behaviors were also investigated, demonstrating the branched chains acted as nucleating agent. Moreover, the branched structure of modified samples gave rise to enhance mechanical properties, especially, the higher impact strength compared with recycled PP. Copyright © 2018 Elsevier Ltd. All rights reserved.

Linking Supply Chain Governance and Biosecurity in the Context of HPAI Control in Western Java: A Value Chain Perspective

PubMed Central

Indrawan, Dikky; Rich, Karl M.; van Horne, Peter; Daryanto, Arief; Hogeveen, Henk

2018-01-01

Despite extensive efforts to control the highly pathogenic avian influenza (HPAI), it remains endemic in Western Java, Indonesia. To understand the limited effectiveness of HPAI control measures, it is important to map the complex structure of the poultry sector. The governance of the poultry value chain in particular, could play a pivotal role, yet there is limited information on the different chain governance structures and their impacts on HPAI control. This article uses value chain analysis (VCA), focusing on an in-depth assessment of governance structures as well as transaction cost economics and quantitative estimates of the market power of different chain actors, to establish a theoretical framework to examine biosecurity and HPAI control in the Western Java poultry chain. During the research, semi-structured interviews were conducted with key value-chain stakeholders, and the economic performance of identified actors was estimated. Results indicated the co-existence of four different poultry value chains in West Java: the integrator chain, the semi-automated slaughterhouse chain, the controlled slaughter-point chain, and the private slaughter-point chain. The integrator chain was characterized by the highest levels of coordination and a tight, hierarchical governance. In contrast, the other three types of value chains were less coordinated. The market power of the different actors within the four value chains also differed. In more integrated chains, slaughterhouses held considerable market power, while in more informal value chains, market power was in the hands of traders. The economic effects of HPAI and biosecurity measures also varied for the identified actors in the different value chains. Implementation of biosecurity and HPAI control measures was strongly related to the governance structure of the chain, with interactions between different chains and governance structures accentuating the risk of HPAI. Our findings highlight that a proper

Linking Supply Chain Governance and Biosecurity in the Context of HPAI Control in Western Java: A Value Chain Perspective.

PubMed

Indrawan, Dikky; Rich, Karl M; van Horne, Peter; Daryanto, Arief; Hogeveen, Henk

2018-01-01

Despite extensive efforts to control the highly pathogenic avian influenza (HPAI), it remains endemic in Western Java, Indonesia. To understand the limited effectiveness of HPAI control measures, it is important to map the complex structure of the poultry sector. The governance of the poultry value chain in particular, could play a pivotal role, yet there is limited information on the different chain governance structures and their impacts on HPAI control. This article uses value chain analysis (VCA), focusing on an in-depth assessment of governance structures as well as transaction cost economics and quantitative estimates of the market power of different chain actors, to establish a theoretical framework to examine biosecurity and HPAI control in the Western Java poultry chain. During the research, semi-structured interviews were conducted with key value-chain stakeholders, and the economic performance of identified actors was estimated. Results indicated the co-existence of four different poultry value chains in West Java: the integrator chain, the semi-automated slaughterhouse chain, the controlled slaughter-point chain, and the private slaughter-point chain. The integrator chain was characterized by the highest levels of coordination and a tight, hierarchical governance. In contrast, the other three types of value chains were less coordinated. The market power of the different actors within the four value chains also differed. In more integrated chains, slaughterhouses held considerable market power, while in more informal value chains, market power was in the hands of traders. The economic effects of HPAI and biosecurity measures also varied for the identified actors in the different value chains. Implementation of biosecurity and HPAI control measures was strongly related to the governance structure of the chain, with interactions between different chains and governance structures accentuating the risk of HPAI. Our findings highlight that a proper

Structure and dynamics of solvated polyethylenimine chains

NASA Astrophysics Data System (ADS)

Beu, Titus A.; Farcaş, Alexandra

2017-12-01

Polimeric gene-delivery carriers have attracted great interest in recent years, owing to their applicability in gene therapy. In particular, cationic polymers represent the most promising delivery vectors for nucleic acids into the cells. This study presents extensive atomistic molecular dynamics simulations of linear polyethylenimine chains. The simulations show that the variation of the chain size and protonation fraction causes a substantial change of the diffusion coefficient. Examination of the solvated chains suggests the possibility of controlling the polymer diffusion mobility in solution.

Fabrication and electrical characterization of Al/diazo compound containing polyoxy chain/p-Si device structure

NASA Astrophysics Data System (ADS)

Birel, Ozgul; Kavasoglu, Nese; Kavasoglu, A. Sertap; Dincalp, Haluk; Metin, Bengul

2013-03-01

Diazo-compounds are important class of chemical compounds in terms of optical and electronic properties which make them potentially attractive for device applications. Diazo compound containing polyoxy chain has been deposited on p-Si. Current-voltage characteristics of Al/diazo compound containing polyoxy chain/p-Si structure present rectifying behaviour. The Schottky barrier height (SBH), diode factor (n), reverse saturation current (Io), interface state density (Nss) of Al/diazo compound containing polyoxy chain/p-Si structure have been calculated from experimental forward bias current-voltage data measured in the temperature range 100-320 K and capacitance-voltage data measured at room temperature and 1 MHz. The calculated values of SBH have ranged from 0.041 and 0.151 eV for the high and low temperature regions. Diode factor values fluctuate between the values 14 and 18 with temperature. Such a high diode factors stem from disordered interface layer in a junction structure as stated by Brötzmann et al. [M. Brötzmann, U. Vetter, H. Hofsäss, J. Appl. Phys. 106 (2009) 063704]. The calculated values of saturation current have ranged from 3×10-11 A to 2.79×10-7 A and interface state density have ranged from 5×1011 eV-1 cm-2 and 4×1013 eV-1 cm-2 as temperature increases. Results show that Al/diazo compound containing polyoxy chain/p-Si structure is a valuable candidate for device applications in terms of low reverse saturation current and low interface state density.

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

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

Kumar, V.S.; Robinson, H.; O-Neall-Hennessey, E.

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 resultmore » provides additional evidence that phosphorylation of the RLC is unlikely to act as an on-switch in regulation of scallop catch muscle myosin.« less

Analysis on the cost structure of product recall for reverse supply chain

NASA Astrophysics Data System (ADS)

Yanhua, Feng; Xuhui, Xia; Zheng, Yang

2017-12-01

The research on the reverse supply chain of product recall mainly focused on the recall network structure, logistics mode and so on. In this paper, when product recall and supply channel are fixed, the specific structure and function expression of cost are analyzed according to the peak season and off-season of recall activities, and whether the assembly manufacturer, supplier and recyclers are cooperated situation, respectively, to build the total cost structure of the function model. Finally, the model is validated correctly through the automotive industry and the electromechanical industry.

Catalytic behavior of ‘Pt-atomic chain encapsulated gold nanotube’: A density functional study

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

Nigam, Sandeep, E-mail: snigam@barc.gov.in; Majumder, Chiranjib

2016-05-23

With an aim to design novel material and explore its catalytic performance towards CO oxidation, Pt atomic chain was introduced inside gold nanotube (Au-NT). Theoretical calculations at the level of first principles formalism was carried out to investigate the atomic and electronic properties of the composite. Geometrically Pt atoms prefer to align in zig-zag fashion. Significant electronic charge transfer from inside Pt atoms to the outer wall Au atoms is observed. Interaction of O{sub 2} with Au-NT wall follows by injection of additional electronic charge in the anti-bonding orbital of oxygen molecule leading to activation of the O-O bond. Furthermore » interaction of CO molecule with the activated oxygen molecule leads to spontaneous oxidation reaction and formation of CO{sub 2}.« less

Connecting Structural and Transport Properties of Ionic Liquids with Cationic Oligoether Chains

DOE PAGES

Lall-Ramnarine, Sharon I.; Zhao, Man; Rodriguez, Chanele; ...

2017-06-01

We used X-ray diffraction and molecular dynamics simulations to probe the structures of two families of ionic liquids containing oligoether tails on the cations. Imidazolium and pyrrolidinium bis(trifluoromethylsulfonyl)amide ILs with side chains ranging from 4 to 10 atoms in length, including both linear alkyl and oligo-ethylene oxide tails, were prepared. Furthermore, their physical properties, such as viscosity, conductivity and thermal profile, were measured and compared for systematic trends. Consistent with earlier literature, a single ether substituent substantially decreases the viscosity of pyrrolidinium and imidazolium ILs compared to their alkyl congeners. Remarkably, as the number of ether units in the pyrrolidiniummore » ILs increases there is hardly any increase in the viscosity, in contrast to alkylpyrrolidinium ILs where the viscosity increases steadily with chain length. Viscosities of imidazolium ether ILs increase with chain length but always remain well below their alkyl congeners. To complement the experimentally determined properties, molecular dynamics simulations were run on the two ILs with the longest ether chains. Our results point to specific aspects that could be useful for researchers designing ILs for specific applications.« less

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.

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

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

Caselli, E.; Powers, R.A.; Blaszczak, L.C.

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 asmore » 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

The structure of 110 tilt boundaries in large area solar silicon

NASA Technical Reports Server (NTRS)

Ast, D. G.; Cunningham, B.; Vaudin, M.

1982-01-01

The models of Hornstra and their connection to the repeating group description of grain boundaries (7-10) are discussed. A model for the Sigma = 27 boundary containing a zig-zag arrangement of dislocations is constructed and it is shown that zig-zag models can account for the contrast features observed in high resolution transmission electron micrographs of second and third order twin boundaries in silicon. The boundaries discussed are symmetric with a 110 tilt axis and a (110) boundary plane in the median lattice (the median plane). The median lattice is identical in structure and halfway in orientation between the crystal lattices either side of the boundary.

Statistical theory for protein combinatorial libraries. Packing interactions, backbone flexibility, and the sequence variability of a main-chain structure.

PubMed

Kono, H; Saven, J G

2001-02-23

Combinatorial experiments provide new ways to probe the determinants of protein folding and to identify novel folding amino acid sequences. These types of experiments, however, are complicated both by enormous conformational complexity and by large numbers of possible sequences. Therefore, a quantitative computational theory would be helpful in designing and interpreting these types of experiment. Here, we present and apply a statistically based, computational approach for identifying the properties of sequences compatible with a given main-chain structure. Protein side-chain conformations are included in an atom-based fashion. Calculations are performed for a variety of similar backbone structures to identify sequence properties that are robust with respect to minor changes in main-chain structure. Rather than specific sequences, the method yields the likelihood of each of the amino acids at preselected positions in a given protein structure. The theory may be used to quantify the characteristics of sequence space for a chosen structure without explicitly tabulating sequences. To account for hydrophobic effects, we introduce an environmental energy that it is consistent with other simple hydrophobicity scales and show that it is effective for side-chain modeling. We apply the method to calculate the identity probabilities of selected positions of the immunoglobulin light chain-binding domain of protein L, for which many variant folding sequences are available. The calculations compare favorably with the experimentally observed identity probabilities.

Correlation Between Chain Architecture and Hydration Water Structure in Polysaccharides.

PubMed

Grossutti, Michael; Dutcher, John R

2016-03-14

The physical properties of confined water can differ dramatically from those of bulk water. Hydration water associated with polysaccharides provides a particularly interesting example of confined water, because differences in polysaccharide structure provide different spatially confined environments for water sorption. 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, dendrimer-like phytoglycogen nanoparticles to those obtained for two unbranched polysaccharides, hyaluronic acid (HA), and chitosan. We find similarities between the water structuring in the two linear polysaccharides and significant differences for phytoglycogen. In particular, the results suggest that the high degree of branching in phytoglycogen leads to a much more well-ordered water structure (low density, high connectivity network water), indicating the strong influence of chain architecture on the structuring of water. These measurements provide unique insight into the relationship between the structure and hydration of polysaccharides, which is important for understanding and exploiting these sustainable nanomaterials in a wide range of applications.

Extinction and the associative structure of heterogeneous instrumental chains.

PubMed

Thrailkill, Eric A; Bouton, Mark E

2016-09-01

Drug abuse, overeating, and smoking are all examples of instrumental behaviors that often involve chains or sequences of behavior. A behavior chain is minimally composed of a procurement response that is required in order for a subsequent consumption response to be reinforced. Despite the translational importance of behavior chains, few studies have attempted to understand what binds them together and takes them apart. This article surveys the development of the heterogeneous instrumental chain method and introduces recent findings that have used extinction to analyze the associative content of (what is learned in) the chain. Chained responses that are occasion-set by their own discriminative stimuli may be directly associated; extinction of the procurement response weakens its associated consumption response, and extinction of the consumption response weakens its associated procurement response. Extinction itself involves learning to inhibit the response. Extinguished chained responses are subject to renewal when they are tested either back in the acquisition context or in a new context. In addition, a consumption response that is extinguished outside its chain is renewed when returned to the context of the preceding response in the chain. Research on heterogeneous behavior chains can provide important insights into an important but often overlooked aspect of instrumental learning. Copyright © 2016 Elsevier Inc. All rights reserved.

Frequent side chain methyl carbon-oxygen hydrogen bonding in proteins revealed by computational and stereochemical analysis of neutron structures.

PubMed

Yesselman, Joseph D; Horowitz, Scott; Brooks, Charles L; Trievel, Raymond C

2015-03-01

The propensity of backbone Cα atoms to engage in carbon-oxygen (CH · · · O) hydrogen bonding is well-appreciated in protein structure, but side chain CH · · · O hydrogen bonding remains largely uncharacterized. The extent to which side chain methyl groups in proteins participate in CH · · · O hydrogen bonding is examined through a survey of neutron crystal structures, quantum chemistry calculations, and molecular dynamics simulations. Using these approaches, methyl groups were observed to form stabilizing CH · · · O hydrogen bonds within protein structure that are maintained through protein dynamics and participate in correlated motion. Collectively, these findings illustrate that side chain methyl CH · · · O hydrogen bonding contributes to the energetics of protein structure and folding. © 2014 Wiley Periodicals, Inc.

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.

Tuning conductivity in boron nanowire by edge geometry

NASA Astrophysics Data System (ADS)

Bhuyan, Prabal Dev; Gupta, Sanjeev K.; Sonvane, Yogesh; Gajjar, P. N.

2018-04-01

In present study, we have investigated electronic and temperature dependent transport properties of carbyne like linear chain and ribbon like zigzag structures of Boron (B) nanowire. The linear chain structure showed higher electric and thermal conductivity, as it is sp-hybridized, than its counterpart ribbon (R) structure. However the conductivity of ribbon structure increases with increases in width due to edge geometry effect. The ribbon (3R) structure showed high electric and thermal conductivity of 8.0×1019 1/Ω m s and 0.59×1015 W/ m K respectively. Interestingly we have observed that B linear chain showed higher thermal conductivity of 0.23×1015 W/ m K than its ribbon R and 2R structure above 600K. Because of high Seebeck co-efficient of boron chain and ribbon (R) structures at low temperature, they could find applications in thermoelectric sensors. Our results show that tuning conductivity property of boron nanowire could be of great interest in research for future electric connector in nanodevices.

Tunable magnetic states on the zigzag edges of hydrogenated and halogenated group-IV nanoribbons

NASA Astrophysics Data System (ADS)

Chuang, Feng-Chuan; Wang, Tzu-Cheng; Hsu, Chia-Hsiu; Huang, Zhi-Quan; Su, Wan-Sheng; Guo, Guang-Yu

The magnetic and electronic properties of hydrogenated and halogenated group-IV zigzag nanoribbons (ZNRs) are investigated by first-principles density functional calculations. Fascinatingly, we find that all the ZNRs have magnetic edges with a rich variety of electronic and magnetic properties tunable by selecting the parent and passivating elements as well as controlling the magnetization direction and external strain. In particular, the electric property of the edge band structure can be tuned from the conducting to insulating with a band gap up to 0.7 eV, depending on the parent and passivating elements as well as the applied strain, magnetic configuration and magnetization orientation. The last controllability would allow us to develop magnetic on-off nano-switches. Furthermore, ZNRs such as SiI, Ge, GeI and SnH, have fully spin-polarized metallic edge states and thus are promising materials for spintronics. The calculated magnetocrystalline anisotropy energy can be as large as 9 meV/edge-site, being 2000 time greater than that of bulk Ni and Fe ( 5 μeV/atom), and thus has great potential for high density magneto-electric data-storage devices. Finally, the calculated exchange coupling strength and thus magnetic transition temperature increases as the applied strain goes from -5 % to 5 %. Our findings thus show that these ZNRs would have exciting applications in next-generation electronic and spintronic nano-devices.

Interaction of CO with an Au monatomic chain at different strains: Electronic structure and ballistic transport

NASA Astrophysics Data System (ADS)

Sclauzero, Gabriele; Dal Corso, Andrea; Smogunov, Alexander

2012-04-01

We study the energetics, the electronic structure, and the ballistic transport of an infinite Au monatomic chain with an adsorbed CO molecule. We find that the bridge adsorption site is energetically favored with respect to the atop site, both at the equilibrium Au-Au spacing of the chain and at larger spacings. Instead, a substitutional configuration requires a very elongated Au-Au bond, well above the rupture distance of the pristine Au chain. The electronic structure properties can be described by the Blyholder model, which involves the formation of bonding/antibonding pairs of 5σ and 2π states through the hybridization between molecular levels of CO and metallic states of the chain. In the atop geometry, we find an almost vanishing conductance due to the 5σ antibonding states giving rise to a Fano-like destructive interference close to the Fermi energy. In the bridge geometry, instead, the same states are shifted to higher energies and the conductance reduction with respect to pristine Au chain is much smaller. We also examine the effects of strain on the ballistic transport, finding opposite behaviors for the atop and bridge conductances. Only the bridge geometry shows a strain dependence compatible with the experimental conductance traces.

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.

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

Structure of the intermediate Zr/sub 2/Br/sub 2/H by neutron diffraction and its structural and bonding relationships to other phases

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

Wijeyesekera, S.D.; Corbett, J.D.

1986-12-17

The structures of the isomorphous Zr/sub 2/Br/sub 2/D and Zr/sub 2/Br/sub 2/H have been solved and refined by using Rietveld techniques on pulsed neutron diffraction data obtained from the powdered samples at 14 K (C2/m, a = 19.437 (3) A, b = 3.5253 (4) A, c = 5.9036 (6) A, ..beta.. = 100.98 (1)/sup 0/, R(profile)/R(expected) = 2.44 for the deuteride). The structure consists of layers sequenced Br-Zr-H-H-Zr-Br and arranged such that hydride lies in zigzag chains of distorted metal tetrahedra (or butterflies) (d(Zr-D) = 2.03-2.20 A; d(D-D) = 2.93 A). The structure is intermediate between ZrBr (ccp) and ZrBrHmore » (hcp heavy atoms, double H in trigonal-antiprismatic interstices) and can be generated by concerted intraslab slippage from either. The hemihydride effectively retains most of the strong Zr-Zr bonding of the ZrBr parent while tetrahedral bonding of hydrogen to metal is gained that is absent in ZrBrH. The energetics associated with the contrasting structures of YClH/sub x/ (ZrBr type) and ZrBrH are considered in terms of the results of extended-Hueckel band calculations. 25 references, 7 figures, 3 tables.« less

Chain-like structure elements in Ni40Ta60 metallic glasses observed by scanning tunneling microscopy

PubMed Central

Pawlak, Rémy; Marot, Laurent; Sadeghi, Ali; Kawai, Shigeki; Glatzel, Thilo; Reimann, Peter; Goedecker, Stefan; Güntherodt, Hans-Joachim; Meyer, Ernst

2015-01-01

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. PMID:26268430

Structural phase transition of magnetic [Ni(dmit)2]- salts induced by supramolecular cation structures of (M+)([12]crown-4)2.

PubMed

Akutagawa, Tomoyuki; Motokizawa, Takeshi; Matsuura, Kazumasa; Nishihara, Sadafumi; Noro, Shin-ichiro; Nakamura, Takayoshi

2006-03-30

Sandwich-type supramolecular cation structures of (M(+))([12]crown-4)(2) complexes (M(+) = Li(+), Na(+), K(+), and Rb(+)) were introduced as countercations to the [Ni(dmit)(2)](-) anion, which bears an S = (1)/(2) spin, to form novel magnetic crystals (dmit(2-) = 2-thione-1,3-dithiole-4,5-dithiolate). The zigzag arrangement of Li(+)([12]crown-4)(2) cations in Li(+)([12]crown-4)(2)[Ni(dmit)(2)](-) salt induced weak intermolecular interactions of [Ni(dmit)(2)](-) dimers, whose magnetic spins were isolated from each other. The molecular arrangements of cations and anions in M(+)([12]crown-4)(2)[Ni(dmit)(2)](-) salts (M(+) = Na(+), K(+), and Rb(+)) were isostructural to each other. In the case of Na(+)([12]crown-4)(2)[Ni(dmit)(2)](-), the space group C2/m changed to C2/c with a lowering in temperature from 298 to 100 K. This structural change occurred at 222.5 K as a first-order phase transition. The space group C2/m (T = 298 K) in the salt K(+)([12]crown-4)(2)[Ni(dmit)(2)](-) also changed to C2/c (T = 100 K), which transition occurred at 270 K. Crystal structural analyses at 298 and 100 K revealed changes in both supramolecular cation conformation and [Ni(dmit)(2)](-) anion arrangements. The transition from C2/m to C2/c crystals generated a dipole moment in the Na(+)([12]crown-4)(2) and K(+)([12]crown-4)(2) structures, which were reconstructed to cancel the net dipole moment of the C2/c crystals. These cation transformations led to changes in intermolecular interactions between the [Ni(dmit)(2)](-) anions via structural rearrangements. The crystal structure of C2/c was stabilized in Rb(+)([12]crown-4)(2)[Ni(dmit)(2)](-) at 298 K. The [Ni(dmit)(2)](-) configuration in these salts with the C2/c space group was a one-dimensional uniform chain, which showed the temperature-dependent magnetic susceptibility of a one-dimensional linear Heisenberg antiferromagnetic chain.

Synthesis, magnetic properties and electronic structure of the S  =  ½ uniform spin chain system InCuPO5

NASA Astrophysics Data System (ADS)

Koteswararao, B.; Hazra, Binoy K.; Rout, Dibyata; Srinivasarao, P. V.; Srinath, S.; Panda, S. K.

2017-07-01

We have studied the structural and magnetic properties and electronic structure of the compound InCuPO5 synthesized by a solid state reaction method. The structure of InCuPO5 comprises S  =  ½ uniform spin chains formed by corner-shared CuO4 units. Magnetic susceptibility (χ(T)) data show a broad maximum at about 65 K, a characteristic feature of one-dimensional (1D) magnetism. The χ(T) data are fitted to the coupled S  =  ½ Heisenberg antiferromagnetic (HAFM) uniform chain model that gives the intra-chain coupling (J/k B) between nearest-neighbor Cu2+ ions as  -100 K and the ratio of inter-chain to intra-chain coupling (J‧/J) as about 0.07. The exchange couplings estimated from the magnetic data analysis are in good agreement with the values computed from the electronic structure calculations based on the density functional theory  +  Hubbard U (DFT  +  U) approach. The combination of theoretical and experimental analysis confirms that InCuPO5 is a candidate material for weakly coupled S  = ½ uniform chains. A detailed theoretical analysis of the electronic structure further reveals that the system is insulating with a gap of 2.4 eV and a local moment of 0.70 µ B/Cu.

Energetically Unfavorable Amide Conformations for N6-Acetyllysine Side Chains in Refined Protein Structures

PubMed Central

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

2013-01-01

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. PMID:23401043

New metal-organic complexes based on bis(tetrazole) ligands: Synthesis, structures and properties

NASA Astrophysics Data System (ADS)

Du, Ceng-Ceng; Fan, Jian-Zhong; Wang, Xin-Fang; Zhou, Sheng-Bin; Wang, Duo-Zhi

2017-04-01

In this paper, a series of new complexes, [Zn2(HL1)2(H2O)4]·H2O (1), [Co2(HL1)2]·TEA (2), [Co3(HL1)2(H2L1)2(H2O)4]n (3), [Cu(HL1)(H2O)2]n (4), {[Cu5(HL2)2(OH)4(ClO4)2]·4H2O}n (5) and [Cu2(L3)]n (6) were successfully prepared by utilizing three bis(tetrazole) ligands [bis-(1H-tetrazol-5-ylmethyl)-amine (H3L1), bis-(1H-tetrazol-5-ylethyl)-amine (H3L2) and 1,5-bis(5-tetrazolo)-3-thiapentane (H2L3)], all of which have been characterized by elemental analyses, FT-IR spectroscopy, powder X-ray diffraction (PXRD), thermogravimetric analyses as well as single-crystal X-ray diffraction analyses showing different dimensionalities (0D, 1D and 3D). Complexes 1 and 2 are 0D structures, 1 shows a dinuclear structure, 2 displays two crystallographically different mononuclear structures, 1 and 2 are further assembled to form 3D supramolecular framework and 2D supramolecular network by hydrogen-bonding interactions, respectively. Complexes 3, 4 and 5 are 1D structures, 3 features a mononuclear unit and a 1D chain, which are arranged into 3D supramolecular architecture by hydrogen-bonding interactions, 4 presents a zigzag chain, 5 shows an infinite chain structure constructed from pentanuclear Cu(II) subunits and ClO4- anions. Complex 6 exhibits a 3D coordination framework based on cyclic [Cu4(L3)2] dimmer subunits as nodes possessing an 8-connected network topology with the point symbol {424·64}. Further, semiconductor behaviors, the solid-state luminescent properties of the complexes 1-3 and 6 were measured and studied seriously at room temperature.

Automatic low-order aberrations compensator for a conduction-cooled end-pumped solid-state zigzag slab laser

NASA Astrophysics Data System (ADS)

Yu, Xin; Dong, Lizhi; Lai, Boheng; Yang, Ping; Wang, Shuai; Wang, Xun; Liu, Yong; Tang, Guomao; Xu, Bing

2017-11-01

In order to solve the problem of large low-order aberrations with solid-state zigzag slab lasers, an automatic compensator has been developed in this paper. In this compensator, three lenses are mounted on a motorized rail, whose positions can be obtained using ray tracing method based on the beam parameters detected by a wave-front sensor. The initial peak to valley (PV) values of the wave-front range up to several tens of microns. Both simulated and experimental results show that the PV values of the wave-front can be reduced to around 1 . 6 μm with the proposed automatic compensator.

Structure of the conversion laws in quantum integrable spin chains with short range interactions

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

Grabowski, M.P.; Mathieu, P.

1995-11-01

The authors present a detailed analysis of the structure of the conservation laws in quantum integrable chains of the XYZ-type and in the Hubbard model. The essential tool for the former class of models is the boost operator, which provides a recursive way of calculating the integrals of motion. With its help, they establish the general form of the XYZ conserved charges in terms of simple polynomials in spin variables and derive recursion relations for the relative coefficients of these polynomials. Although these relations are difficult to solve in general, a subset of the coefficients can be determined. Moreover, formore » two submodels of the XYZ chain, namely the XXX and XY cases, all the charges can be calculated in closed form. Using this approach, the authors rederive the known expressions for the XY charges in a novel way. For the XXX case. a simple description of conserved charges is found in terms of a Catalan tree. This construction is generalized for the su(M) invariant integrable chain. They also investigate the circumstances permitting the existence of a recursive (ladder) operator in general quantum integrable systems. They indicate that a quantum ladder operator can be traced back to the presence of a Hamiltonian mastersymmetry of degree one in the classical continuous version of the model. In this way, quantum chains endowed with a recursive structure can be identified from the properties of their classical relatives. The authors also show that in the quantum continuous limits of the XYZ model, the ladder property of the boost operator disappears. For the Hubbard model they demonstrate the nonexistence of a ladder operator. Nevertheless, the general structure of the conserved charges is indicated, and the expression for the terms linear in the model`s free parameter for all charges is derived in closed form. 62 refs., 4 figs.« less

Tailoring graphene magnetism by zigzag triangular holes: A first-principles thermodynamics study

DOE PAGES

Khan, Muhammad Ejaz; Zhang, P.; Sun, Yi -Yang; ...

2016-03-30

In this study, we discuss the thermodynamic stability and magnetic property of zigzag triangular holes (ZTHs) in graphene based on the results of first-principles density functional theory calculations. We find that ZTHs with hydrogen-passivated edges in mixed sp 2/sp 3 configurations (z 211) could be readily available at experimental thermodynamic conditions, but ZTHs with 100% sp 2 hydrogen-passivation (z 1) could be limitedly available at high temperature and ultra-high vacuum conditions. Graphene magnetization near the ZTHs strongly depends on the type and the size of the triangles. While metallic z 1 ZTHs exhibit characteristic edge magnetism due to the same-sublatticemore » engineering, semiconducting z 211 ZTHs do show characteristic corner magnetism when the size is small < 2 nm. Our findings could be useful for experimentally tailoring metal-free carbon magnetism by simply fabricating triangular holes in graphene.« less

Prediction of Composite Laminate Strength Properties Using a Refined Zigzag Plate Element

NASA Technical Reports Server (NTRS)

Barut, Atila; Madenci, Erdogan; Tessler, Alexander

2013-01-01

This study presents an approach that uses the refined zigzag element, RZE(exp2,2) in conjunction with progressive failure criteria to predict the ultimate strength of composite laminates based on only ply-level strength properties. The methodology involves four major steps: (1) Determination of accurate stress and strain fields under complex loading conditions using RZE(exp2,2)-based finite element analysis, (2) Determination of failure locations and failure modes using the commonly accepted Hashin's failure criteria, (3) Recursive degradation of the material stiffness, and (4) Non-linear incremental finite element analysis to obtain stress redistribution until global failure. The validity of this approach is established by considering the published test data and predictions for (1) strength of laminates under various off-axis loading, (2) strength of laminates with a hole under compression, and (3) strength of laminates with a hole under tension.

Tailoring graphene magnetism by zigzag triangular holes: A first-principles thermodynamics study

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

Khan, Muhammad Ejaz; Zhang, P.; Kim, Yong-Hyun, E-mail: yong.hyun.kim@kaist.ac.kr

We discuss the thermodynamic stability and magnetic property of zigzag triangular holes (ZTHs) in graphene based on the results of first-principles density functional theory calculations. We find that ZTHs with hydrogen-passivated edges in mixed sp{sup 2}/sp{sup 3} configurations (z{sub 211}) could be readily available at experimental thermodynamic conditions, but ZTHs with 100% sp{sup 2} hydrogen-passivation (z{sub 1}) could be limitedly available at high temperature and ultra-high vacuum conditions. Graphene magnetization near the ZTHs strongly depends on the type and the size of the triangles. While metallic z{sub 1} ZTHs exhibit characteristic edge magnetism due to the same-sublattice engineering, semiconducting z{submore » 211} ZTHs do show characteristic corner magnetism when the size is small <2 nm. Our findings could be useful for experimentally tailoring metal-free carbon magnetism by simply fabricating triangular holes in graphene.« less

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[n i(t,z)•n i(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

Coulomb double helical structure

NASA Astrophysics Data System (ADS)

Kamimura, Tetsuo; Ishihara, Osamu

2012-01-01

Structures of Coulomb clusters formed by dust particles in a plasma are studied by numerical simulation. Our study reveals the presence of various types of self-organized structures of a cluster confined in a prolate spheroidal electrostatic potential. The stable configurations depend on a prolateness parameter for the confining potential as well as on the number of dust particles in a cluster. One-dimensional string, two-dimensional zigzag structure and three-dimensional double helical structure are found as a result of the transition controlled by the prolateness parameter. The formation of stable double helical structures resulted from the transition associated with the instability of angular perturbations on double strings. Analytical perturbation study supports the findings of numerical simulations.

Conformation of single block copolymer chain in two-dimensional microphase-separated structure studied by scanning near-field optical microscopy.

PubMed

Sekine, Ryojun; Aoki, Hiroyuki; Ito, Shinzaburo

2009-05-21

The localization and orientation of the symmetric diblock copolymer chain in a quasi-two-dimensional microphase-separated structure were studied by scanning near-field optical microscopy (SNOM). In the monolayer of poly(isobutyl methacrylate)-block-poly(octadecyl methacrylate) (PiBMA-b-PODMA), the individual PiBMA subchains were directly observed by SNOM, and the center of mass (CM) and orientational angle relative to the phase interface were examined at the single chain level. It was found that the position of the CM and the orientation of the PiBMA subchain in the lamellar structure were dependent on the curvature of the PiBMA/PODMA interface. As the interface was bent toward the objective chain, the block chain preferred the CM position closer to the domain center, and the conformation was strongly oriented perpendicularly to the domain interface. With increase of the curvature, the steric hindrance among the block chain increases, resulting in the stretched conformation.

Precise structural analysis of α-helical polypeptide by quantum-chemical calculation related to reciprocal side-chain combination of two L-phenylalanine residues

NASA Astrophysics Data System (ADS)

Niimura, Subaru; Kurosu, Hiromichi; Shoji, Akira

2010-04-01

To clarify the positive role of side-chain conformation in the stability of protein secondary structure (main-chain conformation), we successfully calculated the optimization structure of a series of well-defined α-helical octadecapeptides composed of two L-phenylalanine (Phe) and 16 L-alanine (Ala) residues, based on the molecular orbital calculation with density functional theory (DFT/B3LYP/6-31G(d)). From the total energy calculation and the precise secondary structural analysis, we found that the conformational stability of the α-helix is closely related to the reciprocal side-chain combinations (such as positional relation and side-chain conformation) of two Phe residues in this system. Furthermore, we demonstrated that the 1H, 13C, 15N and 17O isotropic chemical shifts of each Phe residue depend on the respective side-chain conformations of the Phe residue.

Zigzag antiferromagnetic ground state with anisotropic correlation lengths in the quasi-two-dimensional honeycomb lattice compound N a2C o2Te O6

NASA Astrophysics Data System (ADS)

Bera, A. K.; Yusuf, S. M.; Kumar, Amit; Ritter, C.

2017-03-01

The crystal structure, magnetic ground state, and the temperature-dependent microscopic spin-spin correlations of the frustrated honeycomb lattice antiferromagnet N a2C o2Te O6 have been investigated by powder neutron diffraction. A long-range antiferromagnetic (AFM) ordering has been found below TN˜24.8 K . The magnetic ground state, determined to be zigzag antiferromagnetic and characterized by a propagation vector k =(1 /2 0 0 ) , occurs due to the competing exchange interactions up to third-nearest neighbors within the honeycomb lattice. The exceptional existence of a limited magnetic correlation length along the c axis (perpendicular to the honeycomb layers in the a b planes) has been found even at 1.8 K, well below the TN˜24.8 K . The observed limited correlation along the c axis is explained by the disorder distribution of the Na ions within the intermediate layers between honeycomb planes. The reduced ordered moments mCo (1 )=2.77 (3 ) μB/C o2 + and mCo (2 )=2.45 (2 ) μB/C o2 + at 1.8 K reflect the persistence of spin fluctuations in the ordered state. Above TN˜24.8 K , the presence of short-range magnetic correlations, manifested by broad diffuse magnetic peaks in the diffraction patterns, has been found. Reverse Monte Carlo analysis of the experimental diffuse magnetic scattering data reveals that the spin correlations are mainly confined within the two-dimensional honeycomb layers (a b plane) with a correlation length of ˜12 Å at 25 K. The nature of the spin arrangements is found to be similar in both the short-range and long-range ordered magnetic states. This implies that the short-range correlation grows with decreasing temperature and leads to the zigzag AFM ordering at T ≤TN . The present study provides a comprehensive picture of the magnetic correlations over the temperature range above and below the TN and their relation to the crystal structure. The role of intermediate soft Na layers on the magnetic coupling between honeycomb planes is

Cooperativity of halogen, chalcogen, and pnictogen bonds in infinite molecular chains by electronic structure theory.

PubMed

George, Janine; Deringer, Volker L; Dronskowski, Richard

2014-05-01

Halogen bonds (XBs) are intriguing noncovalent interactions that are frequently being exploited for crystal engineering. Recently, similar bonding mechanisms have been proposed for adjacent main-group elements, and noncovalent "chalcogen bonds" and "pnictogen bonds" have been identified in crystal structures. A fundamental question, largely unresolved thus far, is how XBs and related contacts interact with each other in crystals; similar to hydrogen bonding, one might expect "cooperativity" (bonds amplifying each other), but evidence has been sparse. Here, we explore the crucial step from gas-phase oligomers to truly infinite chains by means of quantum chemical computations. A periodic density functional theory (DFT) framework allows us to address polymeric chains of molecules avoiding the dreaded "cluster effects" as well as the arbitrariness of defining a "large enough" cluster. We focus on three types of molecular chains that we cut from crystal structures; furthermore, we explore reasonable substitutional variants in silico. We find evidence of cooperativity in chains of halogen cyanides and also in similar chalcogen- and pnictogen-bonded systems; the bonds, in the most extreme cases, are amplified through cooperative effects by 79% (I···N), 90% (Te···N), and 103% (Sb···N). Two experimentally known organic crystals, albeit with similar atomic connectivity and XB characteristics, show signs of cooperativity in one case but not in another. Finally, no cooperativity is observed in alternating halogen/acetone and halogen/1,4-dioxane chains; in fact, these XBs weaken each other by up to 26% compared to the respective gas-phase dimers.

Structure and phase behavior of a confined nanodroplet composed of the flexible chain molecules.

PubMed

Kim, Soon-Chul; Kim, Eun-Young; Seong, Baek-Seok

2011-04-28

A polymer density functional theory has been employed for investigating the structure and phase behaviors of the chain polymer, which is modelled as the tangentially connected sphere chain with an attractive interaction, inside the nanosized pores. The excess free energy of the chain polymer has been approximated as the modified fundamental measure-theory for the hard spheres, the Wertheim's first-order perturbation for the chain connectivity, and the mean-field approximation for the van der Waals contribution. For the value of the chemical potential corresponding to a stable liquid phase in the bulk system and a metastable vapor phase, the flexible chain molecules undergo the liquid-vapor transition as the pore size is reduced; the vapor is the stable phase at small volume, whereas the liquid is the stable phase at large volume. The wide liquid-vapor coexistence curve, which explains the wide range of metastable liquid-vapor states, is observed at low temperature. The increase of temperature and decrease of pore size result in a narrowing of liquid-vapor coexistence curves. The increase of chain length leads to a shift of the liquid-vapor coexistence curve towards lower values of chemical potential. The coexistence curves for the confined phase diagram are contained within the corresponding bulk liquid-vapor coexistence curve. The equilibrium capillary phase transition occurs at a higher chemical potential than in the bulk phase.

Origin of spin polarization in an edge boron doped zigzag graphene nanoribbon: a potential spin filter.

PubMed

Chakrabarty, Soubhik; Wasey, A H M Abdul; Thapa, Ranjit; Das, G P

2018-08-24

To realize a graphene based spintronic device, the prime challenge is to control the electronic structure of edges. In this work we find the origin of the spin filtering property in edge boron doped zigzag graphene nanoribbons (ZGNRs) and provide a guide to preparing a graphene based next-generation spin filter based device. Here, we unveil the role of orbitals (p-electron) to tune the electronic, magnetic and transport properties of edge B doped ZGNRs. When all the edge carbon atoms at one of the edges of ZGNRs are replaced by B (100% edge B doping), the system undergoes a semiconductor to metal transition. The role of passivation of the edge with single/double atomic hydrogen on the electronic properties and its relation with the p-electron is correlated in-depth. 50% edge B doped ZGNRs (50% of the edge C atoms at one of the edges are replaced by B) also show half-metallicity when the doped edge is left unpassivated. The half-metallic systems show 100% spin filtering efficiency for a wide range of bias voltages. Zero-bias transmission function of the other configurations shows asymmetric behavior for the up and down spin channels, thereby indicating their possible application potential in nano-spintronics.

The Compact and Biologically Relevant Structure of Inter-α-inhibitor Is Maintained by the Chondroitin Sulfate Chain and Divalent Cations.

PubMed

Scavenius, Carsten; Nikolajsen, Camilla Lund; Stenvang, Marcel; Thøgersen, Ida B; Wyrożemski, Łukasz; Wisniewski, Hans-Georg; Otzen, Daniel E; Sanggaard, Kristian W; Enghild, Jan J

2016-02-26

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 Mg(2+) or Mn(2+), but not Ca(2+), 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 Mg(2+) 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. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

The Relaxation of Vicinal (001) with ZigZag [110] Steps

NASA Astrophysics Data System (ADS)

Hawkins, Micah; Hamouda, Ajmi Bh; González-Cabrera, Diego Luis; Einstein, Theodore L.

2012-02-01

This talk presents a kinetic Monte Carlo study of the relaxation dynamics of [110] steps on a vicinal (001) simple cubic surface. This system is interesting because [110] steps have different elementary excitation energetics and favor step diffusion more than close-packed [100] steps. In this talk we show how this leads to relaxation dynamics showing greater fluctuations on a shorter time scale for [110] steps as well as 2-bond breaking processes being rate determining in contrast to 3-bond breaking processes for [100] steps. The existence of a steady state is shown via the convergence of terrace width distributions at times much longer than the relaxation time. In this time regime excellent fits to the modified generalized Wigner distribution (as well as to the Berry-Robnik model when steps can overlap) were obtained. Also, step-position correlation function data show diffusion-limited increase for small distances along the step as well as greater average step displacement for zigzag steps compared to straight steps for somewhat longer distances along the step. Work supported by NSF-MRSEC Grant DMR 05-20471 as well as a DOE-CMCSN Grant.

Zig-zag tape influence in NREL Phase VI wind turbine

NASA Astrophysics Data System (ADS)

Gomez-Iradi, Sugoi; Munduate, Xabier

2014-06-01

Two bladed 10 metre diameter wind turbine was tested in the 24.4m × 36.6m NASA-Ames wind tunnel (Phase VI). These experiments have been extensively used for validation purposes for CFD and other engineering tools. The free transition case (S), has been, and is, the most employed one for validation purposes, and consist in a 3° pitch case with a rotational speed of 72rpm upwind configuration with and without yaw misalignment. However, there is another less visited case (M) where identical configuration was tested but with the inclusion of a zig-zag tape. This was called transition fixed sequence. This paper shows the differences between the free and the fix transition cases, that should be more appropriate for comparison with fully turbulent simulations. Steady k-ω SST fully turbulent computations performed with WMB CFD method are compared with the experiments showing, better predictions in the attached flow region when it is compared with the transition fixed experiments. This work wants to prove the utility of M case (transition fixed) and show its differences respect the S case (free transition) for validation purposes.

On the zigzagging causility model of EPR correlations and on the interpretation of quantum mechanics

NASA Astrophysics Data System (ADS)

de Beauregard, O. Costa

1988-09-01

Being formalized inside the S-matrix scheme, the zigzagging causility model of EPR correlations has full Lorentz and CPT invariance. EPR correlations, proper or reversed, and Wheeler's smoky dragon metaphor are respectively pictured in spacetime or in the momentum-energy space, as V-shaped, A-shaped, or C-shaped ABC zigzags, with a summation at B over virtual states |B>

Crystal structure of 2-oxopyrrolidin-3-yl 4-(2-phenyl-diazen-1-yl)benzoate.

PubMed

Elkin, Igor; Maris, Thierry; Melkoumov, Alexandre; Hildgen, Patrice; Banquy, Xavier; Leclair, Grégoire; Barrett, Christopher

2018-04-01

In the title compound, C 17 H 15 N 3 O 3 , the plane of the pyrrolidone ring is inclined at an angle of 59.791 (2)° to that of the azo-benzene segment, which adopts a configuration close to planar. In the crystal, mol-ecules are oriented pairwise by (2-oxopyrrolidin-3-yl)-oxy moieties at an angle of 76.257 (3)°, linked by hydrogen bonds and π-stacking inter-actions, forming zigzag supra-molecular chains parallel to [010] further linked via additional C-H⋯π inter-actions.

Pb4(OH)4(BrO3)3(NO3): An Example of SHG Crystal in Metal Bromates Containing π-Conjugated Planar Triangle.

PubMed

Kong, Fang; Hu, Chun-Li; Liang, Ming-Li; Mao, Jiang-Gao

2016-01-19

The first example of SHG crystal in the metal bromates containing π-conjugated planar triangle systems, namely, Pb4(OH)4(BrO3)3(NO3), was successfully synthesized via the hydrothermal method. Furthermore, a single crystal of centrosymmetric Pb8O(OH)6(BrO3)6(NO3)2·H2O was also obtained. Both compounds contain similar [Pb4(OH)4] cubane-like tetranuclear clusters, but they display different one-dimensional (1D) chain structures. Pb4(OH)4(BrO3)3(NO3) features a zigzag [Pb4(OH)4(BrO3)3](+) 1D chain, while Pb8O(OH)6(BrO3)6(NO3)2·H2O is composed of two different orthogonal chains: the linear [Pb4(OH)4(BrO3)2](2+) 1D chain along the b-axis and the zigzag [Pb4O2(OH)2(BrO3)4](2-) 1D chain along the a-axis. The NO3 planar triangles of the compounds are all isolated and located in the spaces of the structures. Pb4(OH)4(BrO3)3(NO3) exhibits the first example of SHG crystal in the metal bromates with π-conjugated planar triangle. The second-harmonic generation (SHG) efficiency of Pb4(OH)4(BrO3)3(NO3) is approximately equal to that of KDP and it is phase-matchable. Dipole moment and theory calculations indicate that BrO3, NO3, and PbO4 groups are the origin of its SHG efficiency, although some of the contributions cancel each other out.

Novel Design for Centrifugal Countercurrent Chromatography: II. Studies on Novel Geometries of Zigzag Toroidal Tubing

PubMed Central

Yang, Yi; Aisa, Haji Akber; Ito, Yoichiro

2009-01-01

The toroidal column using a zigzag pattern has been improved in both retention of the stationary phase and peak resolution. To further improve the retention of stationary phase and peak resolution, a series of novel geometric designs of tubing (plain, mid-clamping, flattened and flat-twisted tubing) was evaluated their performance in CCC. The results showed that the tubing which was flattened vertically against centrifugal force (vert-flattened tubing) produced the best peak resolution among them. Using vert-flattened tubing a series of experiments was performed to study the effects of column capacity and sample size. The results indicated that a 0.25 ml capacity column is ideal for analysis of small amount samples. PMID:20454530

Doping of Semiconducting Atomic Chains

NASA Technical Reports Server (NTRS)

Toshishige, Yamada; Kutler, Paul (Technical Monitor)

1997-01-01

Due to the rapid progress in atom manipulation technology, atomic chain electronics would not be a dream, where foreign atoms are placed on a substrate to form a chain, and its electronic properties are designed by controlling the lattice constant d. It has been shown theoretically that a Si atomic chain is metallic regardless of d and that a Mg atomic chain is semiconducting or insulating with a band gap modified with d. For electronic applications, it is essential to establish a method to dope a semiconducting chain, which is to control the Fermi energy position without altering the original band structure. If we replace some of the chain atoms with dopant atoms randomly, the electrons will see random potential along the chain and will be localized strongly in space (Anderson localization). However, if we replace periodically, although the electrons can spread over the chain, there will generally appear new bands and band gaps reflecting the new periodicity of dopant atoms. This will change the original band structure significantly. In order to overcome this dilemma, we may place a dopant atom beside the chain at every N lattice periods (N > 1). Because of the periodic arrangement of dopant atoms, we can avoid the unwanted Anderson localization. Moreover, since the dopant atoms do not constitute the chain, the overlap interaction between them is minimized, and the band structure modification can be made smallest. Some tight-binding results will be discussed to demonstrate the present idea.

Application of Nitrogen and Carbon Stable Isotopes (δ15N and δ13C) to Quantify Food Chain Length and Trophic Structure

PubMed Central

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 (δ15N) and carbon (δ13C) 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 δ15N, and carbon range (CR) using δ13C, 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 δ15N or δ13C from source to consumer) between trophic levels and among food chains. δ15N 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. δ13C 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 δ13C 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 ecological systems

Effects of molecular and lattice structure on the thermal behaviours of some long chain length potassium(I) n-alkanoates

NASA Astrophysics Data System (ADS)

Nelson, Peter N.; Ellis, Henry A.; Taylor, Richard A.

2014-01-01

Lattice structures and thermal behaviours for some long chain potassium carboxylates (nc = 8-18, inclusive) are investigated using Fourier Transform Infrared spectroscopy, X-ray Powder Diffraction, Solid State spin decoupled 13C NMR spectroscopy, Differential Scanning Calorimetry and Thermogravimetry. The measurements show that the carboxyl groups are coordinated to potassium atoms via asymmetric chelating bidentate bonding, with extensive carboxyl intermolecular interactions to yield tetrahedral metal centers, irrespective of chain length. Furthermore, the hydrocarbon chains are crystallized in the fully extended all-trans configuration and are arranged as non-overlapping lamellar bilayer structures with closely packed methyl groups from opposite layers. Additionally, odd-even alternation, observed in density and methyl group chemical shift, is ascribed to the relative vertical distances between layers in the bilayer, that are not in the same plane. Therefore, for even chain homologues, where this distances is less than for odd chain adducts, more intimate packing is indicated. The phase sequences for all compounds show several reversible crystal-crystal transition associated with kinetically controlled gauche-trans isomerism of the polymethylene chains which undergo incomplete fusion when heated to the melt. The compounds degrade above 785 K to yield carbon dioxide, water, potassium oxide and an alkene.

Multicomponent Pt-Based Zigzag Nanowires as Selectivity Controllers for Selective Hydrogenation Reactions.

PubMed

Bai, Shuxing; Bu, Lingzheng; Shao, Qi; Zhu, Xing; Huang, Xiaoqing

2018-06-22

The selective hydrogenation of α, β-unsaturated aldehyde is an extremely important transformation, while developing efficient catalysts with desirable selectivity to highly value-added products is challenging, mainly due to the coexistence of two conjugated unsaturated functional groups. Herein, we report that a series of Pt-based zigzag nanowires (ZNWs) can be adopted as selectivity controllers for α, β-unsaturated aldehyde hydrogenation, where the excellent unsaturated alcohol (UOL) selectivity (>95%) and high saturated aldehyde (SA) selectivity (>94%) are achieved on PtFe ZNWs and PtFeNi ZNWs+AlCl 3 , respectively. The excellent UOL selectivity of PtFe ZNWs is attributed to the lower electron density of the surface Pt atoms, while the high SA selectivity of PtFeNi ZNWs+AlCl 3 is due to synergy between PtFeNi ZNWs and AlCl 3 , highlighting the importance of Pt-based NWs with precisely controlled surface and composition for catalysis and beyond.

Reversible conformational transition gives rise to 'zig-zag' temperature dependence of the rate constant of irreversible thermoinactivation of enzymes.

PubMed

Levitsky VYu; Melik-Nubarov, N S; Siksnis, V A; Grinberg VYa; Burova, T V; Levashov, A V; Mozhaev, V V

1994-01-15

We have obtained unusual 'zig-zag' temperature dependencies of the rate constant of irreversible thermoinactivation (k(in)) of enzymes (alpha-chymotrypsin, covalently modified alpha-chymotrypsin, and ribonuclease) in a plot of log k(in) versus reciprocal temperature (Arrhenius plot). These dependencies are characterized by the presence of both ascending and descending linear portions which have positive and negative values of the effective activation energy (Ea), respectively. A kinetic scheme has been suggested that fits best for a description of these zig-zag dependencies. A key element of this scheme is the temperature-dependent reversible conformational transition of enzyme from the 'low-temperature' native state to a 'high-temperature' denatured form; the latter form is significantly more stable against irreversible thermoinactivation than the native enzyme. A possible explanation for a difference in thermal stabilities is that low-temperature and high-temperature forms are inactivated according to different mechanisms. Existence of the suggested conformational transition was proved by the methods of fluorescence spectroscopy and differential scanning calorimetry. The values of delta H and delta S for this transition, determined from calorimetric experiments, are highly positive; this fact underlies a conclusion that this heat-induced transition is caused by an unfolding of the protein molecule. Surprisingly, in the unfolded high-temperature conformation, alpha-chymotrypsin has a pronounced proteolytic activity, although this activity is much smaller than that of the native enzyme.

Narrow-linewidth, quasi-continuous-wave ASE source based on a multiple-pass Nd:YAG zigzag slab amplifier configuration.

PubMed

Chen, Xiaoming; Lu, Yanhua; Hu, Hao; Tong, Lixin; Zhang, Lei; Yu, Yi; Wang, Juntao; Ren, Huaijin; Xu, Liu

2018-03-05

We present investigations into a narrow-linewidth, quasi-continuous-wave pulsed all-solid-state amplified spontaneous emission (ASE) source by use of a novel multiple-pass zigzag slab amplifier. The SE fluorescence emitted from a Nd:YAG slab active medium acts as the seed and is amplified back and forth 8 times through the same slab. Thanks to the angular multiplexing nature of the zigzag slab, high-intensity 1064-nm ASE output can be produced without unwanted self-lasing in this configuration. Experimentally, the output energy, optical conversion efficiency, pulse dynamics, spectral property, and beam quality of the ASE source are studied when the Nd:YAG slab end-pumped by two high-brightness laser diode arrays. The maximum single pulse energy of 347 mJ is generated with an optical efficiency of ~5.9% and a beam quality of 3.5/17 in the thickness/width direction of the slab. As expected, smooth pulses without relaxing spikes and continuous spectra are achieved. Moreover, the spectral width of the ASE source narrows versus the pump energy, getting a 3-dB linewidth of as narrow as 20 pm (i.e. 5.3 GHz). Via the sum frequency generation, high-intensity, smooth-pulse, and narrow-linewidth ASE sources are preferred for solving the major problem of saturation of the mesospheric sodium atoms and can create a much brighter sodium guide star to meet the needs of adaptive imaging applications in astronomy.

Two novel copper(II) complexes constructed from dicarboxylate ligands with different spacer lengths and 2-phenylimidazo[4,5- f]1,10-phenanthroline (PIP): Synthesis, structures and properties

NASA Astrophysics Data System (ADS)

Wang, X.-L.; Chen, Yongqiang; Liu, Guocheng; Lin, Hongyan; Zhang, Jinxia

2009-09-01

Two novel metal-organic coordination polymers [Cu(PIP)(bpea)(H 2O)]·H 2O ( 1) and [Cu(PIP)(1,4-bdc)] ( 2) have been obtained from hydrothermal reaction of copper(II) with the mixed ligands [biphenylethene-4,4'-dicarboxylic acid (bpea) for 1, benzene-1,4-dicarboxylic acid (1,4-H 2bdc) for 2, and 2-phenylimidazo[4,5- f]1,10-phenanthroline (PIP)]. Both complexes have been structurally characterized by elemental analyses, IR and single-crystal X-ray diffraction analyses. Structural analyses reveal that complex 1 possesses infinite one-dimensional zigzag chain, 2 exhibits a two-dimensional (4,4) network, both of which are extended into three-dimensional supramolecular network by weak interactions. The different structures of the title complexes illustrate the influence of the flexibility (the spacer length of carboxyl groups and the structural rigidity of the spacer) of organic dicarboxylate ligands on the formation of such coordination architectures. Moreover, the thermal properties and the voltammetric behavior of complexes 1 and 2 have been reported.

Communication: electronic band gaps of semiconducting zig-zag carbon nanotubes from many-body perturbation theory calculations.

PubMed

Umari, P; Petrenko, O; Taioli, S; De Souza, M M

2012-05-14

Electronic band gaps for optically allowed transitions are calculated for a series of semiconducting single-walled zig-zag carbon nanotubes of increasing diameter within the many-body perturbation theory GW method. The dependence of the evaluated gaps with respect to tube diameters is then compared with those found from previous experimental data for optical gaps combined with theoretical estimations of exciton binding energies. We find that our GW gaps confirm the behavior inferred from experiment. The relationship between the electronic gap and the diameter extrapolated from the GW values is also in excellent agreement with a direct measurement recently performed through scanning tunneling spectroscopy.

Local Structure Fixation in the Composite Manufacturing Chain

NASA Astrophysics Data System (ADS)

Girdauskaite, Lina; Krzywinski, Sybille; Rödel, Hartmut; Wildasin-Werner, Andrea; Böhme, Ralf; Jansen, Irene

2010-12-01

Compared to metal materials, textile reinforced composites show interesting features, but also higher production costs because of low automation rate in the manufacturing chain at this time. Their applicability is also limited due to quality problems, which restrict the production of complex shaped dry textile preforms. New technologies, design concepts, and cost-effective manufacturing methods are needed in order to establish further fields of application. This paper deals with possible ways to improve the textile deformation process by locally applying a fixative to the structure parallel to the cut. This hinders unwanted deformation in the textile stock during the subsequent stacking and formation steps. It is found that suitable thermoplastic binders, applied in the appropriate manner do not restrict formation of the textile and have no negative influence on the mechanical properties of the composite.

The sequence and structure of snake gourd (Trichosanthes anguina) seed lectin, a three-chain nontoxic homologue of type II RIPs.

PubMed

Sharma, Alok; Pohlentz, Gottfried; Bobbili, Kishore Babu; Jeyaprakash, A Arockia; Chandran, Thyageshwar; Mormann, Michael; Swamy, Musti J; Vijayan, M

2013-08-01

The sequence and structure of snake gourd seed lectin (SGSL), a nontoxic homologue of type II ribosome-inactivating proteins (RIPs), have been determined by mass spectrometry and X-ray crystallography, respectively. As in type II RIPs, the molecule consists of a lectin chain made up of two β-trefoil domains. The catalytic chain, which is connected through a disulfide bridge to the lectin chain in type II RIPs, is cleaved into two in SGSL. However, the integrity of the three-dimensional structure of the catalytic component of the molecule is preserved. This is the first time that a three-chain RIP or RIP homologue has been observed. A thorough examination of the sequence and structure of the protein and of its interactions with the bound methyl-α-galactose indicate that the nontoxicity of SGSL results from a combination of changes in the catalytic and the carbohydrate-binding sites. Detailed analyses of the sequences of type II RIPs of known structure and their homologues with unknown structure provide valuable insights into the evolution of this class of proteins. They also indicate some variability in carbohydrate-binding sites, which appears to contribute to the different levels of toxicity exhibited by lectins from various sources.

BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization

PubMed Central

Ryu, Joonghyun; Lee, Mokwon; Cha, Jehyun; Laskowski, Roman A.; Ryu, Seong Eon; Kim, Deok-Soo

2016-01-01

Many applications, such as protein design, homology modeling, flexible docking, etc. require the prediction of a protein's optimal side-chain conformations from just its amino acid sequence and backbone structure. Side-chain prediction (SCP) is an NP-hard energy minimization problem. Here, we present BetaSCPWeb which efficiently computes a conformation close to optimal using a geometry-prioritization method based on the Voronoi diagram of spherical atoms. Its outputs are visual, textual and PDB file format. The web server is free and open to all users at http://voronoi.hanyang.ac.kr/betascpweb with no login requirement. PMID:27151195

Effect of B, N, Ge, Sn, K doping on electronic-transport properties of (5, 0) zigzag carbon nanotube

NASA Astrophysics Data System (ADS)

Kamalian, Monir; Seyed Jalili, Yousef; Abbasi, Afshin

2018-04-01

In this paper the effect of impurity on the electronic properties and quantum conductance of zigzag (5, 0) carbon nanotube have been studied by using the Density Functional Theory (DFT) combined with Non-Equilibrium Green’s Function (NEGF) formalism with TranSIESTA software. The effect of Boron (B), Nitrogen (N), Germanium (Ge), Tin (Sn) and Potassium (K) impurities on the CNT conduction behavior and physical characteristics, like density of states (DOS), band structure, transmission coefficients and quantum conductance was considered and discussed simultaneously. The current‑voltage (I‑V) curves of all the proposed models were studied for comparative study under low-bias conditions. The distinct changes in conductance reported as the positions, number and type of dopants was varied in central region of the CNT between two electrodes at different bias voltages. This suggested conductance enhancement mechanism for the charge transport in the doped CNT at different positions is important for the design of CNT based nanoelectronic devices. The results show that Germanium, Tin and Potassium dopant atoms has increased the conductance of the model manifold than other doping atoms furthermore 10 Boron and 10 Nitrogen dopant atoms showed the amazing property of Negative Differential Resistance (NDR).

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

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

Lin, Hung-Jui; Liu, Yu-Chiao; Tseng, Yu-Jui

2016-10-15

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){sub n} (solv = H{sub 2}O, CH{sub 3}OH, and none; X= CF{sub 3}CO{sub 2}{sup –}, BF{sub 4}{sup –}, ClO{sub 4}{sup –}, CF{sub 3}SO{sub 3}{sup –}, and SbF{sub 6}{sup –}). 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 inmore » these Ag(I) CPs displays a μ{sub 3}-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. - Graphical abstract: This work has addressed five ligand-dominated Ag(I)–3,4′-bpma polymeric adducts, which show similar one-dimensional non-flat chain structures depicting a “zipper-like” topology rather than a ladder-like or a double-stranded chain structures.« less

Conformational variety for the ansa chain of rifamycins: Comparison of observed crystal structures and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Bacchi, Alessia; Pelizzi, Giancarlo

1999-07-01

The antibiotic activity (via inhibition of DNA-dependent RNA polymerase, DDRP) of rifamycins has been correlated to the conformation of the ansa chain, which can be described by means of 17 torsion angles defined along the ansa backbone. It has been shown that favourable or unfavourable conformations of the ansa chain in rifamycin crystals are generally diagnostic of activity or inactivity against isolated DDRP. The principles of structure correlation suggest that the torsional variety observed in rifamycin crystals should mimic the dynamic flexibility of the ansa chain in solution. Twenty-six crystal structures of rifamycins are grouped into two classes (active and non-active). For each class the variance of the 17 ansa backbone torsion angles is analysed. Active compounds show a well-defined common pattern, while non-active molecules are more scattered, mainly due to steric constraints forcing the molecules into unfavourable conformations. The experimental distributions of torsion angles are compared to the torsional freedom of the ansa chain simulated by molecular dynamics calculations performed at different temperatures and conditions on rifamycin S and rifamycin O, which represent a typical active and a typical sterically constrained molecule, respectively. It is shown that the torsional variety found in the crystalline state samples the dynamic behaviour of the ansa chain for active compounds. The methods of circular statistics are illustrated to describe torsion angle distributions.

Solid-state NMR Study Reveals Collagen I Structural Modifications of Amino Acid Side Chains upon Fibrillogenesis*

PubMed Central

De Sa Peixoto, Paulo; Laurent, Guillaume; Azaïs, Thierry; Mosser, Gervaise

2013-01-01

In vivo, collagen I, the major structural protein in human body, is found assembled into fibrils. In the present work, we study a high concentrated collagen sample in its soluble, fibrillar, and denatured states using one and two dimensional {1H}-13C solid-state NMR spectroscopy. We interpret 13C chemical shift variations in terms of dihedral angle conformation changes. Our data show that fibrillogenesis increases the side chain and backbone structural complexity. Nevertheless, only three to five rotameric equilibria are found for each amino acid residue, indicating a relatively low structural heterogeneity of collagen upon fibrillogenesis. Using side chain statistical data, we calculate equilibrium constants for a great number of amino acid residues. Moreover, based on a 13C quantitative spectrum, we estimate the percentage of residues implicated in each equilibrium. Our data indicate that fibril formation greatly affects hydroxyproline and proline prolyl pucker ring conformation. Finally, we discuss the implication of these structural data and propose a model in which the attractive force of fibrillogenesis comes from a structural reorganization of 10 to 15% of the amino acids. These results allow us to further understand the self-assembling process and fibrillar structure of collagen. PMID:23341452

Non-equilibrium tunneling in zigzag graphene nanoribbon break-junction results in spin filtering

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

Jiang, Liming; Department of Electrical and Electronic Engineering, The University of Melbourne, Parkville 3010; National ICT Australia, The University of Melbourne, Parkville 3010

Spintronic devices promise new faster and lower energy-consumption electronic systems. Graphene, a versatile material and candidate for next generation electronics, is known to possess interesting spintronic properties. In this paper, by utilizing density functional theory and non-equilibrium green function formalism, we show that Fano resonance can be generated by introducing a break junction in a zigzag graphene nanoribbon (ZGNR). Using this effect, we propose a new spin filtering device that can be used for spin injection. Our theoretical results indicate that the proposed device could achieve high spin filtering efficiency (over 90%) at practical fabrication geometries. Furthermore, our results indicatemore » that the ZGNR break junction lattice configuration can dramatically affect spin filtering efficiency and thus needs to be considered when fabricating real devices. Our device can be fabricated on top of spin transport channel and provides good integration between spin injection and spin transport.« less

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

DOS cones along atomic chains

NASA Astrophysics Data System (ADS)

Kwapiński, Tomasz

2017-03-01

The electron transport properties of a linear atomic chain are studied theoretically within the tight-binding Hamiltonian and the Green’s function method. Variations of the local density of states (DOS) along the chain are investigated. They are crucial in scanning tunnelling experiments and give important insight into the electron transport mechanism and charge distribution inside chains. It is found that depending on the chain parity the local DOS at the Fermi level can form cone-like structures (DOS cones) along the chain. The general condition for the local DOS oscillations is obtained and the linear behaviour of the local density function is confirmed analytically. DOS cones are characterized by a linear decay towards the chain which is in contrast to the propagation properties of charge density waves, end states and Friedel oscillations in one-dimensional systems. We find that DOS cones can appear due to non-resonant electron transport, the spin-orbit scattering or for chains fabricated on a substrate with localized electrons. It is also shown that for imperfect chains (e.g. with a reduced coupling strength between two neighboring sites) a diamond-like structure of the local DOS along the chain appears.

Structure and thermodynamics of liquid alkali metals in variational modified hypernetted-chain theory

NASA Astrophysics Data System (ADS)

Chen, H. C.; Lai, S. K.

1992-03-01

The role of the Percus-Yevick hard-sphere bridge function in the modified hypernetted-chain integral equation is examined within the context of Lado's criterion [F. Lado, S. M. Foiles, and N. W. Ashcroft, Phys. Rev. A 28, 2374 (1983)]. It is found that the commonly used Lado's criterion, which takes advantage of the analytical simplicity of the Percus-Yevick hard-sphere bridge function, is inadequate for determining an accurate static pair-correlation function. Following Rosenfeld [Y. Rosenfeld, Phys. Rev. A 29, 2877 (1984)], we reconsider Lado's criterion in the so-called variational modified hypernetted-chain theory. The main idea is to construct a free-energy functional satisfying the virial-energy thermodynamic self-consistency. It turns out that the widely used Gibbs-Bogoliubov inequality is equivalent to this integral approach of Lado's criterion. Detailed comparison between the presently obtained structural and thermodynamic quantities for liquid alkali metals and those calculated also in the modified hypernetted-chain theory but with the one-component-plasma reference system leads us to a better understanding of the universality property of the bridge function.

Regions of recognition by blocking antibodies on the light chain of botulinum neurotoxin A: antigenic structure of the entire toxin.

PubMed

Dolimbek, Behzod Z; Steward, Lance E; Aoki, K Roger; Atassi, M Zouhair

2011-06-01

The continuous regions on botulinum neurotoxin A (BoNT/A) light (L) chain recognized by anti-toxin antibodies (Abs) from mouse, horse and chicken have been mapped. We synthesized a panel of thirty-two 19-residue peptides that overlapped consecutively by 5 residues and encompassed the entire L chain (residues 1-453). Mouse Abs recognized 5 major antigenic regions on the L chain, horse Abs recognized 9 while chicken Abs recognized 8 major antigenic regions. Overall, however, the three host species recognized, to some extent, similar, but not identical, peptides and the levels of Abs directed against a given region varied with the immunized host. Differences in the MHC of the host caused variation in levels of Ab recognition and some epitopes showed right or left frame-shifts among the species. Selected region(s) were also uniquely recognized by one species (e.g., peptide L1 by horse Abs). Mapping of the L chain antigenic regions and the previous localization of the regions on the H chain with the same antisera, has permitted description of the complete antigenic structure of BoNT/A. The locations in the 3-dimensional structure of the antigenic regions of the entire toxin are shown for mouse Abs. In the 3-D structure, the antigenic regions are on the surface of the toxin and when antibodies are bound the enzymatic activity of the light chain is obstructed. Copyright © 2010 Elsevier GmbH. All rights reserved.

Magneto-elastic modeling of composites containing chain-structured magnetostrictive particles

NASA Astrophysics Data System (ADS)

Yin, H. M.; Sun, L. Z.; Chen, J. S.

2006-05-01

Magneto-elastic behavior is investigated for two-phase composites containing chain-structured magnetostrictive particles under both magnetic and mechanical loading. To derive the local magnetic and elastic fields, three modified Green's functions are derived and explicitly integrated for the infinite domain containing a spherical inclusion with a prescribed magnetization, body force, and eigenstrain. A representative volume element containing a chain of infinite particles is introduced to solve averaged magnetic and elastic fields in the particles and the matrix. Effective magnetostriction of composites is derived by considering the particle's magnetostriction and the magnetic interaction force. It is shown that there exists an optimal choice of the Young's modulus of the matrix and the volume fraction of the particles to achieve the maximum effective magnetostriction. A transversely isotropic effective elasticity is derived at the infinitesimal deformation. Disregarding the interaction term, this model provides the same effective elasticity as Mori-Tanaka's model. Comparisons of model results with the experimental data and other models show the efficacy of the model and suggest that the particle interactions have a considerable effect on the effective magneto-elastic properties of composites even for a low particle volume fraction.

Crystal structure of bovine Cu,Zn superoxide dismutase at 3 A resolution: chain tracing and metal ligands.

PubMed Central

Richardson, J; Thomas, K A; Rubin, B H; Richardson, D C

1975-01-01

An electron density map at 3 angstrom resolution has been calculated for Cu2+, Zn2+ superoxide dismutase from bovine erythrocytes, and the course of the main chain has been traced. The dominant structural feature is an 8-stranded barrel of antiparallel beta-pleated sheet. There is one very short helical section and two long loops of non-repetitive structure. The Cu and Zn are bound between the loops and one side of the beta barrel and are about 6 Angstrom apart, with a common histidine ligand. The Cu has four histidine ligands in a somewhat distorted square plane, and the Zn has three histidines and an aspartate in approximately tetrahedral arrangement. The two coppers of a dimer are about 34 Angstrom apart. The two subunits have essentially the same conformation and have an extensive contact area that mainly involves hydrophobic side chain interactions. The overall folding pattern of the polypeptide chain is very similar to that of an immunoglobulin domain. Images PMID:1055410

Chain end distribution of block copolymer in two-dimensional microphase-separated structure studied by scanning near-field optical microscopy.

PubMed

Sekine, Ryojun; Aoki, Hiroyuki; Ito, Shinzaburo

2009-10-01

The chain end distribution of a block copolymer in a two-dimensional microphase-separated structure was studied by scanning near-field optical microscopy (SNOM). In the monolayer of poly(octadecyl methacrylate)-block-poly(isobutyl methacrylate) (PODMA-b-PiBMA), the free end of the PiBMA subchain was directly observed by SNOM, and the spatial distributions of the whole block and the chain end are examined and compared with the convolution of the point spread function of the microscope and distribution function of the model structures. It was found that the chain end distribution of the block copolymer confined in two dimensions has a peak near the domain center, being concentrated in the narrower region, as compared with three-dimensional systems.

Phase stability and large in-plane resistivity anisotropy in the 112-type iron-based superconductor Ca 1 - x La x FeAs 2

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

Kang, Chang-Jong; Birol, Turan; Kotliar, Gabriel

The recently discovered high-T c superconductor Ca 1-xLa xFeAs 2 is a unique compound not just because of its low-symmetry crystal structure but also because of its electronic structure, which hosts Dirac-like metallic bands resulting from (spacer) zigzag As chains. We present a comprehensive first-principles theoretical study of the electronic and crystal structures of Ca 1-xLa xFeAs 2. After discussing the connection between the crystal structure of the 112 family, which Ca 1-xLa xFeAs 2 is a member of, with the other known structures of Fe pnictide superconductors, we check the thermodynamic phase stability of CaFeAs 2, and similar hyphotheticalmore » compounds SrFeAs 2 and BaFeAs 2 which, we find, are slightly higher in energy. We calculate the optical conductivity of Ca 1-xLa xFeAs 2 using the DFT+DMFT method and predict a large in-plane resistivity anisotropy in the normal phase, which does not originate from electronic nematicity, but is enhanced by the electronic correlations. In particular, we predict a 0.34 eV peak in the yy component of the optical conductivity of the 30% La-doped compound, which corresponds to coherent interband transitions within a fast-dispersing band arising from the zigzag As chains, which are unique to this compound. We also study the Landau free energy for Ca 1-xLa xFeAs 2 including the order parameter relevant for the nematic transition and find that the free energy does not have any extra terms that could induce ferro-orbital order. This explains why the presence of As chains does not broaden the nematic transition in Ca 1-xLa xFeAs 2.« less

Phase stability and large in-plane resistivity anisotropy in the 112-type iron-based superconductor Ca 1 - x La x FeAs 2

DOE PAGES

Kang, Chang-Jong; Birol, Turan; Kotliar, Gabriel

2017-01-17

The recently discovered high-T c superconductor Ca 1-xLa xFeAs 2 is a unique compound not just because of its low-symmetry crystal structure but also because of its electronic structure, which hosts Dirac-like metallic bands resulting from (spacer) zigzag As chains. We present a comprehensive first-principles theoretical study of the electronic and crystal structures of Ca 1-xLa xFeAs 2. After discussing the connection between the crystal structure of the 112 family, which Ca 1-xLa xFeAs 2 is a member of, with the other known structures of Fe pnictide superconductors, we check the thermodynamic phase stability of CaFeAs 2, and similar hyphotheticalmore » compounds SrFeAs 2 and BaFeAs 2 which, we find, are slightly higher in energy. We calculate the optical conductivity of Ca 1-xLa xFeAs 2 using the DFT+DMFT method and predict a large in-plane resistivity anisotropy in the normal phase, which does not originate from electronic nematicity, but is enhanced by the electronic correlations. In particular, we predict a 0.34 eV peak in the yy component of the optical conductivity of the 30% La-doped compound, which corresponds to coherent interband transitions within a fast-dispersing band arising from the zigzag As chains, which are unique to this compound. We also study the Landau free energy for Ca 1-xLa xFeAs 2 including the order parameter relevant for the nematic transition and find that the free energy does not have any extra terms that could induce ferro-orbital order. This explains why the presence of As chains does not broaden the nematic transition in Ca 1-xLa xFeAs 2.« less

Majorana Zero-Energy Mode and Fractal Structure in Fibonacci-Kitaev Chain

NASA Astrophysics Data System (ADS)

Ghadimi, Rasoul; Sugimoto, Takanori; Tohyama, Takami

2017-11-01

We theoretically study a Kitaev chain with a quasiperiodic potential, where the quasiperiodicity is introduced by a Fibonacci sequence. Based on an analysis of the Majorana zero-energy mode, we find the critical p-wave superconducting pairing potential separating a topological phase and a non-topological phase. The topological phase diagram with respect to Fibonacci potentials follow a self-similar fractal structure characterized by the box-counting dimension, which is an example of the interplay of fractal and topology like the Hofstadter's butterfly in quantum Hall insulators.

Geometry, bonding and magnetism in planar triangulene graphene molecules with D3h symmetry: Zigzag Cm∗∗2+4m+1H3m+3 (m = 2, …, 15)

NASA Astrophysics Data System (ADS)

Philpott, Michael R.; Cimpoesu, Fanica; Kawazoe, Yoshiyuki

2008-12-01

Ab initio plane wave based all valence electron DFT calculations with geometry optimization are reported for the electronic structure of planar zigzag edged triangular shaped graphene molecules CH where the zigzag ring number m = 2, …, 15. The largest molecule C 286H 48 has a 3.8 nm side length and retains D3h symmetric geometry. The zone in the middle of the molecules, where the geometry and electronic properties resemble infinite single sheet graphite (graphene), expands with increasing ring number m, driving deviations in geometry, charge and spin to the perimeter. If a molecule is viewed as a set of nested triangular rings of carbon, then the zone where the lattice resembles an infinite sheet of graphene with CC = 142 pm, extends to the middle of the penultimate ring. The radial bonds joining the perimeter carbon atoms to the interior are long CC = 144 pm, except near the three apexes where the bonds are shorter. Isometric surfaces of the total charge density show that the two bonds joined at the apex have the highest valence charge. The perimeter CC bonds establish a simple pattern as the zigzag number increases, which shares some features with the zigzag edges in the D2h linear acenes C 4m+2H 2m+4 and the D6h hexangulenes CH6m but not the D6h symmetric annulenes (CH). The two CC bonds forming each apex are short (≈139 pm), next comes one long bond CC ≈ 142 pm and a middle region where all the CC bonds have length ≈141 pm. The homo-lumo gap declines from 0.53 eV at m = 2 to approximately 0.29 V at m = 15, the latter being larger than found for linear or hexagonal shaped graphenes with comparable edge lengths. Across the molecule the charge on the carbon atoms undergoes a small oscillation following the bipartite lattice. The magnitude of the charge in the same nested triangle decreases monotonically with the distance of the row from the center of the molecule. These systems are predicted to have spin polarized ground states with S = ½( m - 1), in

Cubic Zig-Zag Enrichment of the Classical Kirchhoff Kinematics for Laminated and Sandwich Plates

NASA Technical Reports Server (NTRS)

Nemeth, Michael P.

2012-01-01

A detailed anaylsis and examples are presented that show how to enrich the kinematics of classical Kirchhoff plate theory by appending them with a set of continuous piecewise-cubic functions. This analysis is used to obtain functions that contain the effects of laminate heterogeneity and asymmetry on the variations of the inplane displacements and transverse shearing stresses, for use with a {3, 0} plate theory in which these distributions are specified apriori. The functions used for the enrichment are based on the improved zig-zag plate theory presented recently by Tessler, Di Scuva, and Gherlone. With the approach presented herein, the inplane displacements are represented by a set of continuous piecewise-cubic functions, and the transverse shearing stresses and strains are represented by a set of piecewise-quadratic functions that are discontinuous at the ply interfaces.

Crustal structure of an intraplate thrust belt: The Iberian Chain revealed by wide-angle seismic, magnetotelluric soundings and gravity data

NASA Astrophysics Data System (ADS)

Seillé, Hoël; Salas, Ramon; Pous, Jaume; Guimerà, Joan; Gallart, Josep; Torne, Montserrat; Romero-Ruiz, Ivan; Diaz, Jordi; Ruiz, Mario; Carbonell, Ramon; Mas, Ramón

2015-11-01

The Iberian Chain is a Cenozoic intraplate thrust belt located within the Iberian plate. Unlike other belts in the Iberia Peninsula, the scarcity of geophysical studies in this area results in a number of unknowns about its crustal structure. The Iberian Chain crust was investigated by means of a NE-SW refraction/wide-angle reflection seismic transect and two magnetotelluric profiles across the chain, oriented along the same direction. The seismic profile was designed to sample the crust by means of three shots designed to obtain a reversed profile. The resulting velocity-depth model shows a moderate thickening of the crust toward the central part of the profile, where crustal thickness reaches values above 40 km, thinning toward de SW Tajo and NE Ebro foreland basins. The crustal thickening is concentrated in the upper crust. The seismic results are in overall agreement with regional trends of Bouguer gravity anomaly and the main features of the seismic model were reproduced by gravity modeling. The magnetotelluric data consist of 39 sites grouped into two profiles, with periods ranging from 0.01 s to 1000 s. Dimensionality analyses show significant 3D effects in the resistivity structure and therefore we carried out a joint 3D inversion of the full impedance tensor and magnetic transfer functions. The Mesozoic and Cenozoic basins along the Chain are well characterized by shallow high conductive zones and low velocities. Elongated conductors reaching mid-crustal depths evidence the presence of major faults dominating the crustal structure. The results from the interpretation of these complementary geophysical data sets provided the first images of the crustal structure of the Iberian Chain. They are consistent with a Cenozoic shortening responsible of the upper crust thickening as well as of the uplift of the Iberian Chain and the generation of its present day topography.

Structural and magnetic characterization of the one-dimensional S = 5/2 antiferromagnetic chain system SrMn(VO 4)(OH)

DOE PAGES

Sanjeewa, Liurukara D.; Garlea, Vasile O.; McGuire, Michael A.; ...

2016-06-06

The descloizite-type compound, SrMn(VO 4)(OH), was synthesized as large single crystals (1-2mm) using a high-temperature high-pressure hydrothermal technique. X-ray single crystal structure analysis reveals that the material crystallizes in the acentric orthorhombic space group of P2 12 12 1 (no. 19), Z = 4. The structure exhibits a one-dimensional feature, with [MnO 4] chains propagating along the a-axis which are interconnected by VO 4 tetrahedra. Raman and infrared spectra were obtained to identify the fundamental vanadate and hydroxide vibrational modes. Magnetization data reveal a broad maximum at approximately 80 K, arising from one-dimensional magnetic correlations with intrachain exchange constant ofmore » J/k B = 9.97(3) K between nearest Mn neighbors and a canted antiferromagnetic behavior below T N = 30 K. Single crystal neutron diffraction at 4 K yielded a magnetic structure solution in the lower symmetry of the magnetic space group P2 1 with two unique chains displaying antiferromagnetically ordered Mn moments oriented nearly perpendicular to the chain axis. Lastly, the presence of the Dzyaloshinskii Moriya antisymmetric exchange interaction leads to a slight canting of the spins and gives rise to a weak ferromagnetic component along the chain direction.« less

Highly Efficient Carbon Dioxide Hydrogenation to Methanol Catalyzed by Zigzag Platinum-Cobalt Nanowires.

PubMed

Bai, Shuxing; Shao, Qi; Feng, Yonggang; Bu, Lingzheng; Huang, Xiaoqing

2017-06-01

Carbon dioxide (CO 2 ) hydrogenation is an effective strategy for CO 2 utilization, while unsatisfied conversion efficiencies remain great challenges. It is reported herein that zigzag Pt-Co nanowires (NWs) with Pt-rich surfaces and abundant steps/edges can perform as highly active and stable CO 2 hydrogenation catalysts. It is found that tuning the Pt/Co ratio of the Pt-Co NWs, solvents, and catalyst supports could well optimize the CO 2 hydrogenation to methanol (CH 3 OH) with the Pt 4 Co NWs/C exhibiting the best performance, outperforming all the previous catalysts. They are also very durable with limited activity decays after six catalytic cycles. The diffuse reflectance infrared Fourier transform spectroscopy result of CO 2 adsorption shows that the Pt 4 Co NWs/C undergoes the adsorption/activation of CO 2 by forming appropriate carboxylate intermediates, and thus enhancing the CH 3 OH production. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Zigzag nanoribbons of two-dimensional silicene-like crystals: magnetic, topological and thermoelectric properties.

PubMed

Wierzbicki, Michał; Barnaś, Józef; Swirkowicz, Renata

2015-12-09

The effects of electron-electron and spin-orbit interactions on the ground-state magnetic configuration and on the corresponding thermoelectric and spin thermoelectric properties in zigzag nanoribbons of two-dimensional hexagonal crystals are analysed theoretically. The thermoelectric properties of quasi-stable magnetic states are also considered. Of particular interest is the influence of Coulomb and spin-orbit interactions on the topological edge states and on the transition between the topological insulator and conventional gap insulator states. It is shown that the interplay of both interactions also has a significant impact on the transport and thermoelectric characteristics of the nanoribbons. The spin-orbit interaction also determines the in-plane magnetic easy axis. The thermoelectric properties of nanoribbons with in-plane magnetic moments are compared to those of nanoribbons with edge magnetic moments oriented perpendicularly to their plane. Nanoribbons with ferromagnetic alignment of the edge moments are shown to reveal spin thermoelectricity in addition to the conventional one.

Doping Scheme in Atomic Chain Electronics

NASA Technical Reports Server (NTRS)

Toshishige, Yamada

1997-01-01

Due to the dramatic reduction in MOS size, there appear many unwanted effects. In these small devices, the number of dopant atoms in the channel is not macroscopic and electrons may suffer significantly different scattering from device to device since the spatial distribution of dopant atoms is no longer regarded as continuous. This prohibits integration, while it is impossible to control such dopant positions within atomic scale. A fundamental solution is to create electronics with simple but atomically precise structures, which could be fabricated with recent atom manipulation technology. All the constituent atoms are placed as planned, and then the device characteristics are deviation-free, which is mandatory for integration. Atomic chain electronics belongs to this category. Foreign atom chains or arrays form devices, and they are placed on the atomically flat substrate surface. We can design the band structure and the resultant Fermi energy of these structures by manipulating the lattice constant. Using the tight-binding theory with universal parameters, it has been predicted that isolated Si chains and arrays are metallic, Mg chains are insulating, and Mg arrays have metallic and insulating phases [1]. The transport properties along a metallic chain have been studied, emphasizing the role of the contact to electrodes [2]. For electronic applications, it is essential to establish a method to dope a semiconducting chain, which is to control the Fermi energy position without altering the original band structure. If we replace some of the chain atoms with dopant atoms randomly, the electrons will see random potential along die chain and will be localized strongly in space (Anderson localization). However, if we replace periodically, although the electrons can spread over the chain, there will generally appear new bands and band gaps reflecting the new periodicity of dopant atoms. This will change the original band structure significantly. In order to overcome

Binding of DNA-bending non-histone proteins destabilizes regular 30-nm chromatin structure

PubMed Central

Bajpai, Gaurav; Jain, Ishutesh; Inamdar, Mandar M.; Das, Dibyendu; Padinhateeri, Ranjith

2017-01-01

Why most of the in vivo experiments do not find the 30-nm chromatin fiber, well studied in vitro, is a puzzle. Two basic physical inputs that are crucial for understanding the structure of the 30-nm fiber are the stiffness of the linker DNA and the relative orientations of the DNA entering/exiting nucleosomes. Based on these inputs we simulate chromatin structure and show that the presence of non-histone proteins, which bind and locally bend linker DNA, destroys any regular higher order structures (e.g., zig-zag). Accounting for the bending geometry of proteins like nhp6 and HMG-B, our theory predicts phase-diagram for the chromatin structure as a function of DNA-bending non-histone protein density and mean linker DNA length. For a wide range of linker lengths, we show that as we vary one parameter, that is, the fraction of bent linker region due to non-histone proteins, the steady-state structure will show a transition from zig-zag to an irregular structure—a structure that is reminiscent of what is observed in experiments recently. Our theory can explain the recent in vivo observation of irregular chromatin having co-existence of finite fraction of the next-neighbor (i + 2) and neighbor (i + 1) nucleosome interactions. PMID:28135276

BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization.

PubMed

Ryu, Joonghyun; Lee, Mokwon; Cha, Jehyun; Laskowski, Roman A; Ryu, Seong Eon; Kim, Deok-Soo

2016-07-08

Many applications, such as protein design, homology modeling, flexible docking, etc. require the prediction of a protein's optimal side-chain conformations from just its amino acid sequence and backbone structure. Side-chain prediction (SCP) is an NP-hard energy minimization problem. Here, we present BetaSCPWeb which efficiently computes a conformation close to optimal using a geometry-prioritization method based on the Voronoi diagram of spherical atoms. Its outputs are visual, textual and PDB file format. The web server is free and open to all users at http://voronoi.hanyang.ac.kr/betascpweb with no login requirement. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Simulation study of the initial crystallization processes of poly(3-hexylthiophene) in solution: ordering dynamics of main chains and side chains.

PubMed

Takizawa, Yuumi; Shimomura, Takeshi; Miura, Toshiaki

2013-05-23

We study the initial nucleation dynamics of poly(3-hexylthiophene) (P3HT) in solution, focusing on the relationship between the ordering process of main chains and that of side chains. We carried out Langevin dynamics simulation and found that the initial nucleation processes consist of three steps: the ordering of ring orientation, the ordering of main-chain vectors, and the ordering of side chains. At the start, the normal vectors of thiophene rings aligned in a very short time, followed by alignment of main-chain end-to-end vectors. The flexible side-chain ordering took almost 5 times longer than the rigid-main-chain ordering. The simulation results indicated that the ordering of side chains was induced after the formation of the regular stack structure of main chains. This slow ordering dynamics of flexible side chains is one of the factors that cause anisotropic nuclei growth, which would be closely related to the formation of nanofiber structures without external flow field. Our simulation results revealed how the combined structure of the planar and rigid-main-chain backbones and the sparse flexible side chains lead to specific ordering behaviors that are not observed in ordinary linear polymer crystallization processes.

The increase in conductance of a gold single atom chain during elastic elongation

NASA Astrophysics Data System (ADS)

Tavazza, F.; Barzilai, S.; Smith, D. T.; Levine, L. E.

2013-02-01

The conductance of monoatomic gold wires has been studied using ab initio calculations and the transmission was found to vary with the elastic strain. Counter-intuitively, the conductance was found to increase for the initial stages of the elongation, where the structure has a zigzag shape and the bond angles increase from ≈140° toward ≈160°. After a certain elongation limit, where the angles are relatively high, the bond length elongation associated with a Peierls distortion reverses this trend and the conductance decreases. These simulations are in good agreement with previously unexplained experimental results.

Managing risks in the fisheries supply chain using House of Risk Framework (HOR) and Interpretive Structural Modeling (ISM)

NASA Astrophysics Data System (ADS)

Nguyen, T. L. T.; Tran, T. T.; Huynh, T. P.; Ho, T. K. D.; Le, A. T.; Do, T. K. H.

2018-04-01

One of the sectors which contributes importantly to the development of Vietnam economy is fishery industry. However, during recent year, it has been witnessed many difficulties on managing the performance of the fishery supply chain operations as a whole. In this paper, a framework for supply chain risk management (SCRM) is proposed. Initially, all the activities are mapped by using Supply Chain Operations Reference (SCOR) model. Next, the risk ranking is analyzed in House of Risk. Furthermore, interpretive structural modeling (ISM) is used to identify inter-relationships among supply chain risks and to visualize the risks according to their levels. For illustration, the model has been tested in several case studies with fishery companies in Can Tho, Mekong Delta. This study identifies 22 risk events and 20 risk agents through the supply chain. Also, the risk priority could be used for further House of Risk with proactive actions in future studies.

Structure-guided investigation of lipopolysaccharide O-antigen chain length regulators reveals regions critical for modal length control.

PubMed

Kalynych, Sergei; Ruan, Xiang; Valvano, Miguel A; Cygler, Miroslaw

2011-08-01

The O-antigen component of the lipopolysaccharide (LPS) represents a population of polysaccharide molecules with nonrandom (modal) chain length distribution. The number of the repeat O units in each individual O-antigen polymer depends on the Wzz chain length regulator, an inner membrane protein belonging to the polysaccharide copolymerase (PCP) family. Different Wzz proteins confer vastly different ranges of modal lengths (4 to >100 repeat units), despite having remarkably conserved structural folds. The molecular mechanism responsible for the selective preference for a certain number of O units is unknown. Guided by the three-dimensional structures of PCPs, we constructed a panel of chimeric molecules containing parts of two closely related Wzz proteins from Salmonella enterica and Shigella flexneri which confer different O-antigen chain length distributions. Analysis of the O-antigen length distribution imparted by each chimera revealed the region spanning amino acids 67 to 95 (region 67 to 95), region 200 to 255, and region 269 to 274 as primarily affecting the length distribution. We also showed that there is no synergy between these regions. In particular, region 269 to 274 also influenced chain length distribution mediated by two distantly related PCPs, WzzB and FepE. Furthermore, from the 3 regions uncovered in this study, region 269 to 274 appeared to be critical for the stability of the oligomeric form of Wzz, as determined by cross-linking experiments. Together, our data suggest that chain length determination depends on regions that likely contribute to stabilize a supramolecular complex.

A protein-dependent side-chain rotamer library.

PubMed

Bhuyan, Md Shariful Islam; Gao, Xin

2011-12-14

Protein side-chain packing problem has remained one of the key open problems in bioinformatics. The three main components of protein side-chain prediction methods are a rotamer library, an energy function and a search algorithm. Rotamer libraries summarize the existing knowledge of the experimentally determined structures quantitatively. Depending on how much contextual information is encoded, there are backbone-independent rotamer libraries and backbone-dependent rotamer libraries. Backbone-independent libraries only encode sequential information, whereas backbone-dependent libraries encode both sequential and locally structural information. However, side-chain conformations are determined by spatially local information, rather than sequentially local information. Since in the side-chain prediction problem, the backbone structure is given, spatially local information should ideally be encoded into the rotamer libraries. In this paper, we propose a new type of backbone-dependent rotamer library, which encodes structural information of all the spatially neighboring residues. We call it protein-dependent rotamer libraries. Given any rotamer library and a protein backbone structure, we first model the protein structure as a Markov random field. Then the marginal distributions are estimated by the inference algorithms, without doing global optimization or search. The rotamers from the given library are then re-ranked and associated with the updated probabilities. Experimental results demonstrate that the proposed protein-dependent libraries significantly outperform the widely used backbone-dependent libraries in terms of the side-chain prediction accuracy and the rotamer ranking ability. Furthermore, without global optimization/search, the side-chain prediction power of the protein-dependent library is still comparable to the global-search-based side-chain prediction methods.

Role of κ→λ light-chain constant-domain switch in the structure and functionality of A17 reactibody

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

Ponomarenko, Natalia; Chatziefthimiou, Spyros D.; Kurkova, Inna

2014-03-01

Catalytic antibody variants with κ and λ light-chain constant domains show differences in their crystal structures which lead to subtle changes in catalytic efficiency and thermodynamic parameters as well as in their affinity for peptide substrates. The engineering of catalytic function in antibodies requires precise information on their structure. Here, results are presented that show how the antibody domain structure affects its functionality. The previously designed organophosphate-metabolizing reactibody A17 has been re-engineered by replacing its constant κ light chain by the λ chain (A17λ), and the X-ray structure of A17λ has been determined at 1.95 Å resolution. It was foundmore » that compared with A17κ the active centre of A17λ is displaced, stabilized and made more rigid owing to interdomain interactions involving the CDR loops from the V{sub L} and V{sub H} domains. These V{sub L}/V{sub H} domains also have lower mobility, as deduced from the atomic displacement parameters of the crystal structure. The antibody elbow angle is decreased to 126° compared with 138° in A17κ. These structural differences account for the subtle changes in catalytic efficiency and thermodynamic parameters determined with two organophosphate ligands, as well as in the affinity for peptide substrates selected from a combinatorial cyclic peptide library, between the A17κ and A17λ variants. The data presented will be of interest and relevance to researchers dealing with the design of antibodies with tailor-made functions.« less

Recursive formulae and performance comparisons for first mode dynamics of periodic structures

NASA Astrophysics Data System (ADS)

Hobeck, Jared D.; Inman, Daniel J.

2017-05-01

Periodic structures are growing in popularity especially in the energy harvesting and metastructures communities. Common types of these unique structures are referred to in the literature as zigzag, orthogonal spiral, fan-folded, and longitudinal zigzag structures. Many of these studies on periodic structures have two competing goals in common: (a) minimizing natural frequency, and (b) minimizing mass or volume. These goals suggest that no single design is best for all applications; therefore, there is a need for design optimization and comparison tools which first require efficient easy-to-implement models. All available structural dynamics models for these types of structures do provide exact analytical solutions; however, they are complex requiring tedious implementation and providing more information than necessary for practical applications making them computationally inefficient. This paper presents experimentally validated recursive models that are able to very accurately and efficiently predict the dynamics of the four most common types of periodic structures. The proposed modeling technique employs a combination of static deflection formulae and Rayleigh’s Quotient to estimate the first mode shape and natural frequency of periodic structures having any number of beams. Also included in this paper are the results of an extensive experimental validation study which show excellent agreement between model prediction and measurement. Lastly, the proposed models are used to evaluate the performance of each type of structure. Results of this performance evaluation reveal key advantages and disadvantages associated with each type of structure.

Alkyl Chain Length Dependent Structural and Orientational Transformations of Water at Alcohol-Water Interfaces and Its Relevance to Atmospheric Aerosols.

PubMed

Mondal, Jahur A; Namboodiri, V; Mathi, P; Singh, Ajay K

2017-04-06

Although the hydrophobic size of an amphiphile plays a key role in various chemical, biological, and atmospheric processes, its effect at macroscopic aqueous interfaces (e.g., air-water, oil-water, cell membrane-water, etc.), which are ubiquitous in nature, is not well understood. Here we report the hydrophobic alkyl chain length dependent structural and orientational transformations of water at alcohol (C n H 2n+1 OH, n = 1-12)-water interfaces using interface-selective heterodyne-detected vibrational sum frequency generation (HD-VSFG) and Raman multivariate curve resolution (Raman-MCR) spectroscopic techniques. The HD-VSFG results reveal that short-chain alcohols (C n H 2n+1 OH, n < 4, i.e., up to 1-propanol) do not affect the structure (H-bonding) and orientation of water at the air-water interface; the OH stretch band maximum appears at ∼3470 cm -1 , and the water H atoms are pointed toward the bulk water, that is, "H-down" oriented. In contrast, long-chain alcohols (C n H 2n+1 OH, n > 4, i.e., beyond 1-butanol) make the interfacial water more strongly H-bonded and reversely orientated; the OH stretch band maximum appears at ∼3200 cm -1 , and the H atoms are pointed away from the bulk water, that is, "H-up" oriented. Interestingly, for the alcohol of intermediate chain length (C n H 2n+1 OH, n = 4, i.e, 1-butanol), the interface is quite unstable even after hours of its formation and the time-averaged result is qualitatively similar to that of the long-chain alcohols, indicating a structural/orientational crossover of interfacial water at the 1-butanol-water interface. pH-dependent HD-VSFG measurements (with H 2 O as well as isotopically diluted water, HOD) suggest that the structural/orientational transformation of water at the long-chain alcohol-water interface is associated with the adsorption of OH - anion at the interface. Vibrational mapping of the water structure in the hydration shell of OH - anion (obtained by Raman-MCR spectroscopy of NaOH in HOD

Structure of flexible and semiflexible polyelectrolyte chains in confined spaces of slit micro/nanochannels.

PubMed

Jeon, Jonggu; Chun, Myung-Suk

2007-04-21

Understanding the behavior of a polyelectrolyte in confined spaces has direct relevance in design and manipulation of microfluidic devices, as well as transport in living organisms. In this paper, a coarse-grained model of anionic semiflexible polyelectrolyte is applied, and its structure and dynamics are fully examined with Brownian dynamics (BD) simulations both in bulk solution and under confinement between two negatively charged parallel plates. The modeling is based on the nonlinear bead-spring discretization of a continuous chain with additional long-range electrostatic, Lennard-Jones, and hydrodynamic interactions between pairs of beads. The authors also consider the steric and electrostatic interactions between the bead and the confining wall. Relevant model parameters are determined from experimental rheology data on the anionic polysaccharide xanthan reported previously. For comparison, both flexible and semiflexible models are developed accompanying zero and finite intrinsic persistence lengths, respectively. The conformational changes of the polyelectrolyte chain induced by confinements and their dependence on the screening effect of the electrolyte solution are faithfully characterized with BD simulations. Depending on the intrinsic rigidity and the medium ionic strength, the polyelectrolyte can be classified as flexible, semiflexible, or rigid. Confined flexible and semiflexible chains exhibit a nonmonotonic variation in size, as measured by the radius of gyration and end-to-end distance, with changing slit width. For the semiflexible chain, this is coupled to the variations in long-range bond vector correlation. The rigid chain, realized at low ionic strength, does not have minima in size but exhibits a sigmoidal transition. The size of confined semiflexible and rigid polyelectrolytes can be well described by the wormlike chain model once the electrostatic effects are taken into account by the persistence length measured at long length scale.

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 C 16 -alkyl chains on the surface. Gas permeation measurements are performed at temperatures ranging from 0 to 80 °C using Ar, N 2 , and CO 2 . Nonfunctionalized structures feature a gas transport according to Knudsen diffusion with regard to gas flow and selectivity. After C 16 -functionalization, the gas flow is reduced by a factor of 10, and the ideal selectivities deviate from the Knudsen theory. CO 2 adsorption measurements show a decrease in total amount of adsorbed gas and isosteric heat of adsorption. It is hypothesized that the immobilized C 16 -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 C 16 -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 (CO 2 < Ar < N 2 ) 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 C 16 -chains is responsible for the stronger interaction between gas molecules and surface functional groups.

Time-dependent density-functional theory simulation of local currents in pristine and single-defect zigzag graphene nanoribbons

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

He, Shenglai, E-mail: shenglai.he@vanderbilt.edu; Russakoff, Arthur; Li, Yonghui

2016-07-21

The spatial current distribution in H-terminated zigzag graphene nanoribbons (ZGNRs) under electrical bias is investigated using time-dependent density-functional theory solved on a real-space grid. A projected complex absorbing potential is used to minimize the effect of reflection at simulation cell boundary. The calculations show that the current flows mainly along the edge atoms in the hydrogen terminated pristine ZGNRs. When a vacancy is introduced to the ZGNRs, loop currents emerge at the ribbon edge due to electrons hopping between carbon atoms of the same sublattice. The loop currents hinder the flow of the edge current, explaining the poor electric conductancemore » observed in recent experiments.« less

Chain length effect on the structure and stability of antimicrobial peptides of the (RW)n series.

PubMed

Phambu, Nsoki; Almarwani, Bashiyar; Garcia, Arlette M; Hamza, Nafisa S; Muhsen, Amira; Baidoo, Jacqueline E; Sunda-Meya, Anderson

2017-08-01

Three peptides containing (RW) n -NH 2 units (where n=4, 6, and 8) have been chosen to study the effect of the chain length on the structure and stability of the peptide using Fourier transform infrared (FTIR), scanning electron microscopy (SEM), thermogravimetric analysis (TGA), and differential scanning calorimetry (DSC) techniques. Their interactions with Escherichia coli (E. coli) membrane mimetic vesicles are discussed. Infrared results indicate that addition of (RW) n -NH 2 units increases intermolecular H bonds with antiparallel orientation. TGA and DSC results reveal that (RW) 6 -NH 2 shows the optimal chain length in terms of stability and all three peptides show a preferential interaction with one of the anionic lipids in E. coli membranes. SEM images of (RW) 4 -NH 2 present large aggregates while those of (RW) 6 -NH 2 and (RW) 8 -NH 2 present layers of sheet-like structure. In the presence of model membranes, (RW) n -NH 2 show fibrillar peptide superstructures. This study suggests that repeating structures of (RW) n -NH 2 promotes lateral assembly. Copyright © 2017 Elsevier B.V. All rights reserved.

Synthesis and structural characterization of dinuclear Cd2+, Hg2+ and Fe2+ complexes with neutral bi and tetradentate flexible pyrazole-based ligands

NASA Astrophysics Data System (ADS)

Beheshti, Azizolla; Lalegani, Arash; Behvandi, Fatemeh; Safaeiyan, Forough; Sarkarzadeh, Afsoon; Bruno, Giuseppe; Amiri Rudbari, Hadi

2015-02-01

Four new complexes of [Hg2Cl4(bpp)]n (1), [Hg2Cl4(tdmpp)] (2), [Cd2I4(tdmpp)] (3) and [Fe2Cl4(tdmpp)] (4) were prepared by using the neutral N-donor ligands 1,3-bis(3,5-dimethyl-1-pyrazolyl)propane (bpp) and 1,1,3,3-tetrakis(3,5-dimethyl-1-pyrazolyl)propane (tdmpp) with different flexibility and appropriate metal salts of Cd(II), Hg(II) and Fe(II) ions. These compounds were characterized by the infrared spectroscopy, elemental analysis and X-ray crystallography. Flexible ligands and non-covalent Csbnd H⋯Cl hydrogen bonds play a major role in the crystal packing of compounds 1, 2 and 4. In the two-dimensional non-covalent structure of 1, there are two distinctly different coordination modes for the mercury atoms. One mercury atom has pseudo-trigonal bipyramidal geometry and the other adopts a distorted tetrahedral environment. In the dinuclear structures of 2 and 4 the neutral molecules are linked together by the Csbnd H⋯Cl hydrogen bonds, forming an infinite one-dimensional zigzag chain structure. Compounds 2-4 are isostructural with each other.

NMR studies of structure, hydrogen exchange, and main-chain dynamics in a disrupted-core mutant of thioredoxin.

PubMed Central

De Lorimier, R.; Hellinga, H. W.; Spicer, L. D.

1996-01-01

Core-packing mutants of proteins often approach molten globule states, and hence may have attributes of folding intermediates. We have studied a core-packing mutant of thioredoxin, L78K, in which a leucine residue is substituted by lysine, using 15N heteronuclear two- and three-dimensional NMR. Chemical shift differences between the mutant and wild-type main-chain resonances reveal that structural changes caused by the mutation are localized within 12 A of the altered side chain. The majority of resonances are unchanged, as are many 1H-1H NOEs indicative of the main-chain fold, suggesting that the structure of L78K is largely similar to wild type. Hydrogen exchange studies reveal that residues comprising the central beta-sheet of both mutant and wild-type proteins constitute a local unfolding unit, but with the unfolding/folding equilibrium approximately 12 times larger in L78K. The dynamics of main-chain NH bonds in L78K were studied by 15N spin relaxation and compared with a previous study of wild type. Order parameters for angular motion of NH bonds in the mutant are on average lower than in wild type, suggesting greater spatial freedom on a rapid time scale, but may also be related to different rotational correlation times in the two proteins. There is also evidence of greater conformational exchange in the mutant. Differences between mutant and wild type in hydrogen exchange and main-chain dynamics are not confined to the vicinity of the mutation. We infer that mispacking of the protein core in one location affects local dynamics and stability throughout. PMID:8976564

Controllable spin polarization and spin filtering in a zigzag silicene nanoribbon

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

Farokhnezhad, Mohsen, E-mail: Mohsen-farokhnezhad@physics.iust.ac.ir; Esmaeilzadeh, Mahdi, E-mail: mahdi@iust.ac.ir; Pournaghavi, Nezhat

2015-05-07

Using non-equilibrium Green's function, we study the spin-dependent electron transport properties in a zigzag silicene nanoribbon. To produce and control spin polarization, it is assumed that two ferromagnetic strips are deposited on the both edges of the silicene nanoribbon and an electric field is perpendicularly applied to the nanoribbon plane. The spin polarization is studied for both parallel and anti-parallel configurations of exchange magnetic fields induced by the ferromagnetic strips. We find that complete spin polarization can take place in the presence of perpendicular electric field for anti-parallel configuration and the nanoribbon can work as a perfect spin filter. Themore » spin direction of transmitted electrons can be easily changed from up to down and vice versa by reversing the electric field direction. For parallel configuration, perfect spin filtering can occur even in the absence of electric field. In this case, the spin direction can be changed by changing the electron energy. Finally, we investigate the effects of nonmagnetic Anderson disorder on spin dependent conductance and find that the perfect spin filtering properties of nanoribbon are destroyed by strong disorder, but the nanoribbon retains these properties in the presence of weak disorder.« less

Three coordination polymers constructed from 5-(4-(tetrazol-5-yl)phenyl)isophthalic acid: Synthesis, crystal structure and properties

NASA Astrophysics Data System (ADS)

Zhai, Dandan; Sun, Wujuan; Fan, Fei; Liao, Xuzhao; Chen, Sanping; Yang, Xuwu

2017-04-01

Three new coordination polymers, namely, {[Co2(TPA)(μ3-O)3]·0.5DMA}n (1), {[Co(H2TPA)(bibp)(H2O)3]·H2O}n (2) and {[Cd3(TPA)2(phen)4]·4H2O}n (3), (H3TPA = 5-(4-(tetrazol-5-yl)phenyl)isophthalic acid, bibp = 4,4'-bis(imidazolyl)biphenyl, phen = 1,10-phenanthroline and DMA = N,N-dimethylacetamide), have been synthesized under solvothermal conditions and structurally characterized by elemental analysis, IR spectroscopy, powder X-ray diffraction (PXRD) and single-crystal X-ray diffraction analysis. Polymer 1 exhibits a three-dimensional (3D) structure constructed from 5-connected secondary building units (SBUs) [Co3(μ3-O)] and 3-connected H3TPA ligands. Polymer 2 has a 1D zigzag polymer chain connected by H3TPA and bibp ligands. Polymer 3 features an unusual 3D framework with a (3,4,2)-connected {4; 6;8}{4; 62;83} topology. Moreover, the thermal stabilities of 1-3 and photoluminescence properties of 3 have been investigated. Magnetic susceptibility measurements indicate that polymers 1-2 display antiferromagnetic exchange properties.

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.

Detecting Memory and Structure in Human Navigation Patterns Using Markov Chain Models of Varying Order

PubMed Central

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. PMID:25013937

¹⁵N, ¹³C and ¹H resonance assignments and secondary structure determination of a variable heavy domain of a heavy chain antibody.

PubMed

Prosser, Christine E; Waters, Lorna C; Muskett, Frederick W; Veverka, Vaclav; Addis, Philip W; Griffin, Laura M; Baker, Terry S; Lawson, Alastair D G; Wernery, Ulrich; Kinne, Jorg; Henry, Alistair J; Taylor, Richard J; Carr, Mark D

2014-04-01

Heavy chain antibodies differ in structure to conventional antibodies lacking both the light chain and the first heavy chain constant domain (CH1). Characteristics of the antigen-binding variable heavy domain of the heavy chain antibody (VHH) including the smaller size, high solubility and stability make them an attractive alternative to more traditional antibody fragments for detailed NMR-based structural analysis. Here we report essentially complete backbone and side chain (15)N, (13)C and (1)H assignments for a free VHH. Analysis of the backbone chemical shift data obtained indicates that the VHH is comprised predominantly of β-sheets corresponding to nearly 60% of the protein backbone.

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.

Method of repairing discontinuity in fiberglass structures

NASA Technical Reports Server (NTRS)

Gelb, L. L.; Helbert, W. B., Jr.; Enie, R. B.; Mulliken, R. F. (Inventor)

1974-01-01

Damaged fiberglass structures are repaired by substantially filling the irregular surfaced damaged area with a liquid, self-curing resin, preferably an epoxy resin mixed with chopped fiberglass, and then applying to the resin surface the first of several woven fiberglass swatches which has stitching in a zig-zag pattern parallel to each of its edges and a fringe of warp and fill glass fibers about the edges outward of the stitching. The method is especially applicable to repair of fiberglass rocket engine casings and is particularly advantageous since it restores the repaired fiberglass structure to substantially its original strength without any significant changes in the geometry or mass of the structure.

Electronic Structures of Silicene Nanoribbons: Two-Edge-Chemistry Modification and First-Principles Study.

PubMed

Yao, Yin; Liu, Anping; Bai, Jianhui; Zhang, Xuanmei; Wang, Rui

2016-12-01

In this paper, we investigate the structural and electronic properties of zigzag silicene nanoribbons (ZSiNRs) with edge-chemistry modified by H, F, OH, and O, using the ab initio density functional theory method and local spin-density approximation. Three kinds of spin polarized configurations are considered: nonspin polarization (NM), ferromagnetic spin coupling for all electrons (FM), ferromagnetic ordering along each edge, and antiparallel spin orientation between the two edges (AFM). The H, F, and OH groups modified 8-ZSiNRs have the AFM ground state. The directly edge oxidized (O1) ZSiNRs yield the same energy and band structure for NM, FM, and AFM configurations, owning to the same s p (2) hybridization. And replacing the Si atoms on the two edges with O atoms (O2) yields FM ground state. The edge-chemistry-modified ZSiNRs all exhibit metallic band structures. And the modifications introduce special edge state strongly localized at the Si atoms in the edge, except for the O1 form. The modification of the zigzag edges of silicene nanoribbons is a key issue to apply the silicene into the field effect transistors (FETs) and gives more necessity to better understand the experimental findings.

Degree of polymerization of glucan chains shapes the structure fluctuations and melting thermodynamics of a cellulose microfibril.

PubMed

Chang, Rakwoo; Gross, Adam S; Chu, Jhih-Wei

2012-07-19

A Staggered LATtice (SLAT) model is developed for modeling cellulose microfibrils. The simple representation of molecular packing and interactions employed in SLAT allows simulations of structure fluctuations and phase transition of cellulose microfibrils at sufficiently long and large scales for comparison with experiments. Glucan chains in the microfibril are modeled as connected monomers, each corresponding to a cellobiose subunit, and the surrounding space around the cellulose is composed of solvent cells. Interaction parameters of monomer-monomer interactions were parametrized based on the results of atomistic molecular dynamics simulations. The monomer-solvent interaction was optimized to give a melting temperature of ∼695 K for the 36-glucan chain model cellulose microfibril, which is consistent with the estimation based on experimental data. Monte Carlo simulations of the SLAT model also capture experimentally measured X-ray diffraction patterns of cellulose as a function of temperature, including the region of melting transition, as well as predict the highly flexible regions in the microfibril. Beyond the diameter of ∼3 nm, we found that melting temperature of the cellulose microfibril is not significantly shifted by changing the thickness. On the other hand, a slight decrease in the degree of polymerization of glucan chains is shown to enhance structure fluctuations through the ends of glucan chains, i.e., the defect sites, and thereby significantly reduce the melting temperature. Analysis of the sizes, densities, and lifetimes of defect structures in the microfibril indicates a significant extent of fluctuations on the surfaces even at room temperature and that defect statistics are strong but distinct functions of temperature and solvent quality. The SLAT model is the first of its kind for simulating cellulosic materials, and this work shows that it can be used to incorporate information obtained from atomistic simulations and experimental data to

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.

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.

Crystal structure of 2-meth-oxy-2-[(4-meth-oxy-phen-yl)sulfan-yl]-1-phenyl-ethanone.

PubMed

Caracelli, Ignez; Olivato, Paulo R; Traesel, Henrique J; Valença, Jéssica; Rodrigues, Daniel N S; Tiekink, Edward R T

2015-09-01

In the title β-thio-carbonyl compound, C16H16O3S, the adjacent meth-oxy and carbonyl O atoms are synperiplanar [the O-C-C-O torsion angle is 19.8 (4)°] and are separated by 2.582 (3) Å. The dihedral angle between the rings is 40.11 (16)°, and the meth-oxy group is coplanar with the benzene ring to which it is connected [the C-C-O-C torsion angle is 179.1 (3)°]. The most notable feature of the crystal packing is the formation of methine and methyl C-H⋯O(carbon-yl) inter-actions that lead to a supra-molecular chain with a zigzag topology along the c axis. Chains pack with no specific inter-molecular inter-actions between them.

Wavefront improvement in an end-pumped high-power Nd:YAG zigzag slab laser.

PubMed

Shin, Jae Sung; Cha, Yong-Ho; Lim, Gwon; Kim, Yonghee; Kwon, Seong-Ouk; Cha, Byung Heon; Lee, Hyeon Cheor; Kim, Sangin; Koh, Kwang Uoong; Kim, Hyun Tae

2017-08-07

Techniques for wavefront improvement in an end-pumped Nd:YAG zigzag slab laser amplifier were proposed and demonstrated experimentally. First, a study on the contact materials was conducted to improve the heat transfer between the slab and cooling blocks and to increase the cooling uniformity. Among many attempts, only the use of silicon oil showed an improvement in the wavefront. Thus, the appropriate silicone oil was applied to the amplifier as a contact material. In addition, the wavefront compensation method using a glass rod array was also applied to the amplifier. A very low wavefront distortion was obtained through the use of a silicone-oil contact and glass rod array. The variance of the optical path difference for the entire beam height was 3.87 μm at a pump power of 10.6 kW, and that for the 80% section was 1.69 μm. The output power from the oscillator was 3.88 kW, which means the maximum output extracted from the amplifier at a pump power of 10.6 kW.

Role of the constant region domain in the structural diversity of human antibody light chains.

PubMed

Hifumi, Emi; Taguchi, Hiroaki; Kato, Ryuichi; Uda, Taizo

2017-04-01

Issues regarding the structural diversity (heterogeneity) of an antibody molecule have been the subject of discussion along with the development of antibody drugs. Research on heterogeneity has been extensive in recent years, but no clear solution has been reached. Heterogeneity is also observed in catalytic antibody κ light chains (CLs). In this study, we investigated how the constant region domain of CLs concerns structural diversity because it is a simple and good example for elucidating heterogeneity. By means of cation-exchange chromatography, SDS-PAGE, and 2-dimensional electrophoresis for the CL, multimolecular forms consisting of different electrical charges and molecular sizes coexisted in the solution, resulting in the similar heterogeneity of the full length of CLs. The addition of copper ion could cause the multimolecular forms to change to monomolecular forms. Copper ion contributed greatly to the enrichment of the dimer form of CL and the homogenization of the differently charged CLs. Two molecules of the CL protein bound one copper ion. The binding affinity of the ion was 48.0 μM -1 Several divalent metal ions were examined, but only zinc showed a similar effect.-Hifumi, E., Taguchi, H., Kato, R., Uda, T. Role of the constant region domain in the structural diversity of human antibody light chains. © FASEB.

Side-chain-side-chain interactions and stability of the helical state

NASA Astrophysics Data System (ADS)

Zangi, Ronen

2014-01-01

Understanding the driving forces that lead to the stability of the secondary motifs found in proteins, namely α-helix and β-sheet, is a major goal in structural biology. The thermodynamic stability of these repetitive units is a result of a delicate balance between many factors, which in addition to the peptide chain involves also the solvent. Despite the fact that the backbones of all amino acids are the same (except of that of proline), there are large differences in the propensity of the different amino acids to promote the helical structure. In this paper, we investigate by explicit-solvent molecular dynamics simulations the role of the side chains (modeled as coarse-grained single sites) in stabilizing α helices in an aqueous solution. Our model systems include four (six-mer-nine-mer) peptide lengths in which the magnitude of the effective attraction between the side chains is systematically increased. We find that these interactions between the side chains can induce (for the nine-mer almost completely) a transition from a coil to a helical state. This transition is found to be characterized by three states in which the intermediate state is a partially folded α-helical conformation. In the absence of any interactions between the side chains the free energy change for helix formation has a small positive value indicating that favorable contributions from the side chains are necessary to stabilize the helical conformation. Thus, the helix-coil transition is controlled by the effective potentials between the side-chain residues and the magnitude of the required attraction per residue, which is on the order of the thermal energy, reduces with the length of the peptide. Surprisingly, the plots of the population of the helical state (or the change in the free energy for helix formation) as a function of the total effective interactions between the side chains in the helical state for all peptide lengths fall on the same curve.

Structured versus long-chain triglycerides: a safety, tolerance, and efficacy randomized study in colorectal surgical patients.

PubMed

Bellantone, R; Bossola, M; Carriero, C; Malerba, M; Nucera, P; Ratto, C; Crucitti, P; Pacelli, F; Doglietto, G B; Crucitti, F

1999-01-01

After trauma or surgery, researchers have suggested that medium-chain triglycerides have metabolic advantages, although they are toxic in large doses. To try to reduce this potential toxicity, structured lipids, which provide a higher oxidation rate, faster clearance from blood, improved nitrogen balance, and less accumulation in the reticuloendothelial system, could be used. Therefore, we evaluated, through a blind randomized study, the safety, tolerance, and efficacy of structured triglycerides, compared with long-chain triglycerides (LCT), in patients undergoing colorectal surgery. Nineteen patients were randomized to receive long-chain or structured triglycerides as a lipid source. They received the same amount of calories (27.2/kg/d), glucose (4 g/kg/d), protein (0.2 g/kg/d), and lipids (11.2 kcal/kg/d). Patients were evaluated during and after the treatment for clinical and laboratory variables, daily and cumulative nitrogen balance, urinary excretion of 3-methyl-histidine, and urinary 3-methylhistidine/creatinine ratio. No adverse effect that required the interruption of the treatment was observed. Triglyceride levels and clinical and laboratory variables were similar in the two groups. A predominantly positive nitrogen balance was observed from day 2 until day 5 in the LCT group and from day 1 until day 4 in the structured triglycerides group. The cumulative nitrogen balance (in grams) for days 1 to 3 was 9.7+/-5.2 in the experimental group and 4.4+/-11.8 in the control group (p = .2). For days 1 to 5 it was 10.7+/-10.5 and 6.5+/-17.9 (p = .05), respectively. The excretion of 3-methylhistidine was higher in the control group but decreased in the following days and was similar to the experimental group on day 5. This study represents the first report in which structured triglycerides are administered in postoperative patients to evaluate safety, tolerance, and efficacy. It suggests that Fe73403 is safe, well tolerated, and efficacious in terms of nitrogen

Structural diversity and electronic properties in potassium silicides

NASA Astrophysics Data System (ADS)

Hao, Chun-Mei; Li, Yunguo; Huang, Hong-Mei; Li, Yan-Ling

2018-05-01

Stable potassium silicides in the complete compositional landscape were systematically explored up to 30 GPa using the variable-composition evolutionary structure prediction method. The results show that K4Si, K3Si, K5Si2, K2Si, K3Si2, KSi, KSi2, KSi3, and K8Si46 have their stability fields in the phase diagram. The spatial dimensional diversity of polymerized silicon atoms (0D "isolated" anion, dimer, Si4 group, 1D zigzag chain, 2D layer, and 3D network) under the potassium sublattice was uncovered as silicon content increases. Especially, the 2D layered silicon presents interestingly a variety of shapes, such as the "4 + 6" ring, "4 + 8"ring, and 8-membered ring. K-Si bonding exhibits a mixed covalency and ionicity, while Si-Si bonding is always of covalent character. Semiconductivity or metallicity mainly depends on the form of sublattices and K:Si ratio, which allows us to find more semiconductors in the Si-rich side when closed-shell K cations are encompassed by polymerized Si. The semiconducting silicides present strong absorption in the infrared and visible light range. These findings open up the avenue for experimental synthesis of alkali metal-IVA compounds and potential applications as battery electrode materials or photoelectric materials.

Role of antennary structure of N-linked sugar chains in renal handling of recombinant human erythropoietin.

PubMed

Misaizu, T; Matsuki, S; Strickland, T W; Takeuchi, M; Kobata, A; Takasaki, S

1995-12-01

To elucidate the role of the branched structure of sugar chains of human erythropoietin (EPO) in the expression of in vivo activity, the pharmacokinetic profile of a less active recombinant human EPO sample (EPO-bi) enriched with biantennary sugar chains was compared with that of a highly active control EPO sample enriched with tetraantennary sugar chains. After an intravenous injection in rats, 125I-EPO-bi disappeared from the plasma with 3.2 times greater total body clearance (Cltot) than control 125I-EPO. Whole-body autoradiography after 20 minutes of administration indicated that the overall distribution of radioactivity is similar, but 125I-EPO-bi showed a higher level of radioactivity in the kidneys than control 125I-EPO. Quantitative determination of radioactivity in the tissues also indicated that radioactivity of 125I-EPO-bi in the kidneys was two times higher than that of control 125I-EPO. The difference in plasma disappearance between 125I-EPO-bi and control 125I-EPO was not observed in bilaterally nephrectomized rats. The distribution of 125I-EPO-bi to bone marrow and spleen was similarly inhibited by simultaneous injection of excess amounts of either the nonlabeled EPO-bi or control EPO. These results indicate that the low in vivo biologic activity of EPO-bi results from rapid clearance from the systemic circulation by renal handling. Thus, the well-branched structure of the N-linked sugar chain of EPO is suggested to play an important role in maintaining its higher plasma level, which guarantees an effective transfer to target organs and stimulation of erythroid progenitor cells.

Electronic and transport properties of zigzag carbon nanotubes with the presence of periodical antidot and boron/nitride doping defects

NASA Astrophysics Data System (ADS)

Zoghi, Milad; Yazdanpanah Goharrizi, Arash; Mirjalili, Seyed Mohammad; Kabir, M. Z.

2018-06-01

Electronic and transport properties of Carbon nanotubes (CNTs) are affected by the presence of physical or chemical defects in their structures. In this paper, we present novel platforms of defected zigzag CNTs (Z-CNTs) in which two topologies of antidot and Boron/Nitride (BN) doping defects are periodically imposed throughout the length of perfect tubes. Using the tight binding model and the non-equilibrium Green’s function method, it is realized that the quantum confinement of Z-CNTs is modified by the presence of such defects. This new quantum confinement results in the appearance of mini bands and mini gaps in the transmission spectra, as well as a modified band structure and band gap size. The modified band gap could be either larger or smaller than the intrinsic band gap of a perfect tube, which is determined by the category of Z-CNT. The in-depth analysis shows that the size of the modified band gap is the function of several factors consisting of: the radii of tube (D r), the distance between adjacent defects (d d), the utilized defect topology, and the kind of defect (antidot or BN doping). Furthermore, taking advantage of the tunable band gap size of Z-CNT with the presence of periodical defects, new platforms of defect-based Z-CNT resonant tunneling diode (RTD) are proposed for the first time. Our calculations demonstrate the apparition of resonances in transmission spectra and the negative differential resistance in the I-V characteristics for such RTD platforms.

Structure-based design and mechanisms of allosteric inhibitors for mitochondrial branched-chain α-ketoacid dehydrogenase kinase

PubMed Central

Qi, Xiangbing; Gui, Wen-Jun; Morlock, Lorraine K.; Wallace, Amy L.; Ahmed, Kamran; Laxman, Sunil; Campeau, Philippe M.; Lee, Brendan H.; Hutson, Susan M.; Tu, Benjamin P.; Williams, Noelle S.; Tambar, Uttam K.; Wynn, R. Max; Chuang, David T.

2013-01-01

The branched-chain amino acids (BCAAs) leucine, isoleucine, and valine are elevated in maple syrup urine disease, heart failure, obesity, and type 2 diabetes. BCAA homeostasis is controlled by the mitochondrial branched-chain α-ketoacid dehydrogenase complex (BCKDC), which is negatively regulated by the specific BCKD kinase (BDK). Here, we used structure-based design to develop a BDK inhibitor, (S)-α-chloro-phenylpropionic acid [(S)-CPP]. Crystal structures of the BDK-(S)-CPP complex show that (S)-CPP binds to a unique allosteric site in the N-terminal domain, triggering helix movements in BDK. These conformational changes are communicated to the lipoyl-binding pocket, which nullifies BDK activity by blocking its binding to the BCKDC core. Administration of (S)-CPP to mice leads to the full activation and dephosphorylation of BCKDC with significant reduction in plasma BCAA concentrations. The results buttress the concept of targeting mitochondrial BDK as a pharmacological approach to mitigate BCAA accumulation in metabolic diseases and heart failure. PMID:23716694

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

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.

Structural analysis of poly-SUMO chain recognition by the RNF4-SIMs domain.

PubMed

Kung, Camy C-H; Naik, Mandar T; Wang, Szu-Huan; Shih, Hsiu-Ming; Chang, Che-Chang; Lin, Li-Ying; Chen, Chia-Lin; Ma, Che; Chang, Chi-Fon; Huang, Tai-Huang

2014-08-15

The E3 ubiquitin ligase RNF4 (RING finger protein 4) contains four tandem SIM [SUMO (small ubiquitin-like modifier)-interaction motif] repeats for selective interaction with poly-SUMO-modified proteins, which it targets for degradation. We employed a multi-faceted approach to characterize the structure of the RNF4-SIMs domain and the tetra-SUMO2 chain to elucidate the interaction between them. In solution, the SIM domain was intrinsically disordered and the linkers of the tetra-SUMO2 were highly flexible. Individual SIMs of the RNF4-SIMs domains bind to SUMO2 in the groove between the β2-strand and the α1-helix parallel to the β2-strand. SIM2 and SIM3 bound to SUMO with a high affinity and together constituted the recognition module necessary for SUMO binding. SIM4 alone bound to SUMO with low affinity; however, its contribution to tetra-SUMO2 binding avidity is comparable with that of SIM3 when in the RNF4-SIMs domain. The SAXS data of the tetra-SUMO2-RNF4-SIMs domain complex indicate that it exists as an ordered structure. The HADDOCK model showed that the tandem RNF4-SIMs domain bound antiparallel to the tetra-SUMO2 chain orientation and wrapped around the SUMO protamers in a superhelical turn without imposing steric hindrance on either molecule.

Chemical scissors cut phosphorene nanostructures

NASA Astrophysics Data System (ADS)

Peng, Xihong; Wei, Qun

2014-12-01

Phosphorene, a recently fabricated two-dimensional puckered honeycomb structure of phosphorus, showed promising properties for applications in nano-electronics. In this work, we report a chemical scissors effect on phosphorene, using first-principles method. It was found that chemical species, such as H, OH, F, and Cl, can act as scissors to cut phosphorene. Phosphorus nanochains and nanoribbons can be obtained. The scissors effect results from the strong bonding between the chemical species and phosphorus atoms. Other species such as O, S and Se fail to cut phosphorene nanostructures due to their weak bonding with phosphorus. The electronic structures of the produced P-chains reveal that the hydrogenated chain is an insulator while the pristine chain is a one-dimensional Dirac material, in which the charge carriers are massless fermions travelling at an effective speed of light ˜8 × 105 m s-1. The obtained zigzag phosphorene nanoribbons show either metallic or semiconducting behaviors, depending on the treatment of the edge phosphorus atoms.

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. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

Six complexes based on bis(imidazole/benzimidazole-1-yl)pyridazine ligands: Syntheses, structures and properties

NASA Astrophysics Data System (ADS)

Wang, Xin-Fang; Du, Ceng-Ceng; Zhou, Sheng-Bin; Wang, Duo-Zhi

2017-01-01

Herein we reported six new Ni(II)/Cu(II)/Zn(II) complexes, namely, [Ni(L1)4(OH)2] (1), [Cu(L1)4(OH)2] (2), [Cu(L1)2(SiF6)]n (3), {[Cu(L2)(HCOO)2]·H2O·CH3OH}n (4), [Ni(L2)2(NO3)2]n (5) and {[Zn(L2)Cl2]·DMF}n (6) (L1 = 3,6-bis(imidazole-1-yl)pyridazine, L2 = 3,6-bis(benzimidazole-1-yl)pyridazine), which were characterized by single-crystal X-ray diffraction, elemental analysis, IR, PXRD. These complexes have been successfully constructed under interface diffusion process, heating reflux or hydrothermal conditions. The structures of 1 and 2 are mononuclear complexes. Complex 3 exhibits a 6-connected 3D topology network with the Schläfli symbol of (412·63). In complex 4, two Cu(II) were connected through two HCOO- anions to form dinuclear structure unit, which is arranged into a 1D ladder-like structure by μ2-L2 ligands. Complexes 5 and 6 are 1D zigzag chains connected by L2 ligands, but the Ni(II) ion is six-coordinated in 5 and the Zn(II) ion is four-coordinated in 6. Moreover, the solid-state luminescence property and UV-vis diffuse reflection spectrum of complex 6 have been investigated and discussed.

New oxyfluorotellurates(IV): MTeO3F (M = FeIII, GaIII and CrIII).

PubMed

Laval, Jean Paul; Jennene Boukharrata, Nefla; Thomas, Philippe

2008-02-01

The crystal structures of the new isomorphous compounds iron(III) oxyfluorotellurate(IV), FeTeO(3)F, gallium(III) oxyfluorotellurate(IV), GaTeO(3)F, and chromium(III) oxyfluorotellurate(IV), CrTeO(3)F, consist of zigzag chains of MO(4)F(2) distorted octahedra alternately sharing O-O and F-F edges and connected via TeO(3) trigonal pyramids. A full O/F anionic ordering is observed and the electronic lone pair of the Te(IV) cation is stereochemically active.

Structured medium and long chain triglycerides show short-term increases in fat oxidation, but no changes in adiposity in men.

PubMed

Roynette, Catherine E; Rudkowska, Iwona; Nakhasi, Dilip K; Jones, Peter J H

2008-05-01

Medium chain triglycerides (MCT) have been suggested as modulators of human energy expenditure (EE) and thus may influence total and regional body fat distribution. To investigate in overweight men the effects of structured medium and long chain triglycerides on EE, substrate oxidation and body adiposity, compared to extra virgin olive oil (OO). In a 6 week single-blind crossover study, 23 overweight men were randomly assigned to consume a standard high-fat diet of which 75% total fat was provided as either structured medium and long chain triglycerides referred to as structured oil (StO), or OO. EE and body composition were measured using indirect calorimetry and magnetic resonance imaging, respectively, at weeks 1 and 6 of each phase. Body weight decreased (p<0.01) from baseline to end-point during consumption of both the StO (-1.46+/-0.4k g) and OO (-1.17+/-0.4 kg); however, no significant treatment differences were observed. There were no changes in body composition among treatment groups. No differences between diets for EE measurements were reported. Fat oxidation rates did not differ between oils, but were reduced (p<0.05) in the StO group between baseline (0.0020+/-0.0003 g/kg fat free mass per min) in comparison to after week 6 (0.0013+/-0.0001 g/kg fat free mass per min). No differences in carbohydrate oxidation rate were noted across diets or time. The present structured medium and long chain triglyceride oil increases short-term fat oxidation but fails to modulate body weight or adiposity through a change in EE.

Influence of alkyl chain length compatibility on microemulsion structure and solubilization

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

Bansal, V.K.; O'Connell, J.P.; Shah, D.O.

1980-06-01

The water solubilization capacity of water/oil microemulsions is studied as a function of alkyl chain length of oil (C/sub 8/ to C/sub 16/), surfactant (C/sub 14/ and C/sub 18/ fatty acid soaps), and alcohol (C/sub 4/ to C/sub 7/). Sodium stearate and sodium myristate were used as surfactants. For n-butanol microemulsions the maximum amount of water solubilized in the microemulsion decreased continuously with increasing oil chain length; for n-heptanol it increased continuously. For n-pentanol and n-hexanol systems, water solubilization reached a maximum when the oil chain length plus alcohol chain length was equal to that of the surfactant. The electricmore » resistance and dielectric constant of the microemulsions also are measured as a function of alkyl chain length of the oil. 48 references.« less

Structure of a short-chain dehydrogenase/reductase (SDR) within a genomic island from a clinical strain of Acinetobacter baumannii

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

Shah, Bhumika S., E-mail: bhumika.shah@mq.edu.au; Tetu, Sasha G.; Harrop, Stephen J.

2014-09-25

The structure of a short-chain dehydrogenase encoded within genomic islands of A. baumannii strains has been solved to 2.4 Å resolution. This classical SDR incorporates a flexible helical subdomain. The NADP-binding site and catalytic side chains are identified. Over 15% of the genome of an Australian clinical isolate of Acinetobacter baumannii occurs within genomic islands. An uncharacterized protein encoded within one island feature common to this and other International Clone II strains has been studied by X-ray crystallography. The 2.4 Å resolution structure of SDR-WM99c reveals it to be a new member of the classical short-chain dehydrogenase/reductase (SDR) superfamily. Themore » enzyme contains a nucleotide-binding domain and, like many other SDRs, is tetrameric in form. The active site contains a catalytic tetrad (Asn117, Ser146, Tyr159 and Lys163) and water molecules occupying the presumed NADP cofactor-binding pocket. An adjacent cleft is capped by a relatively mobile helical subdomain, which is well positioned to control substrate access.« less

Modulational Instability and Quantum Discrete Breather States of Cold Bosonic Atoms in a Zig-Zag Optical Lattice

NASA Astrophysics Data System (ADS)

Chang, Xia; Xie, Jiayu; Wu, Tianle; Tang, Bing

2018-07-01

A theoretical study on modulational instability and quantum discrete breather states in a system of cold bosonic atoms in zig-zag optical lattices is presented in this work. The time-dependent Hartree approximation is employed to deal with the multiple body problem. By means of a linear stability analysis, we analytically study the modulational instability, and estimate existence conditions of the bright stationary localized solutions for different values of the second-neighbor hopping constant. On the other hand, we get analytical bright stationary localized solutions, and analyze the influence of the second-neighbor hopping on their existence conditions. The predictions of the modulational instability analysis are shown to be reliable. Using these stationary localized single-boson wave functions, the quantum breather states corresponding to the system with different types of nonlinearities are constructed.

Optimal Harvesting in a Periodic Food Chain Model with Size Structures in Predators

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

Zhang, Feng-Qin, E-mail: zhafq@263.net; Liu, Rong; Chen, Yuming, E-mail: ychen@wlu.ca

In this paper, we investigate a periodic food chain model with harvesting, where the predators have size structures and are described by first-order partial differential equations. First, we establish the existence of a unique non-negative solution by using the Banach fixed point theorem. Then, we provide optimality conditions by means of normal cone and adjoint system. Finally, we derive the existence of an optimal strategy by means of Ekeland’s variational principle. Here the objective functional represents the net economic benefit yielded from harvesting.

Effects of molecular structure on microscopic heat transport in chain polymer liquids.

PubMed

Matsubara, Hiroki; Kikugawa, Gota; Bessho, Takeshi; Yamashita, Seiji; Ohara, Taku

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 (0.7Tc) 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.

Antibody side chain conformations are position-dependent.

PubMed

Leem, Jinwoo; Georges, Guy; Shi, Jiye; Deane, Charlotte M

2018-04-01

Side chain prediction is an integral component of computational antibody design and structure prediction. Current antibody modelling tools use backbone-dependent rotamer libraries with conformations taken from general proteins. Here we present our antibody-specific rotamer library, where rotamers are binned according to their immunogenetics (IMGT) position, rather than their local backbone geometry. We find that for some amino acid types at certain positions, only a restricted number of side chain conformations are ever observed. Using this information, we are able to reduce the breadth of the rotamer sampling space. Based on our rotamer library, we built a side chain predictor, position-dependent antibody rotamer swapper (PEARS). On a blind test set of 95 antibody model structures, PEARS had the highest average χ 1 and χ1+2 accuracy (78.7% and 64.8%) compared to three leading backbone-dependent side chain predictors. Our use of IMGT position, rather than backbone ϕ/ψ, meant that PEARS was more robust to errors in the backbone of the model structure. PEARS also achieved the lowest number of side chain-side chain clashes. PEARS is freely available as a web application at http://opig.stats.ox.ac.uk/webapps/pears. © 2018 Wiley Periodicals, Inc.

SCit: web tools for protein side chain conformation analysis.

PubMed

Gautier, R; Camproux, A-C; Tufféry, P

2004-07-01

SCit is a web server providing services for protein side chain conformation analysis and side chain positioning. Specific services use the dependence of the side chain conformations on the local backbone conformation, which is described using a structural alphabet that describes the conformation of fragments of four-residue length in a limited library of structural prototypes. Based on this concept, SCit uses sets of rotameric conformations dependent on the local backbone conformation of each protein for side chain positioning and the identification of side chains with unlikely conformations. The SCit web server is accessible at http://bioserv.rpbs.jussieu.fr/SCit.

SCit: web tools for protein side chain conformation analysis

PubMed Central

Gautier, R.; Camproux, A.-C.; Tufféry, P.

2004-01-01

SCit is a web server providing services for protein side chain conformation analysis and side chain positioning. Specific services use the dependence of the side chain conformations on the local backbone conformation, which is described using a structural alphabet that describes the conformation of fragments of four-residue length in a limited library of structural prototypes. Based on this concept, SCit uses sets of rotameric conformations dependent on the local backbone conformation of each protein for side chain positioning and the identification of side chains with unlikely conformations. The SCit web server is accessible at http://bioserv.rpbs.jussieu.fr/SCit. PMID:15215438

Crystal structure of N-de­acetyl­lappa­coni­tine

PubMed Central

Shi, Xin-Wei; Lu, Qiang-Qiang; Zhou, Jun-Hui; Cui, Xin-Ai

2015-01-01

The title compound, C30H42N2O7 [systematic name: (1S,4S,5S,7S,8S,9S,10S,11S,13R,14S,16S,17R)-20-ethyl-4,8,9-trihy­droxy-1,14,16-tri­meth­oxy­aconitan-4-yl 2-amino­benzoate], isolated from roots of Aconitum sinomontanum Nakai, is a typical aconitane-type C19-diterpenoid alkaloid, which crystallizes with two independent mol­ecules in the asymmetric unit. The conformations of the two independent mol­ecules are closely similar. Each mol­ecule comprises four six-membered rings (A, B, D and E) including one six-membered N-containing heterocyclic ring (E), and two five-membered rings (C and F). Rings A, B and E adopt chair conformations, while ring D displays a boat conformation. Five-membered rings C and F exhibit envelope conformations. IntramolecularN—H⋯O hydrogen bonds between the amino group and carbonyl O atom help to stabilize molecular structure. In the crystal, O—H⋯O hydrogen bonds link the mol­ecules into zigzag chains propagating in [010]. PMID:26396805

Peppytides: Interactive Models of Polypeptide Chains

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

Zuckermann, Ron; Chakraborty, Promita; Derisi, Joe

2014-01-21

Peppytides are scaled, 3D-printed models of polypeptide chains that can be folded into accurate protein structures. Designed and created by Berkeley Lab Researcher, Promita Chakraborty, and Berkeley Lab Senior Scientist, Dr. Ron Zuckermann, Peppytides are accurate physical models of polypeptide chains that anyone can interact with and fold intro various protein structures - proving to be a great educational tool, resulting in a deeper understanding of these fascinating structures and how they function. Build your own Peppytide model and learn about how nature's machines fold into their intricate architectures!

Peppytides: Interactive Models of Polypeptide Chains

ScienceCinema

Zuckermann, Ron; Chakraborty, Promita; Derisi, Joe

2018-06-08

Peppytides are scaled, 3D-printed models of polypeptide chains that can be folded into accurate protein structures. Designed and created by Berkeley Lab Researcher, Promita Chakraborty, and Berkeley Lab Senior Scientist, Dr. Ron Zuckermann, Peppytides are accurate physical models of polypeptide chains that anyone can interact with and fold intro various protein structures - proving to be a great educational tool, resulting in a deeper understanding of these fascinating structures and how they function. Build your own Peppytide model and learn about how nature's machines fold into their intricate architectures!

Confinement dynamics of a semiflexible chain inside nano-spheres

NASA Astrophysics Data System (ADS)

Fathizadeh, A.; Heidari, Maziar; Eslami-Mossallam, B.; Ejtehadi, M. R.

2013-07-01

We study the conformations of a semiflexible chain, confined in nano-scaled spherical cavities, under two distinct processes of confinement. Radial contraction and packaging are employed as two confining procedures. The former method is performed by gradually decreasing the diameter of a spherical shell which envelopes a confined chain. The latter procedure is carried out by injecting the chain inside a spherical shell through a hole on the shell surface. The chain is modeled with a rigid body molecular dynamics simulation and its parameters are adjusted to DNA base-pair elasticity. Directional order parameter is employed to analyze and compare the confined chain and the conformations of the chain for two different sizes of the spheres are studied in both procedures. It is shown that for the confined chains in the sphere sizes of our study, they appear in spiral or tennis-ball structures, and the tennis-ball structure is more likely to be observed in more compact confinements. Our results also show that the dynamical procedure of confinement and the rate of the confinement are influential parameters of the structure of the chain inside spherical cavities.

Quantum conductance oscillation in linear monatomic silicon chains

NASA Astrophysics Data System (ADS)

Liu, Fu-Ti; Cheng, Yan; Yang, Fu-Bin; Chen, Xiang-Rong

2014-02-01

The conductance of linear silicon atomic chains with n=1-8 atoms sandwiched between Au electrodes is investigated by using the density functional theory combined with non-equilibrium Green's function. The results show that the conductance oscillates with a period of two atoms as the number of atoms in the chain is varied. We optimize the geometric structure of nanoscale junctions in different distances, and obtain that the average bond-length of silicon atoms in each chain at equilibrium positions is 2.15±0.03 Å. The oscillation of average Si-Si bond-length can explain the conductance oscillation from the geometric structure of atomic chains. We calculate the transmission spectrum of the chains in the equilibrium positions, and explain the conductance oscillation from the electronic structure. The transport channel is mainly contributed by px and py orbital electrons of silicon atoms. The even-odd oscillation is robust under external voltage up to 1.2 V.

Folding of polyglutamine chains

NASA Astrophysics Data System (ADS)

Chopra, Manan; Reddy, Allam S.; Abbott, N. L.; de Pablo, J. J.

2008-10-01

Long polyglutamine chains have been associated with a number of neurodegenerative diseases. These include Huntington's disease, where expanded polyglutamine (PolyQ) sequences longer than 36 residues are correlated with the onset of symptoms. In this paper we study the folding pathway of a 54-residue PolyQ chain into a β-helical structure. Transition path sampling Monte Carlo simulations are used to generate unbiased reactive pathways between unfolded configurations and the folded β-helical structure of the polyglutamine chain. The folding process is examined in both explicit water and an implicit solvent. Both models reveal that the formation of a few critical contacts is necessary and sufficient for the molecule to fold. Once the primary contacts are formed, the fate of the protein is sealed and it is largely committed to fold. We find that, consistent with emerging hypotheses about PolyQ aggregation, a stable β-helical structure could serve as the nucleus for subsequent polymerization of amyloid fibrils. Our results indicate that PolyQ sequences shorter than 36 residues cannot form that nucleus, and it is also shown that specific mutations inferred from an analysis of the simulated folding pathway exacerbate its stability.

Synthesis, Crystal Structure, and Magnetic Properties of the Linear-Chain Cobalt Oxide Sr 5Pb 3CoO 12

NASA Astrophysics Data System (ADS)

Yamaura, K.; Huang, Q.; Takayama-Muromachi, E.

2002-02-01

The novel spin-chain cobalt oxide Sr5Pb3CoO12 [Poverline6×2m, a=10.1093(2) Å and c=3.562 51(9) Å at 295 K] is reported. A polycrystalline sample of the compound was studied by neutron diffraction (at 6 and 295 K) and magnetic susceptibility measurements (5 to 390 K). The cobalt oxide was found to be analogous to the copper oxide Sr5Pb3CuO12, which is comprised of magnetic-linear chains at an interchain distance of 10 Å. Although the cobalt oxide chains (μeff of 3.64 μB per Co) are substantially antiferromagnetic (θW=-38.8 K), neither low-dimensional magnetism nor long-range ordering has been found; a local-structure disorder in the chains might have an impact on the magnetism. This compound is highly electrically insulating.

Structure of gel phase saturated lecithin bilayers: temperature and chain length dependence.

PubMed Central

Sun, W J; Tristram-Nagle, S; Suter, R M; Nagle, J F

1996-01-01

Systematic low-angle and wide-angle x-ray scattering studies have been performed on fully hydrated unoriented multilamamellar vesicles of saturated lecithins with even chain lengths N = 16, 18, 20, 22, and 24 as a function of temperature T in the normal gel (L beta') phase. For all N, the area per chain Ac increases linearly with T with an average slope dAc/dT = 0.027 A2/degree C, and the lamellar D-spacings also increase linearly with an average slope dD/dT = 0.040 A/degree C. At the same T, longer chain length lecithins have more densely packed chains, i.e., smaller Ac's, than shorter chain lengths. The chain packing of longer chain lengths is found to be more distorted from hexagonal packing than that of smaller N, and the distortion epsilon of all N approaches the same value at the respective transition temperatures. The thermal volume expansion of these lipids is accounted for by the expansion in the hydrocarbon chain region. Electron density profiles are constructed using four orders of low-angle lamellar peaks. These show that most of the increase in D with increasing T is due to thickening of the bilayers that is consistent with a decrease in tilt angle theta and with little change in water spacing with either T or N. Because of the opposing effects of temperature on area per chain Ac and tilt angle 0, the area expansivity alpha A is quite small. A qualitative theoretical model based on competing head and chain interactions accounts for our results. PMID:8842227

Influence of HMW tail chains on the structural evolution of HDPE induced by second melt penetration.

PubMed

Zhu, Chun-Xia; Xia, Xiao-Chao; Huang, Yan-Hao; Xie, Dan-Dan; Chen, Rui; Yang, Ming-Bo

2017-07-21

It is widely accepted that the role of the high molecular weight (HMW) component is cooperative in shear-induced crystallization, owing to entanglements among long chains. However, this paper demonstrates that the HMW component has a novel effect on structural evolution during the process of multi-melt multi-injection molding (M 3 IM), organized as follows. First, the appropriate HDPE system with an incremental concentration of HMW tails was established. Second, the crystalline morphologies and orientation behaviors of the M 3 IM samples were characterized using a combination of scanning electron microscopy (SEM) and two-dimensional small angle X-ray scattering (2D-SAXS), and these suggested that the amount of shish-kebabs was not monotonically promoted with an increasing content of HMW tails but tended to reduce at a certain value. Third, in order to explain this phenomenon, the special temperature and shear profiles of M 3 IM were depicted subsequently, and finally the mechanism of hierarchical structure formation with the influence of various amounts of HMW tail chains was discussed, based on the classical rheological viewpoint.

First-principles investigation on structural and electronic properties of antimonene nanoribbons and nanotubes

NASA Astrophysics Data System (ADS)

Nagarajan, V.; Chandiramouli, R.

2018-03-01

The electronic properties of antimonene nanotubes and nanoribbons hydrogenated along the zigzag and armchair borders are investigated with the help of density functional theory (DFT) method. The structural stability of antimonene nanostructures is confirmed with the formation energy. The electronic properties of hydrogenated zigzag and armchair antimonene nanostructures are studied in terms of highest occupied molecular orbital (HOMO) & lowest unoccupied molecular orbital (LUMO) gap and density of states (DOS) spectrum. Moreover, due to the influence of buckled orientation, hydrogen passivation and width of antimonene nanostructures, the HOMO-LUMO gap widens in the range of 0.15-0.41 eV. The findings of the present study confirm that the electronic properties of antimonene nanostructures can be tailored with the influence of width, orientation of the edges, passivation with hydrogen and morphology of antimonene nanostructures (nanoribbons, nanotubes), which can be used as chemical sensor and for spintronic devices.

Fabrication and Optimal Design of Biodegradable Polymeric Stents for Aneurysms Treatments

PubMed Central

Han, Xue; Wu, Xia; Kelly, Michael; Chen, Xiongbiao

2017-01-01

An aneurysm is a balloon-like bulge in the wall of blood vessels, occurring in major arteries of the heart and brain. Biodegradable polymeric stent-assisted coiling is expected to be the ideal treatment of wide-neck complex aneurysms. This paper presents the development of methods to fabricate and optimally design biodegradable polymeric stents for aneurysms treatment. Firstly, a dispensing-based rapid prototyping (DBRP) system was developed to fabricate coil and zigzag structures of biodegradable polymeric stents. Then, compression testing was carried out to characterize the radial deformation of the stents fabricated with the coil or zigzag structure. The results illustrated the stent with a zigzag structure has a stronger radial stiffness than the one with a coil structure. On this basis, the stent with a zigzag structure was chosen for the development of a finite element model for simulating the real compression tests. The result showed the finite element model of biodegradable polymeric stents is acceptable within a range of radial deformation around 20%. Furthermore, the optimization of the zigzag structure was performed with ANSYS DesignXplorer, and the results indicated that the total deformation could be decreased by 35.7% by optimizing the structure parameters, which would represent a significant advance of the radial stiffness of biodegradable polymeric stents. PMID:28264515

Structured Mono- and Diacylglycerols with a High Content of Medium Chain Fatty Acids.

PubMed

Esperón-Rojas, Alaina A; Baeza-Jiménez, R; Cano-Sarmiento, Cynthia; García, Hugo S

2017-09-01

In the present work, direct enzyme-catalysed esterification of medium chain fatty acids (MCFA) from three different sources (Medium chain triacylglycerols, MCT; saponified MCT and a mixture of free MCFA) was evaluated to obtain structured mono- and diacylglycerols. The esterifications were carried out mixing the different sources of MCFA with glycerol at two weight ratios (1:1 and 4:1, w/w), using three immobilized lipases: Novozym 435, Lipozyme RM IM and Lipozyme TL IM; different reaction times (t = 0, 15, 30, 60, 120 min); enzyme loadings (5, 10 or 15% with respect to the total weight of substrates). The extent of esterification was determined by gas chromatography (GC) analysis of the acylglycerols produced. The highest incorporation of free MCFA into glycerol was obtained for a 1:1 (w/w) glycerol to free MCFA ratio, 5% of Novozym 435, at 50°C, 300 rpm, 10% of molecular sieves and a commercial MCFA mixture as starting material. Under these conditions, incorporation of at least 90% of MCFA into glycerol was achieved after 30 min of reaction.

Alignment between chain quality management and chain governance in EU pork supply chains: a Transaction-Cost-Economics perspective.

PubMed

Wever, Mark; Wognum, Nel; Trienekens, Jacques; Omta, Onno

2010-02-01

Although inter-firm coordination of quality management is increasingly important for meeting end-customer demand in agri-food chains, few researchers focus on the relation between inter-firm quality management systems (QMS) and inter-firm governance structures (GS). However, failure to align QMSs and GSs may lead to inefficiencies in quality management because of high transaction-costs. In addition, misalignment is likely to reduce the quality of end-customer products. This paper addresses this gap in research by empirically examining the relation between QMSs and GSs in pork meat supply chains. Transaction-Cost-Economic theory is used to develop propositions about the relation between three aspects of QMSs--ownership, vertical scope and scale of adoption--and the use of different types of GSs in pork meat supply chains. To validate the propositions, seven cases are examined from four different countries. The results show that the different aspects of QMSs largely relate to specific GSs used in chains in the manner predicted by the propositions. This supports the view that alignment between QMSs and GSs is important for the efficient coordination of quality management in (pork meat) supply chains.

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.

Space Survivability of Main-Chain and Side-Chain POSS-Kapton Polyimides

NASA Astrophysics Data System (ADS)

Tomczak, Sandra J.; Wright, Michael E.; Guenthner, Andrew J.; Pettys, Brian J.; Brunsvold, Amy L.; Knight, Casey; Minton, Timothy K.; Vij, Vandana; McGrath, Laura M.; Mabry, Joseph M.

2009-01-01

Kapton® polyimde (PI) is extensively used in solar arrays, spacecraft thermal blankets, and space inflatable structures. Upon exposure to atomic oxygen (AO) in low Earth orbit (LEO), Kapton® is severely degraded. An effective approach to prevent this erosion is chemically bonding polyhedral oligomeric silsesquioxane (POSS) into the polyimide matrix by copolymerization of POSS-diamine with the polyimide monomers. POSS is a silicon and oxygen cage-like structure surrounded by organic groups and can be polymerizable. The copolymerization of POSS provides Si and O in the polymer matrix on the nano level. During POSS polyimide exposure to atomic oxygen, organic material is degraded and a silica passivation layer is formed. This silica layer protects the underlying polymer from further degradation. Ground-based studies and MISSE-1 and MISSE-5 flight results have shown that POSS polyimides are resistant to atomic-oxygen attack in LEO. In fact, 3.5 wt% Si8O11 main-chain POSS polyimide eroded about 2 μm during the 3.9 year flight in LEO, whereas 32 μm of 0 wt% POSS polyimide would have eroded within 4 mos. The atomic-oxygen exposure of main-chain POSS polyimides and new side-chain POSS polyimides has shown that copolymerized POSS imparts similar AO resistance to polyimide materials regardless of POSS monomer structure.

Modification of the band offset in boronitrene

NASA Astrophysics Data System (ADS)

Obodo, K. O.; Andrew, R. C.; Chetty, N.

2011-10-01

Using density functional methods within the generalized gradient approximation implemented in the Quantum Espresso codes, we modify the band offset in a single layer of boronitrene by substituting a double line of carbon atoms. This effectively introduces a line of dipoles at the interface. We considered various junctions of this system within the zigzag and armchair orientations. Our results show that the “zigzag-short” structure is energetically most stable, with a formation energy of 0.502 eV and with a band offset of 1.51 eV. The “zigzag-long” structure has a band offset of 1.99 eV. The armchair structures are nonpolar, while the zigzag-single structures show a charge accumulation for the C-substituted B and charge depletion for the C-substituted N at the junction. Consequently there is no shifting of the bands.

Magneto-electronic properties of graphene nanoribbons with various edge structures passivated by phosphorus and hydrogen atoms.

PubMed

Yu, Z L; Wang, D; Zhu, Z; Zhang, Z H

2015-10-07

The electronic and magnetic structures of graphene nanoribbons (GNRs) with various edge structures passivated by P atoms are investigated systematically, and compared with H passivation as well. GNRs with the entire reconstructed Klein edge or armchair edge are found to be nonmagnetic regardless of P or H passivation. However, if the edge of GNRs is a mixture of zigzag edge and reconstructed Klein edge, they are nonmagnetic for H passivation but significantly magnetic for P passivation, which could be attributed to the "charge transfer doping" effect. And the corresponding magnetic device shows a noticeable negative differential resistance phenomenon and an excellent spin filtering effect under AP configuration, which originate from the special energy band structure. The GNRs with zigzag edge, reconstructed Klein edge, or mixed edge shapes are all metals in the nonmagnetic state regardless of the H or P atoms involved. The relationship between the energy gap and the width in armchair-edged GNRs by P passivation with a dimer structure also satisfies the 3p periodicity, but different in detail from the case of H passivation. The calculated edge formation energy indicates that P-passivated GNRs are energetically more favorable, suggesting that they can stably exist in the experiment.

Synthesis, structural analysis, and magnetic properties of ethylmalonate-manganese(II) complexes.

PubMed

Déniz, Mariadel; Pasán, Jorge; Ferrando-Soria, Jesús; Fabelo, Oscar; Cañadillas-Delgado, Laura; Yuste, Consuelo; Julve, Miguel; Cano, Joan; Ruiz-Pérez, Catalina

2011-11-07

Five manganese(II) complexes of formulas [Mn(2)(Etmal)(2)(H(2)O)(2)(L)](n) (1-4) and {[Mn(Etmal)(2)(H(2)O)][Mn(H(2)O)(4)]}(n) (5) with H(2)Etmal = ethylmalonic acid (1-5) and L = 1,2-bis(4-pyridyl)ethane (bpa) (1), 4,4'-azobispyridine (azpy) (2), 4,4'-bipyridyl (4,4'-bpy) (3), and 1,2-bis(4-pyridyl)ethylene (bpe) (4) were synthesized and structurally characterized by single crystal X-ray diffraction. Their thermal behavior and variable-temperature magnetic properties were also investigated. The structure of the compounds 1-4 consists of corrugated layers of aquamanganese(II) units with intralayer carboxylate-ethylmalonate bridges in the anti-syn (equatorial-equatorial) coordination mode which are linked through bis-monodentate bpa (1), azpy (2), 4,4'-bpy (3), and bpe (4) ligands to build up a three-dimensional (3D) framework. The structure of compound 5 is made up by zigzag chains of manganese(II) ions with a regular alternation of [Mn(H(2)O)(4)](2+) and chiral (either Δ or λ enantiomeric forms) [Mn(Etmal)(2)(H(2)O)](2-) units within each chain. In contrast to the bidentate/bis-monodentate coordination mode of the Etmal ligand in 1-4, it adopts the bidentate/monodentate coordination mode in 5 with the bridging carboxylate-ethylmalonate also exhibiting the anti-syn conformation but connecting one equatorial and an axial position from adjacent metal centers. The manganese-manganese separation through the carboxylate-ethylmalonate bridge in 1-5 vary in the range 5.3167(4)-5.5336(7) Å. These values are much shorter than those across the extended bis-monodentate N-donors in 1-4 with longest/shortest values of 11.682(3) (3)/13.9745(9) Å (4). Compounds 1-5 exhibit an overall antiferromagnetic behavior, where the exchange pathway is provided by the carboxylate-ethylmalonate bridge. Monte Carlo simulations based on the classical spin approach (1-5) were used to successfully reproduce the magnetic data of 1-5. © 2011 American Chemical Society

On Substrate for Atomic Chain Electronics

NASA Technical Reports Server (NTRS)

Yamada, Toshishige; Bauschlicher, Charles W., Jr.; Partridge, Harry; Saini, Subhash (Technical Monitor)

1998-01-01

A substrate for future atomic chain electronics, where adatoms are placed at designated positions and form atomically precise device components, is studied theoretically. The substrate has to serve as a two-dimensional template for adatom mounting with a reasonable confinement barrier and also provide electronic isolation, preventing unwanted coupling between independent adatom structures. However, the two requirements conflict. For excellent electronic isolation, we may seek adatom confinement via van der Waals interaction without chemical bonding to the substrate atoms, but the confinement turns out to be very weak and hence unsatisfactory. An alternative chemical bonding scheme with excellent structural strength is examined, but even fundamental adatom chain properties such as whether chains are semiconducting or metallic are strongly influenced by the nature of the chemical bonding, and electronic isolation is not always achieved. Conditions for obtaining semiconducting chains with well-localized surface-modes, leading to good isolation, are clarified and discussed.

Experimental observation of boron nitride chains.

PubMed

Cretu, Ovidiu; Komsa, Hannu-Pekka; Lehtinen, Ossi; Algara-Siller, Gerardo; Kaiser, Ute; Suenaga, Kazu; Krasheninnikov, Arkady V

2014-12-23

We report the formation and characterization of boron nitride atomic chains. The chains were made from hexagonal boron nitride sheets using the electron beam inside a transmission electron microscope. We find that the stability and lifetime of the chains are significantly improved when they are supported by another boron nitride layer. With the help of first-principles calculations, we prove the heteroatomic structure of the chains and determine their mechanical and electronic properties. Our study completes the analogy between various boron nitride and carbon polymorphs, in accordance with earlier theoretical predictions.

Motion of spin label side chains in cellular retinol-binding protein: correlation with structure and nearest-neighbor interactions in an antiparallel beta-sheet.

PubMed

Lietzow, Michael A; Hubbell, Wayne L

2004-03-23

A goal in the development of site-directed spin labeling in proteins is to correlate the motion of a nitroxide side chain with local structure, interactions, and dynamics. Significant progress toward this goal has been made using alpha-helical proteins of known structure, and the present study is the first step in a similar exploration of a beta-sheet protein, cellular retinol-binding protein (CRBP). Nitroxide side chains were introduced along both interior and edge strands. At sites in interior strands, the side-chain motion is strongly influenced by interactions with side chains of neighboring strands, giving rise to a rich variety of dynamic modes (weakly ordered, strongly ordered, immobilized) and complex electron paramagnetic resonance spectra that are modulated by strand twist. The interactions giving rise to the dynamic modes are explored using mutagenesis, and the results demonstrate the particular importance of the non-hydrogen-bonded neighbor residue in giving rise to highly ordered states. Along edge strands of the beta-sheet, the motion of the side chain is simple and weakly ordered, resembling that at solvent-exposed surfaces of an alpha-helix. A simple working model is proposed that can account for the wide variety of dynamic modes encountered. Collectively, the results suggest that the nitroxide side chain is an effective probe of side-chain interactions, and that site-directed spin labeling should be a powerful means of monitoring conformational changes that involve changes in beta-sheet topology.

Influence of chain topology on polymer crystallization: poly(ethylene oxide) (PEO) rings vs. linear chains.

PubMed

Zardalidis, George; Mars, Julian; Allgaier, Jürgen; Mezger, Markus; Richter, Dieter; Floudas, George

2016-10-04

The absence of entanglements, the more compact structure and the faster diffusion in melts of cyclic poly(ethylene oxide) (PEO) chains have consequences on their crystallization behavior at the lamellar and spherulitic length scales. Rings with molecular weight below the entanglement molecular weight (M < M e ), attain the equilibrium configuration composed from twice-folded chains with a lamellar periodicity that is half of the corresponding linear chains. Rings with M > M e undergo distinct step-like conformational changes to a crystalline lamellar with the equilibrium configuration. Rings melt from this configuration in the absence of crystal thickening in sharp contrast to linear chains. In general, rings more easily attain their extended equilibrium configuration due to strained segments and the absence of entanglements. In addition, rings have a higher equilibrium melting temperature. At the level of the spherulitic superstructure, growth rates are much faster for rings reflecting the faster diffusion and more compact structure. With respect to the segmental dynamics in their semi-crystalline state, ring PEOs with a steepness index of ∼34 form some of the "strongest" glasses.

Action-derived molecular dynamics simulations for the migration and coalescence of vacancies in graphene and carbon nanotubes.

PubMed

Lee, Alex Taekyung; Ryu, Byungki; Lee, In-Ho; Chang, K J

2014-03-19

We report the results of action-derived molecular dynamics simulations for the migration and coalescence processes of monovacancies in graphene and carbon nanotubes with different chiralities. In carbon nanotubes, the migration pathways and barriers of a monovacancy depend on the tube chirality, while there is no preferential pathway in graphene due to the lattice symmetry and the absence of the curvature effect. The probable pathway changes from the axial to circumferential direction as the chirality varies from armchair to zigzag. The chirality dependence is attributed to the preferential orientation of the reconstructed bond formed around each vacancy site. It is energetically more favourable for two monovacancies to coalesce into a divacancy via alternative movements rather than simultaneous movements. The energy barriers for coalescence are generally determined by the migration barrier for the monovacancy, although there are some variations due to interactions between two diffusing vacancies. In graphene and armchair nanotubes, two monovacancies prefer to migrate along different zigzag atomic chains rather than a single atomic chain connecting these vacancies. On the other hand, in zigzag tubes, the energy barrier for coalescence increases significantly unless monovacancies lie on the same circumference.

Structural and Electronic Properties of α2-Graphyne Nanotubes: A Density Functional Theory Study

NASA Astrophysics Data System (ADS)

Majidi, Roya

2018-02-01

Another form of carbon-based two-dimensional material in the graphene family, named the α2-graphyne sheet, was predicted very recently. The α2-graphyne sheet was created by doubling each acetylenic linker in an α-graphyne sheet. It exhibited semimetallic Dirac point features similar to graphene and α-graphyne sheets. In the present work, single -walled carbon nanotubes based on an α2-graphyne sheet was introduced. The structural and electronic properties of these nanotubes were studied using density functional theory. It was found that armchair α2-graphyne nanotubes showed metallic behavior, while zigzag α2-graphyne nanotubes were found to have semiconducting or metallic properties depending on tube size. The energy band gap of zigzag α2-graphyne nanotubes decreased with increasing tube diameter. The results indicated that the α2-graphyne sheet and its nanotubes can be proper materials for future nanoelectronics.

Syntheses, structures and properties of four 3D microporous lanthanide coordination polymers based on 3,5-pyrazoledicarboxylate and oxalate ligands

NASA Astrophysics Data System (ADS)

Song, Juan; Wang, Ji-Jiang; Hu, Huai-Ming; Wu, Qing-Ran; Xie, Juan; Dong, Fa-Xin; Yang, Meng-Lin; Xue, Gang-Lin

2014-04-01

Four three-dimensional lanthanide coordination polymers with reversible structural interconversions, [Ln2(Hpdc)2(C2O4)(H2O)4]n·2nH2O [Ln=Sm (1), Eu (2), Tb (3) and Dy (4)], have been synthesized by hydrothermal reactions of lanthanide nitrates with 3,5-pyrazoledicarboxylic (H3pdc) and oxalic acids. It is noteworthy that there is an in situ reaction in 1, in which H3pdc was decomposed into (ox)2- with Cu(II)-Sm(III) synergistic effect under hydrothermal conditions. These compounds are isostructural and crystallized in the monoclinic P21/c space group. The Ln(III) ions are eight-coordinated with dodecahedron coordination geometry. These polyhedra are linked by oxalate groups to form 1D zigzag chain, which are further connected by 3,5-pyrazoledicarboxylate to extend similar 3D frameworks with channels along c-axis in 1-4. These coordination polymers display the characteristic emission bands of the Ln(III) ions in the solid state and possess good thermal stabilities.

A comparison of the thermal and hydraulic performances between miniature pin fin heat sink and microchannel heat sink with zigzag flow channel together with using nanofluids

NASA Astrophysics Data System (ADS)

Duangthongsuk, Weerapun; Wongwises, Somchai

2018-05-01

In this study, a comparison of the convective heat transfer, pressure drop, and performance index characteristics of heat sinks with a miniature circular pin-fin inline arrangement (MCFHS) and a zigzag flow channel with single cross-cut structures (CCZ-HS) is presented. SiO2-water nanofluids with different particle concentrations are used as the coolant. The effects of the heat sink type, particle concentration and fluid flow rate on the thermal and hydraulic performances are evaluated. The testing conditions are performed at the wall heat fluxes of 10 to 60 kW/m2 and at a mass flow rate ranging from 0.18 to 0.6 kg/s. The dimension of heat sinks is equally designed at 28 × 33 mm. The heat transfer area of MCFHS and of CCZ-HS is 1430 and 1238 mm2, respectively. Similarly, the hydraulic diameter of the flow channel of MCFHS and of CCZ-HS is 1.2 and 1.0 mm, respectively. The measured data indicate that the cooling performances of CCZ-HS are about 24-55% greater than that of MCFHS. The effects of the channel diameter and single cross-cut of the flow channel are more dominant than the effects of the fin structure and heat transfer area.

Structured triglycerides were well tolerated and induced increased whole body fat oxidation compared with long-chain triglycerides in postoperative patients.

PubMed

Sandström, R; Hyltander, A; Körner, U; Lundholm, K

1995-01-01

It has been proposed, on the basis of animal experiments, that medium-chain triglycerides (MCT) may exert more favorable effects on whole body metabolism of injured animals than long-chain triglycerides (LCT). Therefore, the present study was designed to evaluate whether structured triglycerides are associated with increased whole body fat oxidation without promotion of ketogenesis in postoperative patients. A structured lipid emulsion (73403 Pharmacia, Sweden) containing medium- and long-chain fatty acids, esterified randomly to glycerol in a triglyceride structure, was used. Whole body fat oxidation was determined by indirect calorimetry in the postoperative period. Patients were randomized to receive structured lipids 1 day followed by LCT (Intralipid, Pharmacia) the next day or vice versa during 6 postoperative days. In part 1 of the study patients received fat at 1.0 g/kg per day in the presence of 80% of the basal requirement of nonprotein calories. In part 2 patients received fat at 1.5 g/kg per day in the presence of 120% of the nonprotein caloric requirement. Amino acids were always provided at 0.15 g N/kg per day. Structured lipids were not associated with any side effects, were rapidly cleared from the plasma compartment, and were rapidly oxidized without any significant hyperlipidemia or ketosis. Provision of structured lipids in the presence of excess of nonprotein calories (part 2) caused a significantly higher whole body fat oxidation (2.4 +/- 0.05 g/kg per day) compared with LCT provision (1.9 +/- 0.06 g/kg per day) (p < .0001) examined in the same patients. The results demonstrated for the first time in man that provision of structured triglycerides were associated with increased whole body fat oxidation in stressed postoperative patients, which is in line with the original metabolic and biochemical concept for structured triglycerides. The study provided evidence to support that structured lipids may represent a next generation of IV fat emulsions

Stability of suspended gold and silver alloy monatomic chains

NASA Astrophysics Data System (ADS)

Fa, Wei; Dong, Jinming

2008-06-01

Using the first-principles plane wave pseudopotential method, we have studied the structures and stability of gold and silver alloy monatomic chains. It is found that minimizing system's enthalpy instead of its energy is critical to identify the stability of stretched alloy chains at zero temperature since the string tension can efficiently suppress the self-purification. Our simulations show that all the gold-containing chains do exhibit a local enthalpy minimum, giving a reasonable interpretation for the experimental observations of gold and silver alloy chains with different Ag concentrations [Bettini et al., Nat. Nanotechnol. 1, 182 (2006)]. These alloy chains are stabilized by the combined actions of the gold's relativistic effect and the string tension applied by the tip contacts, having similar geometrical structures to those of the pure gold chains.

Dynamical ion transfer between coupled Coulomb crystals in a double-well potential.

PubMed

Klumpp, Andrea; Zampetaki, Alexandra; Schmelcher, Peter

2017-09-01

We investigate the nonequilibrium dynamics of coupled Coulomb crystals of different sizes trapped in a double well potential. The dynamics is induced by an instantaneous quench of the potential barrier separating the two crystals. Due to the intra- and intercrystal Coulomb interactions and the asymmetric population of the potential wells, we observe a complex reordering of ions within the two crystals as well as ion transfer processes from one well to the other. The study and analysis of the latter processes constitutes the main focus of this work. In particular, we examine the dependence of the observed ion transfers on the quench amplitude performing an analysis for different crystalline configurations ranging from one-dimensional ion chains via two-dimensional zigzag chains and ring structures to three-dimensional spherical structures. Such an analysis provides us with the means to extract the general principles governing the ion transfer dynamics and we gain some insight on the structural disorder caused by the quench of the barrier height.

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

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.

Controlled self-assembling structures of ferrocene-dipeptide conjugates composed of Ala-Pro-NHCH2CH2SH chain.

PubMed

Moriuchi, Toshiyuki; Nishiyama, Taiki; Tayano, Yoshiki; Hirao, Toshikazu

2017-12-01

Bioorganometallic ferrocene-dipeptide conjugates with the Ala-Pro-cysteamine chain, Fc-L-Ala-L-Pro-NHCH 2 CH 2 SH (2) and Fc-L-Ala-D-Pro-NHCH 2 CH 2 SH (4) (Fc=ferrocenoyl), were prepared by the reduction of the ferrocene-dipeptide conjugates, Fc-L-Ala-L-Pro-cystamine-L-Pro-L-Ala-Fc (1) or Fc-L-Ala-D-Pro-cystamine-D-Pro-L-Ala-Fc (3), respectively. Control of the self-assembling structures of the ferrocene-dipeptide conjugates was demonstrated by changing the chirality of the amino acid. The molecular structure of 2 composed of the L-Ala-L-Pro-NHCH 2 CH 2 SH chain confirmed the formation of intramolecular hydrogen bond of N-H⋯N pattern between the NH of cysteamine moiety and the nitrogen of Pro moiety. Furthermore, intermolecular hydrogen bonds between NH (Ala) and CO (Pro of another molecule) and between NH (cysteamine) and CO (the ferrocenoyl moiety of another molecule) were formed, wherein each molecule is connected to four neighboring molecules by continuous intermolecular hydrogen bonds to form the hydrogen-bonded molecular assembling structure. On the contrary, the left-handed helical assembly through an intermolecular hydrogen-bonding network of 15-membered intermolecularly hydrogen-bonded ring between NH (Ala) and CO (the ferrocenoyl moiety of another molecule) and between NH (the cysteamine moiety of another molecule) and CO (Ala) was observed in the crystal packing of 4 composed of the L-Ala-D-Pro-NHCH 2 CH 2 SH chain. Copyright © 2017 Elsevier Inc. All rights reserved.

Myosin light chains: Teaching old dogs new tricks

PubMed Central

Heissler, Sarah M; Sellers, James R

2014-01-01

The myosin holoenzyme is a multimeric protein complex consisting of heavy chains and light chains. Myosin light chains are calmodulin family members which are crucially involved in the mechanoenzymatic function of the myosin holoenzyme. This review examines the diversity of light chains within the myosin superfamily, discusses interactions between the light chain and the myosin heavy chain as well as regulatory and structural functions of the light chain as a subunit of the myosin holoenzyme. It covers aspects of the myosin light chain in the localization of the myosin holoenzyme, protein-protein interactions and light chain binding to non-myosin binding partners. Finally, this review challenges the dogma that myosin regulatory and essential light chain exclusively associate with conventional myosin heavy chains while unconventional myosin heavy chains usually associate with calmodulin. PMID:26155737

Effects of molecular structure on microscopic heat transport in chain polymer liquids

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

Matsubara, Hiroki, E-mail: matsubara@microheat.ifs.tohoku.ac.jp; Kikugawa, Gota; Ohara, Taku

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 newmore » 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.« less

Crystal structures of 5-amino-N-phenyl-3H-1,2,4-di-thia-zol-3-iminium chloride and 5-amino-N-(4-chloro-phen-yl)-3H-1,2,4-di-thia-zol-3-iminium chloride monohydrate.

PubMed

Yeo, Chien Ing; Tan, Yee Seng; Tiekink, Edward R T

2015-10-01

The crystal and mol-ecular structures of the title salt, C8H8N3S2 (+)·Cl(-), (I), and salt hydrate, C8H7ClN3S2 (+)·Cl(-)·H2O, (II), are described. The heterocyclic ring in (I) is statistically planar and forms a dihedral angle of 9.05 (12)° with the pendant phenyl ring. The comparable angle in (II) is 15.60 (12)°, indicating a greater twist in this cation. An evaluation of the bond lengths in the H2N-C-N-C-N sequence of each cation indicates significant delocalization of π-electron density over these atoms. The common feature of the crystal packing in (I) and (II) is the formation of charge-assisted amino-N-H⋯Cl(-) hydrogen bonds, leading to helical chains in (I) and zigzag chains in (II). In (I), these are linked by chains mediated by charge-assisted iminium-N(+)-H⋯Cl(-) hydrogen bonds into a three-dimensional architecture. In (II), the chains are linked into a layer by charge-assisted water-O-H⋯Cl(-) and water-O-H⋯O(water) hydrogen bonds with charge-assisted iminium-N(+)-H⋯O(water) hydrogen bonds providing the connections between the layers to generate the three-dimensional packing. In (II), the chloride anion and water mol-ecules are resolved into two proximate sites with the major component being present with a site occupancy factor of 0.9327 (18).

Bridging the gap between atomic microstructure and electronic properties of alloys: The case of (In,Ga)N

NASA Astrophysics Data System (ADS)

Chan, J. A.; Liu, J. Z.; Zunger, Alex

2010-07-01

The atomic microstructure of alloys is rarely perfectly random, instead exhibiting differently shaped precipitates, clusters, zigzag chains, etc. While it is expected that such microstructural features will affect the electronic structures (carrier localization and band gaps), theoretical studies have, until now, been restricted to investigate either perfectly random or artificial “guessed” microstructural features. In this paper, we simulate the alloy microstructures in thermodynamic equilibrium using the static Monte Carlo method and study their electronic structures explicitly using a pseudopotential supercell approach. In this way, we can bridge atomic microstructures with their electronic properties. We derive the atomic microstructures of InGaN using (i) density-functional theory total energies of ˜50 ordered structures to construct a (ii) multibody cluster expansion, including strain effects to which we have applied (iii) static Monte Carlo simulations of systems consisting of over 27000 atoms to determine the equilibrium atomic microstructures. We study two types of alloy thermodynamic behavior: (a) under lattice incoherent conditions, the formation enthalpies are positive and thus the alloy system phase-separates below the miscibility-gap temperature TMG , (b) under lattice coherent conditions, the formation enthalpies can be negative and thus the alloy system exhibits ordering tendency. The microstructure is analyzed in terms of structural motifs (e.g., zigzag chains and InnGa4-nN tetrahedral clusters). The corresponding electronic structure, calculated with the empirical pseudopotentials method, is analyzed in terms of band-edge energies and wave-function localization. We find that the disordered alloys have no electronic localization but significant hole localization, while below the miscibility gap under the incoherent conditions, In-rich precipitates lead to strong electron and hole localization and a reduction in the band gap.

A combinatorial approach to protein docking with flexible side chains.

PubMed

Althaus, Ernst; Kohlbacher, Oliver; Lenhof, Hans-Peter; Müller, Peter

2002-01-01

Rigid-body docking approaches are not sufficient to predict the structure of a protein complex from the unbound (native) structures of the two proteins. Accounting for side chain flexibility is an important step towards fully flexible protein docking. This work describes an approach that allows conformational flexibility for the side chains while keeping the protein backbone rigid. Starting from candidates created by a rigid-docking algorithm, we demangle the side chains of the docking site, thus creating reasonable approximations of the true complex structure. These structures are ranked with respect to the binding free energy. We present two new techniques for side chain demangling. Both approaches are based on a discrete representation of the side chain conformational space by the use of a rotamer library. This leads to a combinatorial optimization problem. For the solution of this problem, we propose a fast heuristic approach and an exact, albeit slower, method that uses branch-and-cut techniques. As a test set, we use the unbound structures of three proteases and the corresponding protein inhibitors. For each of the examples, the highest-ranking conformation produced was a good approximation of the true complex structure.

Linear rheology and structure of molecular bottlebrushes with short side chains

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

López-Barrón, Carlos R., E-mail: carlos.r.lopez-barron@exxonmobil.com; Brant, Patrick; Crowther, Donna J.

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,more » 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.« less

Spin-polarized electron transport in hybrid graphene-BN nanoribbons

NASA Astrophysics Data System (ADS)

Gao, Song; Lu, Wei; Zheng, Guo-Hui; Jia, Yalei; Ke, San-Huang

2017-05-01

The experimental realization of hybrid graphene and h-BN provides a new way to modify the electronic and transport properties of graphene-based materials. In this work, we investigate the spin-polarized electron transport in hybrid graphene-BN zigzag nanoribbons by performing first-principles nonequilibrium Green’s function method calculations. A 100% spin-polarized electron transport in a large energy window around the Fermi level is found and this behavior is independent of the ribbon width as long as there contain 3 zigzag carbon chains. This behavior may be useful in making perfect spin filters.

Residues with similar hexagon neighborhoods share similar side-chain conformations.

PubMed

Li, Shuai Cheng; Bu, Dongbo; Li, Ming

2012-01-01

We present in this study a new approach to code protein side-chain conformations into hexagon substructures. Classical side-chain packing methods consist of two steps: first, side-chain conformations, known as rotamers, are extracted from known protein structures as candidates for each residue; second, a searching method along with an energy function is used to resolve conflicts among residues and to optimize the combinations of side chain conformations for all residues. These methods benefit from the fact that the number of possible side-chain conformations is limited, and the rotamer candidates are readily extracted; however, these methods also suffer from the inaccuracy of energy functions. Inspired by threading and Ab Initio approaches to protein structure prediction, we propose to use hexagon substructures to implicitly capture subtle issues of energy functions. Our initial results indicate that even without guidance from an energy function, hexagon structures alone can capture side-chain conformations at an accuracy of 83.8 percent, higher than 82.6 percent by the state-of-art side-chain packing methods.

Fibrin chain cross-linking, fibrinolysis, and in vivo sealing efficacy of differently structured fibrin sealants.

PubMed

Hedrich, Hans Christian; Simunek, Manuela; Reisinger, Sonja; Ferguson, James; Gulle, Heinz; Goppelt, Andreas; Redl, Heinz

2012-08-01

In this study, we compared the sealing characteristics and efficacy of a fibrin sealant with reduced plasminogen (FS-rplg) and a fibrin sealant with aprotinin as a fibrinolysis inhibitor (FS-apr). The relevant sealing characteristics including clot structure, fibrin chain cross-linking, and clot lysis were tested in the laboratory. The sealing efficacy was then investigated in a follow-up animal model to determine differences in the in vivo sealing properties. A total of 46 animals were available for the final analysis with 23 animals in each treatment arm. In conclusion, we saw differences in vitro between FS-rplg and FS-apr in ultrastructure and α-chain cross-linking rates as well as in the rate of fibrinolysis. These differences may explain the significantly enhanced sealing efficacy in FS-apr compared to FS-rplg shown in vivo in a rabbit intestinal model. Copyright © 2012 Wiley Periodicals, Inc.

Precise Nanoelectronics with Adatom Chains

NASA Technical Reports Server (NTRS)

Yamada, Toshishige

1999-01-01

Adatom chains on an atomically regulated substrate will be building components in future precise nanoelectronics. Adatoms need to be secured with chemical bonding, but then electronic isolation between the adatom and substrate systems is not guaranteed. A one-dimensional model shows that good isolation with existence of surface states is expected on an s-p crossing substrate such as Si, Ge, or GaAs, reflecting the bulk nature of the substrate. Isolation is better if adatoms are electronically similar to the substrate atoms, and can be manipulated by hydrogenation. Chain structures with group IV adatoms with two chemical bonds, or group III adatoms with one chemical bond, are semiconducting, reflecting the surface nature of the substrate. These structures are unintentionally doped due to the charge transfer across the chemical bonds. Physical properties of adatom chains have to be determined for the unified adatom-substrate system.

Theoretical modeling of the electronic structure and exchange interactions in a Cu(II)Pc one-dimensional chain

NASA Astrophysics Data System (ADS)

Wu, Wei; Fisher, A. J.; Harrison, N. M.

2011-07-01

We calculate the electronic structure and exchange interactions in a copper(II)phthalocyanine [Cu(II)Pc] crystal as a one-dimensional molecular chain using hybrid exchange density functional theory (DFT). In addition, the intermolecular exchange interactions are also calculated in a molecular dimer using Green’s function perturbation theory (GFPT) to illustrate the underlying physics. We find that the exchange interactions depend strongly on the stacking angle, but weakly on the sliding angle (defined in the text). The hybrid DFT calculations also provide an insight into the electronic structure of the Cu(II)Pc molecular chain and demonstrate that on-site electron correlations have a significant effect on the nature of the ground state, the band gap, and magnetic excitations. The exchange interactions predicted by our DFT calculations and GFPT calculations agree qualitatively with the recent experimental results on newly found η-Cu(II)Pc and the previous results for the α and β phases. This work provides a reliable theoretical basis for the further application of Cu(II)Pc to molecular spintronics and organic-based quantum information processing.

The Synthesis and Structural Characterization of Graft Copolymers Composed of γ-PGA Backbone and Oligoesters Pendant Chains

NASA Astrophysics Data System (ADS)

Kwiecień, Iwona; Radecka, Iza; Kowalczuk, Marek; Jelonek, Katarzyna; Orchel, Arkadiusz; Adamus, Grażyna

2017-10-01

The novel copolymers composed of poly-γ-glutamic acid (γ-PGA) and oligoesters have been developed. The structures of the obtained copolymers including variety of end groups were determined at the molecular level with the aid of electrospray ionization multistage mass spectrometry (ESI-MSn). The fragmentation experiment performed for the selected sodium adducts of the copolymers confirmed that the developed methods lead to the formation of graft copolymers composed of poly-γ-glutamic acid (γ-PGA) backbone and oligoesters pendant chains. Moreover, it was established that fragmentation of selected sodium adducts of graft copolymers proceeded via random breakage of amide bonds along the backbone and ester bonds of the oligoesters pendant chains. Considering potential applications of the synthesized copolymers in the area of biomaterials, the hydrolytic degradation under laboratory conditions and in vitro cytotoxicity tests were performed. The ESI-MSn technique applied in this study has been proven to be a useful tool in structural studies of novel graft copolymers as well as their degradation products. [Figure not available: see fulltext.

Relationship between sugar chain structure and biological activity of recombinant human erythropoietin produced in Chinese hamster ovary cells.

PubMed Central

Takeuchi, M; Inoue, N; Strickland, T W; Kubota, M; Wada, M; Shimizu, R; Hoshi, S; Kozutsumi, H; Takasaki, S; Kobata, A

1989-01-01

Two forms of erythropoietin, EPO-bi and EPO-tetra, with different biological activities were isolated from the culture medium of a recombinant Chinese hamster ovary cell line, B8-300, into which the human erythropoietin gene had been introduced. EPO-bi, an unusual form, showed only one-seventh the in vivo activity and 3 times higher in vitro activity of the previously described recombinant human EPO (standard EPO). In contrast, EPO-tetra showed both in vivo and in vitro activities comparable to those of the standard EPO. EPO-bi, EPO-tetra, and the standard EPO had the same amino acid composition and immunoreactivity. However, structural analyses of their N-linked sugar chains revealed that EPO-bi contains the biantennary complex type as the major sugar chain, while EPO-tetra and the standard EPO contain the tetraantennary complex type as the major sugar chain. From examination of various preparations of recombinant human EPO, we found a positive correlation between the in vivo activity of EPO and the ratio of tetraantennary to biantennary oligosaccharides. These results suggest that higher branching of the N-linked sugar chains is essential for effective expression of in vivo biological activity of EPO. PMID:2813359

Crystal structure of carnidazole form II from synchrotron X-ray powder diffraction: structural comparison with form I, the hydrated form and the low energy conformations in vacuo.

PubMed

de Armas, Héctor Novoa; Peeters, Oswald M; Blaton, Norbert; Van den Mooter, Guy; De Ridder, Dirk J A; Schenk, Henk

2006-10-01

The crystal structure of carnidazole form II, O-methyl [2-(2-methyl-5-nitro-1H-imidazole-1-yl)ethyl]thiocarbamate, has been determined using synchrotron X-ray powder diffraction in combination with simulated annealing and whole profile pattern matching, and refined by the Rietveld method. For structure solution, 12 degrees of freedom were defined: one motion group and six torsions. Form II crystallizes in space group P2(1)/n, Z=4, with unit cell parameters after Rietveld refinement: a=13.915(4), b=8.095(2), c=10.649(3) A, beta=110.83(1) degrees, and V=1121.1(5) A3. The two polymorphic forms, as well as the hydrate, crystallize in the monoclinic space group P2(1)/n having four molecules in the cell. In form II, the molecules are held together by forming two infinite zig-zag chains via hydrogen bonds of the type N--H...N, the same pattern as in form I. A conformational study of carnidazole, at semiempirical PM3 level, was performed using stochastic approaches based on modification of the flexible torsion angles. The values of the torsion angles for the molecules of the two polymorphic forms and the hydrate of carnidazole are compared to those obtained from the conformational search. Form I and form II are enantiotropic polymorphic pairs this agrees with the fact that the two forms are conformational polymorphs. Copyright (c) 2006 Wiley-Liss, Inc. and the American Pharmacists Association

How to realize a spin-dependent Seebeck diode effect in metallic zigzag γ-graphyne nanoribbons?

PubMed

Wu, Dan-Dan; Liu, Qing-Bo; Fu, Hua-Hua; Wu, Ruqian

2017-11-30

The spin-dependent Seebeck effect (SDSE) is one of the core topics of spin caloritronics. In the traditional device designs of spin-dependent Seebeck rectifiers and diodes, finite spin-dependent band gaps of materials are required to realize the on-off characteristic in thermal spin currents, and nearly zero charge current should be achieved to reduce energy dissipation. Here, we propose that two ferromagnetic zigzag γ-graphyne nanoribbons (ZγGNRs) without any spin-dependent band gaps around the Fermi level can not only exhibit the SDSE, but also display rectifier and diode effects in thermal spin currents characterized by threshold temperatures, which originates from the compensation effect occurring in spin-dependent transmissions but not from the spin-splitting band gaps in materials. The metallic characteristics of ZγGNRs bring about an advantage that the gate voltage is an effective route to adjust the symmetry of spin-splitting bands to obtain pure thermal spin currents. The results provide a new mechanism to realize spin-Seebeck rectifier and diode effects in 2D materials and expand material candidates towards spin-Seebeck device applications.

Influence of alkyl chain length and anion species on ionic liquid structure at the graphite interface as a function of applied potential

NASA Astrophysics Data System (ADS)

Li, Hua; Wood, Ross J.; Endres, Frank; Atkin, Rob

2014-07-01

Atomic force microscopy (AFM) force measurements elucidate the effect of cation alkyl chain length and the anion species on ionic liquid (IL) interfacial structure at highly ordered pyrolytic graphite (HOPG) surfaces as a function of potential. Three ILs are examined: 1-hexyl-3-methylimidazolium tris(pentafluoroethyl)trifluorophosphate ([HMIM] FAP), 1-ethyl-3-methylimidazolium tris(pentafluoroethyl)trifluorophosphate ([EMIM] FAP), and 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([EMIM] TFSA). The step-wise force-distance profiles indicate the ILs adopt a multilayered morphology near the surface. When the surface is biased positively or negatively versus Pt quasireference electrode, both the number of steps, and the force required to rupture each step increase, indicating stronger interfacial structure. At all potentials, push-through forces for [HMIM] FAP are the highest, because the long alkyl chain results in strong cohesive interactions between cations, leading to well-formed layers that resist the AFM tip. The most layers are observed for [EMIM] FAP, because the C2 chains are relatively rigid and the dimensions of the cation and anion are similar, facilitating neat packing. [EMIM] TFSA has the smallest push-through forces and fewest layers, and thus the weakest interfacial structure. Surface-tip attractive forces are measured for all ILs. At the same potential, the attractions are the strongest for [EMIM] TFSA and the weakest for [HMIM] FAP because the interfacial layers are better formed for the longer alkyl chain cation. This means interfacial forces are stronger, which masks the weak attractive forces.

Intense conductivity suppression by edge defects in zigzag MoS2 and WSe2 nanoribbons: a density functional based tight-binding study.

PubMed

Silva, F W N; Costa, A L M T; Liu, Lei; Barros, E B

2016-11-04

The effects of edge vacancies on the electron transport properties of zigzag MoS2/WSe2 nanoribbons are studied using a density functional theory (DFT)-based tight-binding model with a sp(3)d(5) basis set for the electronic structure calculation and applying the Landauer-Büttiker approach for the electronic transport. Our results show that the presence of a single edge vacancy, with a missing MoS2/WSe2 triplet, is enough to suppress the conductance of the system by almost one half for most energies around the Fermi level. Furthermore, the presence of other single defects along the same edge has little effect on the overall conductance, indicating that the conductance of that particular edge has been strongly suppressed by the first defect. The presence of another defect on the opposite edge further suppresses the quantum conductance, independently of the relative position between the two defects in opposite edges. The introduction of other defects cause the suppression to be energy dependent, leading to conductance peaks which depend on the geometry of the edges. The strong conductance dependence on the presence of edge defects is corroborated by DFT calculations using SIESTA, which show that the electronic bands near the Fermi energy are strongly localized at the edge.

Syntheses and crystal structures of "unligated" copper(I) and copper(II) trifluoroacetates.

PubMed

Cotton, F A; Dikarev, E V; Petrukhina, M A

2000-12-25

Two extremely unstable copper trifluoroacetates with no exogenous ligands, namely, Cu(O2CCF3) (1) and Cu(O2CCF3)2 (2), are prepared for the first time and obtained in crystalline form by deposition from the vapor phase. Their structures are determined by X-ray crystallography. The crystallographic parameters are as follows: for 1, monoclinic space group P2(1)/c, with a = 9.7937(6) A, b = 15.322(1) A, c = 12.002(1) A, beta = 106.493(9) degrees, and Z = 4; for 2, orthorhombic space group Pcca, with a = 16.911(1) A, b = 10.5063(9) A, c = 9.0357(6) A, and Z = 4. Both structures are unique among other CuI and CuII carboxylates, as well as among metal carboxylates in general. Compound 1 consists of a planar rhombus of four copper atoms with sides of 2.719(1)-2.833(1) A and trifluoroacetate ligands bridging the pairs of adjacent metal atoms alternately above and below the plane. The tetrameric units are further aggregated in a polymeric zigzag ribbon [Cu4(O2CCF3)4]infinity by virtue of intermolecular Cu...O contacts. The structure of 2 is built on cis bis-bridged dimers in which every metal atom is also connected with two copper atoms of the neighboring units. The stacking planes in this extended chain are almost perpendicular to one another. The Cu...Cu distance inside the dimer is 3.086(2) A, indicating a nonbonding interaction.

Effect of room temperature lattice vibration on the electron transport in graphene nanoribbons

NASA Astrophysics Data System (ADS)

Liu, Yue-Yang; Li, Bo-Lin; Chen, Shi-Zhang; Jiang, Xiangwei; Chen, Ke-Qiu

2017-09-01

We observe directly the lattice vibration and its multifold effect on electron transport in zigzag graphene nanoribbons in simulation by utilizing an efficient combined method. The results show that the electron transport fluctuates greatly due to the incessant lattice vibration of the nanoribbons. More interestingly, the lattice vibration behaves like a double-edged sword that it boosts the conductance of symmetric zigzag nanoribbons (containing an even number of zigzag chains along the width direction) while weakens the conductance of asymmetric nanoribbons. As a result, the reported large disparity between the conductances of the two kinds of nanoribbons at 0 K is in fact much smaller at room temperature (300 K). We also find that the spin filter effect that exists in perfect two-dimensional symmetric zigzag graphene nanoribbons is destroyed to some extent by lattice vibrations. Since lattice vibrations or phonons are usually inevitable in experiments, the research is very meaningful for revealing the important role of lattice vibrations play in the electron transport properties of two-dimensional materials and guiding the application of ZGNRs in reality.

Multimode Bose-Hubbard model for quantum dipolar gases in confined geometries

NASA Astrophysics Data System (ADS)

Cartarius, Florian; Minguzzi, Anna; Morigi, Giovanna

2017-06-01

We theoretically consider ultracold polar molecules in a wave guide. The particles are bosons: They experience a periodic potential due to an optical lattice oriented along the wave guide and are polarized by an electric field orthogonal to the guide axis. The array is mechanically unstable by opening the transverse confinement in the direction orthogonal to the polarizing electric field and can undergo a transition to a double-chain (zigzag) structure. For this geometry we derive a multimode generalized Bose-Hubbard model for determining the quantum phases of the gas at the mechanical instability, taking into account the quantum fluctuations in all directions of space. Our model limits the dimension of the numerically relevant Hilbert subspace by means of an appropriate decomposition of the field operator, which is obtained from a field theoretical model of the linear-zigzag instability. We determine the phase diagrams of small systems using exact diagonalization and find that, even for tight transverse confinement, the aspect ratio between the two transverse trap frequencies controls not only the classical but also the quantum properties of the ground state in a nontrivial way. Convergence tests at the linear-zigzag instability demonstrate that our multimode generalized Bose-Hubbard model can catch the essential features of the quantum phases of dipolar gases in confined geometries with a limited computational effort.

AFM Imaging of Hybridization Chain Reaction Mediated Signal Transmission between Two DNA Origami Structures.

PubMed

Helmig, Sarah; Gothelf, Kurt Vesterager

2017-10-23

Signal transfer is central to the controlled exchange of information in biology and advanced technologies. Therefore, the development of reliable, long-range signal transfer systems for artificial nanoscale assemblies is of great scientific interest. We have designed such a system for the signal transfer between two connected DNA nanostructures, using the hybridization chain reaction (HCR). Two sets of metastable DNA hairpins, one of which is immobilized at specific points along tracks on DNA origami structures, are polymerized to form a continuous DNA duplex, which is visible using atomic force microscopy (AFM). Upon addition of a designed initiator, the initiation signal is efficiently transferred more than 200 nm from a specific location on one origami structure to an end point on another origami structure. The system shows no significant loss of signal when crossing from one nanostructure to another and, therefore, has the potential to be applied to larger multi-component DNA assemblies. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Design of BAs-AlN monolayered honeycomb heterojunction structures: A first-principles study

NASA Astrophysics Data System (ADS)

Camacho-Mojica, Dulce C.; López-Urías, Florentino

2016-04-01

BAs and AlN are semiconductor materials with an indirect and direct gap respectively in the bulk phase. Recently, electronic calculations have demonstrated that a single-layer or few layers of BAs and AlN exhibit a graphite-like structure with interesting electronic properties. In this work, infinite sheets single-layer heterojunction structures based on alternated strips with honeycomb BAs and AlN layers are investigated using first-principles density functional theory calculations. Optimized geometries, density of states, band-gaps, formation energies, and wave functions are studied for different strip widths joined along zigzag and armchair edges. Results in optimized heterojunction geometries revealed that BAs narrow strips exhibit a corrugation effect due to a lattice mismatch. It was found that zigzag heterojunctions are more energetically favored than armchair heterojunctions. Furthermore, the formation energy presents a maximum at the point where the heterojunction becomes a planar structure. Electronic charge density results yielded a more ionic behavior in Alsbnd N bonds than the Bsbnd As bonds in accordance with monolayer results. It was observed that the conduction band minimum for both heterojunctions exhibit confined states located mainly at the entire AlN strips whereas the valence band maximum exhibits confined states located mainly at BAs strips. We expect that the present investigation will motivate more experimental and theoretical studies on new layered materials made of III-V semiconductors.

Hsc70-induced Changes in Clathrin-Auxilin Cage Structure Suggest a Role for Clathrin Light Chains in Cage Disassembly

PubMed Central

Young, Anna; Stoilova-McPhie, Svetla; Rothnie, Alice; Vallis, Yvonne; Harvey-Smith, Phillip; Ranson, Neil; Kent, Helen; Brodsky, Frances M; Pearse, Barbara M F; Roseman, Alan; Smith, Corinne J

2013-01-01

The molecular chaperone, Hsc70, together with its co-factor, auxilin, facilitates the ATP-dependent removal of clathrin during clathrin-mediated endocytosis in cells. We have used cryo-electron microscopy to determine the 3D structure of a complex of clathrin, auxilin401-910 and Hsc70 at pH 6 in the presence of ATP, frozen within 20 seconds of adding Hsc70 in order to visualize events that follow the binding of Hsc70 to clathrin and auxilin before clathrin disassembly. In this map, we observe density beneath the vertex of the cage that we attribute to bound Hsc70. This density emerges asymmetrically from the clathrin vertex, suggesting preferential binding by Hsc70 for one of the three possible sites at the vertex. Statistical comparison with a map of whole auxilin and clathrin previously published by us reveals the location of statistically significant differences which implicate involvement of clathrin light chains in structural rearrangements which occur after Hsc70 is recruited. Clathrin disassembly assays using light scattering suggest that loss of clathrin light chains reduces the efficiency with which auxilin facilitates this reaction. These data support a regulatory role for clathrin light chains in clathrin disassembly in addition to their established role in regulating clathrin assembly. PMID:23710728

Alcohol-to-acid ratio and substrate concentration affect product structure in chain elongation reactions initiated by unacclimatized inoculum.

PubMed

Liu, Yuhao; Lü, Fan; Shao, Liming; He, Pinjing

2016-10-01

The objective of the study was to investigate whether the ratio of ethanol to acetate affects yield and product structure in chain elongation initiated by unacclimatized mixed cultures. The effect of varying the substrate concentration, while maintaining the same ratio of alcohol to acid, was also investigated. With a high substrate concentration, an alcohol to acid ratio >2:1 provided sufficient electron donor capacity for the chain elongation reaction. With an ethanol to acetate ratio of 3:1 (300mM total carbon), the highest n-caproate concentration (3033±98mg/L) was achieved during the stable phase of the reaction. A lower substrate concentration (150mM total carbon) gave a lower yield of products and led to reduced carbon transformation efficiency compared with other reaction conditions. The use of unacclimatized inoculum in chain elongation can produce significant amounts of odd-carbon-number carboxylates as a result of protein hydrolysis. Copyright © 2016 Elsevier Ltd. All rights reserved.

Optically Unraveling the Edge Chirality-Dependent Band Structure and Plasmon Damping in Graphene Edges.

PubMed

Duan, Jiahua; Chen, Runkun; Cheng, Yuan; Yang, Tianzhong; Zhai, Feng; Dai, Qing; Chen, Jianing

2018-05-01

The nontrivial topological origin and pseudospinorial character of electron wavefunctions make edge states possess unusual electronic properties. Twenty years ago, the tight-binding model calculation predicted that zigzag termination of 2D sheets of carbon atoms have peculiar edge states, which show potential application in spintronics and modern information technologies. Although scanning probe microscopy is employed to capture this phenomenon, the experimental demonstration of its optical response remains challenging. Here, the propagating graphene plasmon provides an edge-selective polaritonic probe to directly detect and control the electronic edge state at ambient condition. Compared with armchair, the edge-band structure in the bandgap gives rise to additional optical absorption and strongly absorbed rim at zigzag edge. Furthermore, the optical conductivity is reconstructed and the anisotropic plasmon damping in graphene systems is revealed. The reported approach paves the way for detecting edge-specific phenomena in other van der Waals materials and topological insulators. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structural basis of light chain amyloidogenicity: comparison of the thermodynamic properties, fibrillogenic potential and tertiary structural features of four vλ6 proteins

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

Wall, J.S.; Gupta, V.; Wilkerson, M.

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 acidsmore » 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

Flexible mechanism of magnetic microbeads chains in an oscillating field

NASA Astrophysics Data System (ADS)

Li, Yan-Hom; Yen, Chia-Yen

2018-05-01

To investigate the use of magnetic microbeads for swimming at low Reynolds number, the flexible structure of microchains comprising superparamagnetic microbeads under the influence of oscillating magnetic fields is examined experimentally and theoretically. For a ductile chain, each particle has its own phase angle trajectory and phase-lag angle to the overall field. This present study thoroughly discusses the synchronicity of the local phase angle trajectory between each dyad of beads and the external field. The prominently asynchronous trajectories between the central and outer beads significantly dominate the flexible structure of the oscillating chain. In addition, the dimensionless local Mason number (Mnl) is derived as the solo controlling parameter to evaluate the structure of each dyad of beads in a flexible chain. The evolution of the local Mason number within an oscillating period implies the most unstable position locates near the center of the chain around 0.6Pchain with a certain length in the influence of the oscillating field would behave the most significant deformation and have the most flexible structure.