bluuebunny/crossref_metadata_2025 huggingface dataset:
A table-top, repetitive pulsed magnet for nonlinear and ultrafast spectroscopy in high magnetic fields up to 30 T
Authors: Noe G. Timothy , Nojiri Hiroyuki , Lee Joseph , Woods Gary L. , Léotin Jean , Kono Junichiro
Published: December 2013

We have developed a mini-coil pulsed magnet system with direct optical access, ideally suited for nonlinear and ultrafast spectroscopy studies of materials in high magnetic fields up to 30 T. The apparatus consists of a small coil in a liquid nitrogen cryostat coupled with a helium flow cryostat to provide sample temperatures down to below 10 K. Direct optical access to the sample is achieved with the use of easily interchangeable windows separated by a short distance of ∼135 mm on either side of the coupled cryostats with numerical apertures of 0.20 and 0.03 for measurements employing the Faraday geometry. As a demonstration, we performed time-resolved and time-integrated photoluminescence measurements as well as transmission measurements on InGaAs quantum wells.
L
2-stability of the Vlasov-Maxwell-Boltzmann system near global Maxwellians
Authors: Ha Seung-Yeal , Xiao Qinghua , Xiong Linjie , Zhao Huijiang
Published: December 2013

We present a L2-stability theory of the Vlasov-Maxwell-Boltzmann system for the two-species collisional plasma. We show that in a perturbative regime of a global Maxwellian, the L2-distance between two strong solutions can be controlled by that between initial data in a Lipschitz manner. Our stability result extends earlier results [Ha, S.-Y. and Xiao, Q.-H., “A revisiting to the L2-stability theory of the Boltzmann equation near global Maxwellians,” (submitted) and Ha, S.-Y., Yang, X.-F., and Yun, S.-B., “L2 stability theory of the Boltzmann equation near a global Maxwellian,” Arch. Ration. Mech. Anal. 197, 657–688 (2010)] on the L2-stability of the Boltzmann equation to the Boltzmann equation coupled with self-consistent external forces. As a direct application of our stability result, we show that classical solutions in Duan et al. [“Optimal large-time behavior of the Vlasov-Maxwell-Boltzmann system in the whole space,” Commun. Pure Appl. Math. 24, 1497–1546 (2011)] and Guo [“The Vlasov-Maxwell-Boltzmann system near Maxwellians,” Invent. Math. 153(3), 593–630 (2003)] satisfy a uniform L2-stability estimate. This is the first result on the L2-stability of the Boltzmann equation coupled with self-consistent field equations in three dimensions.
Existence of multi-bump solutions for a class of Kirchhoff type problems in $\mathbb {R}^3$R3
Authors: Liang Sihua , Shi Shaoyun
Published: December 2013

Using variational methods, we establish existence of multi-bump solutions for a class of Kirchhoff type problems \documentclass[12pt]{minimal}\begin{document}$-(a+b\int _{\mathbb {R}^3}|\nabla u|^2dx)\Delta u + \lambda V(x)u = f(u)$\end{document}−(a+b∫R3|∇u|2dx)Δu+λV(x)u=f(u), where f is a continuous function with subcritical growth, V(x) is a critical frequency in the sense that \documentclass[12pt]{minimal}\begin{document}$\inf _{x\in \mathbb {R}^3}V(x)=0$\end{document}infx∈R3V(x)=0. We show that if the zero set of V(x) has several isolated connected components Ω1, …, Ωk such that the interior of Ωi is not empty and ∂Ωi is smooth, then for λ > 0 large there exists, for any non-empty subset J ⊂ {1, …, k}, a bump solution is trapped in a neighborhood of ∪j ∈ JΩj.
Non-modular lattices generated by the causal structure
Authors: Cegła Wojciech , Jancewicz Bernard
Published: December 2013

A lattice structure approach is used for investigation of the causal structure of space-time. Two lattices are considered: the first one generated by the chronological relation based on a time-like curve, the second one generated by the causal relation based on a causal path.
Existence of time-periodic weak solutions to the stochastic Navier-Stokes equations around a moving body
Authors: Chen Feng , Han Yuecai
Published: December 2013

The existence of time-periodic stochastic motions of an incompressible fluid is obtained. Here the fluid is subject to a time-periodic body force and an additional time-periodic stochastic force that is produced by a rigid body moves periodically stochastically with the same period in the fluid.
Mimetic discretization of the Abelian Chern-Simons theory and link invariants
Authors: Di Bartolo Cayetano , Grau Javier , Leal Lorenzo
Published: December 2013

A mimetic discretization of the Abelian Chern-Simons theory is presented. The study relies on the formulation of a theory of differential forms in the lattice, including a consistent definition of the Hodge duality operation. Explicit expressions for the Gauss Linking Number in the lattice, which correspond to their continuum counterparts are given. A discussion of the discretization of metric structures in the space of transverse vector densities is presented. The study of these metrics could serve to obtain explicit formulae for knot an link invariants in the lattice.
Built-in electric field in ZnO based semipolar quantum wells grown on (101¯2) ZnO substrates
Authors: Chauveau J.-M. , Xia Y. , Ben Taazaet-Belgacem I. , Teisseire M. , Roland B. , Nemoz M. , Brault J. , Damilano B. , Leroux M. , Vinter B.
Published: December 2013

We report on the properties of semipolar (Zn,Mg)O/ZnO quantum wells homoepitaxially grown by molecular beam epitaxy on (101¯2) R-plane ZnO substrates. We demonstrate that atomically flat interfaces can be achieved with fully relaxed quantum wells because the mismatch between (Zn,Mg)O and ZnO is minimal for this growth orientation. The photoluminescence properties evidence a quantum confined Stark effect with an internal electric field estimated to 430 kV/cm for a 17% Mg content in the barriers. The quantum well emission is strongly polarized along the [1¯21¯0] direction and a comparison with the semipolar bulk ZnO luminescence polarization points to the effect of the confinement.
Formation of ionic complexes in cryogenic matrices: A case study using co-deposition of Cu− with rare gas cations in solid argon
Authors: Ludwig Ryan M. , Moore David T.
Published: December 2013

Matrix isolation spectra have been obtained for ionic species formed from a beam of mass-selected ions, with a coincident beam of externally generated counter-ions used to provide charge balance. Infrared spectra were obtained for copper carbonyl complexes formed following deposition of Cu− ions with rare-gas counter-cations into CO-doped argon matrices. Both anionic and neutral copper carbonyl complexes Cu(CO)nq (n = 1–3; q = 0, −1) were observed in the spectra, with peak positions corresponding to previously reported assignments; new partially resolved bands appearing in the range 1830–1845 cm−1 are assigned to larger [Cu(CO)3•(CO)n]− aggregates, having additional CO ligands in the second solvation shell. The experimental geometry ensures that all Cu-centers initially arrive at the matrix as anions, so the relative abundance of anionic relative to neutral complexes is much higher than in previous studies employing alternative methods for ion deposition; this allows for monitoring of electron-transfer processes between anions and cations in the matrix. Comparison of time-dependent vs. temperature-dependent trends reveals that there are two distinct mechanisms by which the population of anionic complexes is converted into neutral complexes: short-range electron transfer between a cation-anion pair following diffusion, and long-range electron transfer involving photodetachment of an electron from the anion into the conduction band of solid argon, resulting in eventual recombination of the electron with a cation in a remote matrix site. The spectra also show a marked dependence on the deposition temperature and dopant concentration, in that 100-fold higher CO concentrations were required during deposition with the sample window at 10 K compared to that used at 20 K, in order to obtain a similar distribution of copper carbonyl complexes. Furthermore, although no carbonyl complexes are observed initially when low concentrations of CO are used at 10 K, upon warming the matrix to 15 K, the neutral di- and tricarbonyl peaks appear abruptly, which is attributed to fast diffusion of CO stimulated by the energy released upon short-range electron-transfer between Cu−:counter-cation pairs.
A self-consistent field study of diblock copolymer/charged particle system morphologies for nanofiltration membranes
Authors: Zhang Bo , Ye Xianggui , Edwards Brian J.
Published: December 2013

A combination of self-consistent field theory and density functional theory was used to examine the stable, 3-dimensional equilibrium morphologies formed by diblock copolymers with a tethered nanoparticle attached either between the two blocks or at the end of one of the blocks. Both neutral and interacting particles were examined, with and without favorable/unfavorable energetic potentials between the particles and the block segments. The phase diagrams of the various systems were constructed, allowing the identification of three types of ordered mesophases composed of lamellae, hexagonally packed cylinders, and spheroids. In particular, we examined the conditions under which the mesophases could be generated wherein the tethered particles were primarily located within the interface between the two blocks of the copolymer. Key factors influencing these properties were determined to be the particle position along the diblock chain, the interaction potentials of the blocks and particles, the block copolymer composition, and molecular weight of the copolymer.
Effect of chain flexibility on master curve behavior for diffusion coefficient
Authors: Budzien Joanne , Heffernan Julieanne V. , McCoy John D.
Published: December 2013

The diffusion coefficients of simple chain models are analyzed as a function of packing fraction, η, and as a function of a parameter C that is the density raised to a power divided by temperature to look at scalar metrics to find master curves. The central feature in the analysis is the mapping onto an effective hard site diameter, d. For the molecular models lacking restrictions on dihedral angle (e.g., freely jointed), simple mappings of molecular potential to d work very well, and the reduced diffusion coefficient, D*, collapses into a single-valued function of η. Although this does not work for the dihedral angle restriction case, assuming that d is inversely proportional to temperature to a power results in collapse behavior for an empirically selected value of the power. This is equivalent to D* being a single-valued function of C. The diffusion coefficient of a single-site penetrant in the chain systems also is found to be a scalar metric that can reduce the chain diffusion data for a given system to a single master curve.
Transport enhancement and suppression in turbulent magnetic reconnection: A self-consistent turbulence model
Authors: Yokoi N. , Higashimori K. , Hoshino M.
Published: December 2013

Through the enhancement of transport, turbulence is expected to contribute to the fast reconnection. However, the effects of turbulence are not so straightforward. In addition to the enhancement of transport, turbulence under some environment shows effects that suppress the transport. In the presence of turbulent cross helicity, such dynamic balance between the transport enhancement and suppression occurs. As this result of dynamic balance, the region of effective enhanced magnetic diffusivity is confined to a narrow region, leading to the fast reconnection. In order to confirm this idea, a self-consistent turbulence model for the magnetic reconnection is proposed. With the aid of numerical simulations where turbulence effects are incorporated in a consistent manner through the turbulence model, the dynamic balance in the turbulence magnetic reconnection is confirmed.
High and low frequency instabilities driven by a single electron beam in two-electron temperature space plasmas
Authors: Mbuli L. N. , Maharaj S. K. , Bharuthram R.
Published: December 2013

In an attempt to understand the excitation mechanisms of broadband electrostatic noise, beam-generated electrostatic instabilities are investigated using kinetic theory in a four-component magnetised plasma model composed of beam electrons (magnetic field-aligned), background hot and cool electrons and ions. All species are fully magnetised and considered to be Maxwellian. The dependence of the instability growth rates and real frequencies on various plasma parameters such as beam speed, particle densities and temperatures, magnetic field strength, wave propagation angle, and temperature anisotropy of the beam are examined. In this study we have found that the electron-acoustic, electron beam-resonant and ion-acoustic instabilities are excited. Our studies have focused on three velocity regimes, namely, the low (vdbz<Ch), intermediate (Ch<vdbz<2 Ch), and high velocity (vdbz>2 Ch) regimes, where vdbz (Ch) is the electron beam drift speed (thermal speed of the hot electrons). Plasma parameters from satellite measurements are used where applicable to provide realistic predictions.
First principles investigation of Ti adsorption and migration on Si(100) surfaces
Authors: Briquet Ludovic G. V. , Wirtz Tom , Philipp Patrick
Published: December 2013

The titanium adsorption on Si(100) is investigated using first principles computer modelling methods. Two new subsurface adsorption sites are described. They are located at the edge of the cavity topped by a surface silicon dimer. The migration of the titanium from the surface to the subsurface sites is facilitated when occurring via one of these sites. The ejection of one of the silicon atoms forming the surface dimer is also investigated. The actual step of the ejection requires more energy than previously thought although, when considering the global picture of a titanium atom on the surface leading to the ejection of a silicon atom, the overall rate is compensated by the facilitated migration of the titanium to the subsurface sites. The consecutive adsorption of a second and third titanium atom is also investigated. It is shown that titanium grows evenly on the surface in normal condition, showing no intermixing of the titanium and silicon beyond the silicon layer.
Fracture problems of a superconducting slab with a central kinked crack
Authors: Gao S. W. , Feng W. J. , Liu J. X.
Published: December 2013

In this work, the central kinked crack problem is investigated for a long rectangular superconducting slab under electromagnetic forces. The distributions of both the current density and the magnetic flux density in the slab are obtained analytically in the Kim critical state model for both the zero-field cooling and the field cooling magnetization processes. And based on the finite element method, the stress intensity factors at the crack tips for decreasing magnetic fields are numerically calculated. Numerical results obtained show that the zero-field cooling activation process generally has more significant influence on the stress intensity factors than the field cooling activation process, and that for every activation process, as the applied field decreases, the superconducting slab is most dangerous when the currents in the crack region are just be influenced. In general, both the maximal mode-I stress intensity factors (SIFs) and mode-II SIFs decrease with the increasing of either the introduced dimensionless parameter p in the Kim model or the crack length. However, the effects of kinked angles on the SIFs are complex. The present study should be helpful to the design and application of high-temperature superconductors.
Analysis of the hole transport through valence band states in heavy Al doped 4H-SiC by ion implantation
Authors: Parisini A. , Nipoti R.
Published: December 2013

The temperature dependence of the Hall hole density and the Hall mobility data of heavy doped p-type 4H-SiC(Al) materials obtained by Al+ ion implantation have been analysed in the frame of the charge neutrality condition and the relaxation time approximation. Samples with implanted Al concentrations in the range 1019–1020 cm−3 and 1950 °C/5 min conventional annealing have been taken into account. The reliability of the calculation has been critically discussed by focusing the attention on both the validity limits of the models for the impurity scattering mechanisms and the adopted Hall factor. By introducing empirical mass anisotropy factors, reasons were given in favour of a generalized use of the unique experimental evaluation of the Hall factor reported by the literature for p-type 4H-SiC, assessed for an Al acceptor density in the range of 1.8 × 1015 cm−3–2 × 1018 cm−3. The simultaneous fits of the Hall hole density and mobility data indicate an electrical activation of the Al impurities of the order or higher than 70% and a compensation of about 10% of the Al acceptors.
Investigation of optical limiting properties of Aluminium nanoparticles prepared by pulsed laser ablation in different carrier media
Authors: Kuladeep Rajamudili , Jyothi L. , Prakash P. , Mayank Shekhar S. , Durga Prasad M. , Narayana Rao D.
Published: December 2013

In this communication, we carried out the systematic investigation of nonlinear absorption and scattering properties of Aluminium nanoparticles (Al NPs) in various polar and non-polar solvents. Al NPs were synthesized with pulsed Nd:YAG laser operated at 1064 nm by ablating Al target in polar and non-polar liquid environment like chloroform, chlorobenzene, toluene, benzene, and carbon tetrachloride. Synthesized Al NPs colloids of various solvents differ in appearance and UV-Vis extinction spectra exhibit absorption in the UV region. The characterization of Al NPs performed by Transmission electron microscopy (TEM) studies reveal that NPs are made up of a well crystallized Al inner part (bright zone) embedded with an amorphous metal Al shell (dark region). Growth, aggregation, and precipitation mechanisms which influence the optical properties and stability of NPs are found to be related to the dipole moment of the surrounding liquid environment. The nonlinear absorption and scattering studies are performed by open aperture Z-scan technique with 532 nm under nanosecond pulse excitation. The Z-scan measurements are fitted theoretically to estimate both two-photon absorption (TPA) and nonlinear scattering (NLS) coefficients. In polar solvents like chlorobenzene, chloroform synthesized Al NPs exhibited higher TPA, NLS coefficient values, and lower optical limiting threshold values in comparison with partially polar solvent like toluene and non-polar solvents like benzene and carbontetrachloride. These results indicate the potential use of Al NPs as a versatile optical limiting material.
The Snell law for quaternionic potentials
Authors: De Leo Stefano , Ducati Gisele C.
Published: December 2013

By using the analogy between optics and quantum mechanics, we obtain the Snell law for the planar motion of quantum particles in the presence of quaternionic potentials.
Evidence and control of bifurcations in a respiratory system
Authors: Goldin Matías A. , Mindlin Gabriel B.
Published: December 2013

We studied the pressure patterns used by domestic canaries in the production of birdsong. Acoustically different sound elements (“syllables”) were generated by qualitatively different pressure gestures. We found that some ubiquitous transitions between syllables can be interpreted as bifurcations of a low dimensional dynamical system. We interpreted these results as evidence supporting a model in which different timescales interact nonlinearly.
Influence of tungsten substitution and oxygen deficiency on the thermoelectric properties of CaMnO3−δ
Authors: Thiel Philipp , Eilertsen James , Populoh Sascha , Saucke Gesine , Döbeli Max , Shkabko Andrey , Sagarna Leyre , Karvonen Lassi , Weidenkaff Anke
Published: December 2013

Polycrystalline tungsten-substituted CaMn1−xWxO3−δ (0.00 ≤ x ≤ 0.05) powders were synthesized from a polymeric precursor, pressed and sintered to high density. The impact of tungsten substitution on the crystal structure, thermal stability, phase transition, electronic and thermal transport properties is assessed. Tungsten acts as an electron donator and strongly affects high-temperature oxygen stoichiometry. Oxygen vacancies form in the high figure-of-merit (ZT)-region starting from about T = 1000 K and dominate the carrier concentration and electronic transport far more than the tungsten substitution. The analysis of the transport properties yields that in the investigated regime the band filling is sufficiently high to overcome barriers of polaron transport. Therefore, the Cutler-Mott approach describes the electrical transport more accurately than the Mott approach for small polaron transport. The lattice thermal conductivity near room temperature is strongly suppressed with increasing tungsten concentration due to mass-difference impurity scattering. A ZT of 0.25 was found for x = 0.04 at 1225 K.
A geometrical model for the description of the AlN shell morphology in GaN-AlN core-shell nanowires
Authors: Hestroffer Karine , Daudin Bruno
Published: December 2013

A geometrical model based on the one formulated by Foxon et al. [J. Cryst. Growth 311, 3423 (2009)] is developed to describe the morphology of AlN shells in GaN-AlN core-shell nanowires grown by plasma-assisted molecular beam epitaxy. The shell aspect ratio is studied as a function of the atomic beam flux incidence angles and of the ratio between Al and N species. The comparison between experimental data and the developed geometrical model suggests the diffusion of about 55% of Al atoms from the side walls to the top surface.
Dependence of phosphorus gettering and hydrogen passivation efficacy on grain boundary type in multicrystalline silicon
Authors: Karzel P. , Ackermann M. , Gröner L. , Reimann C. , Zschorsch M. , Meyer S. , Kiessling F. , Riepe S. , Hahn G.
Published: December 2013

This investigation analyzes the dependency of minority charge carrier lifetime values at grain boundaries in multicrystalline silicon on the grain boundary type after P gettering and/or firing of SiNx:H layers deposited by plasma enhanced chemical vapor deposition. To get a broad statistics, a new method to determine the coincidence site lattice grain boundary types on large scale throughout entire 50 × 50 mm2 samples is combined with spatially resolved lifetime-calibrated photoluminescence measurements and mappings of the interstitial iron concentration. As an evaluation of the lifetime data at grain boundaries in comparison to the recombination activity of the bordering grains, lifetime contrast values are calculated. The correlation of this dependency on the grain boundary type with the impurity concentration is analyzed by the investigation of multicrystalline samples from two different ingots grown by directional solidification with different crucible material qualities. A dependency of the efficacy of all applied processes on the grain boundary type is shown based on broad statistics—higher coincidence site lattice indexes correlate with a decrease of median lifetime values after all processes. Hydrogenation of both grains and grain boundaries is found to be more effective in cleaner samples. Extended getter sinks, as a P emitter, are also beneficial to the efficacy of hydrogenation. The lifetime contrast values are dependent on the degree of contamination of the multicrystalline silicon material. In cleaner samples, they rather decrease after the processes; in standard solar-grade material, they increase after POCl3 diffusion and decrease again after subsequent hydrogenation. No correlation with the interstitial iron concentration is found.
Ion-beam-induced magnetic and structural phase transformation of Ni-stabilized face-centered-cubic Fe films on Cu(100)
Authors: Gloss Jonas , Shah Zaman Sameena , Jonner Jakub , Novotny Zbynek , Schmid Michael , Varga Peter , Urbánek Michal
Published: December 2013

Metastable face-centered cubic (fcc) Fe/Cu(100) thin films are good candidates for ion-beam magnetic patterning due to their magnetic transformation upon ion-beam irradiation. However, pure fcc Fe films undergo spontaneous transformation when their thickness exceeds 10 ML. This limit can be extended to approximately 22 ML by deposition of Fe at increased CO background pressures. We show that much thicker films can be grown by alloying with Ni for stabilizing the fcc γ phase. The amount of Ni necessary to stabilize nonmagnetic, transformable fcc Fe films in dependence on the residual background pressure during the deposition is determined and a phase diagram revealing the transformable region is presented.
Graded-index separate confinement heterostructure InGaN laser diodes
Authors: Stańczyk S. , Czyszanowski T. , Kafar A. , Goss J. , Grzanka S. , Grzanka E. , Czernecki R. , Bojarska A. , Targowski G. , Leszczyński M. , Suski T. , Kucharski R. , Perlin P.
Published: December 2013

We demonstrate graded-index-separate-confinement-heterostructure InGaN laser diodes (GRINSCH) grown by metal organic vapor phase epitaxy. In this type of structure, the optical mode is confined close to the active region by cladding layers with linearly changing Al content. The virtue of this structure lies in simultaneous improvement of injection efficiency through the funneling effect and mode confinement. After a careful modeling we demonstrate that GRINSCH InGaN laser indeed possess very encouraging properties. Low threshold current density of around 3.5 kA/cm2 accompanied by high differential gain (dG/dJ = 14.93 cm kA−1) make these devices an interesting alternative for the classical step-index structure.
Unipolar poling-induced high switching speed and improved imprint behaviors for poly(vinylidene fluoride-trifluoroethylene) copolymer ultrathin films
Authors: Hou Ying , Lü Zhaoyue , Pu Tiansong , Zhang Yuan , Meng Xiangjian , Xu Haisheng
Published: December 2013

The polarization switching and imprint behaviors with different pulse and unipolar poling processes for ferroelectric poly(vinylidene fluoride-trifluoroethylene) (P(VDF-TrFE)) copolymer ultrathin films have been studied. Compared with results for samples only through the certain protocol we studied previously, the much faster switching speed and lower voltage shift are observed for films with certain protocol as well as certain unipolar poling. The analyses show that these properties are strongly dependent on the directions of the switching and unipolar poling field. The results provide another effective route to design the optimum protocol for ferroelectric random access memory based on P(VDF-TrFE) copolymer ultrathin film.
Sub-wavelength quarter-wave plate based on plasmonic patch antennas
Authors: Zhao Hang , Yang Yuanqing , Li Qiang , Qiu Min
Published: December 2013

A quarter-wave plate using plasmonic patch antennas has been investigated. The nanostructures can convert linear polarized light into circular polarized light in the visible range (633 nm). By further exploiting the dimer patch antenna structure composed of different metals, directional emission (with a directivity of 4.8) of circular polarized light (with a conversion efficiency of 27.8%) in an oblique direction with respect to the incident light is enabled. Compared with previous designs, the proposed structures are ultra-thin, and are more suitable for integration applications.
Strain-induced vertical self-organization of semiconductor quantum dots: A computational study
Authors: Shtinkov N.
Published: December 2013

Atomistic strain simulations based on the valence force field method are employed to study the vertical arrangements of semiconductor quantum dot (QD) multilayers. The effects of the QD shape, dimensions, and materials parameters are systematically investigated, varying independently the following parameters: spacer width H, QD lateral spacing D, base b, and height h, slope of the side facets, elastic properties of the dot and the substrate materials, and lattice mismatch between the dot and the substrate. The transition between vertically aligned and anti-aligned structures is found to be determined mainly by the ratios H/D and b/D, as well as by the strain anisotropy of the substrate and to a lesser extent of the QD. The dependence on the QD height h is significant only for steep side facets and large aspect ratios h/b, and the effects of the lattice mismatch strain and the bulk elastic moduli are found to be negligible. The comparison with experimental data shows an excellent agreement with the results from the simulations, demonstrating that the presented analysis results in precise theoretical predictions for the vertical self-organization regime in a wide range of QD materials systems.
Self-powered solid-state photodetector based on TiO2 nanorod/spiro-MeOTAD heterojunction
Authors: Xie Yanru , Wei Lin , Li Qinghao , Wei Guodong , Wang Dong , Chen Yanxue , Jiao Jun , Yan Shishen , Liu Guolei , Mei Liangmo
Published: December 2013

A nanostructured solid-state photodetector based on an inorganic/organic semiconductor heterojunction of TiO2 nanorod/spiro-MeOTAD is constructed. Spiro-MeOTAD serves as the active absorption layer and TiO2 offers a direct pathway for electron transport. A maximum photoresponsivity of 0.01 A/W was observed under illumination of 410 nm at 0 V bias. The time response (decay time is 0.06 s and rise time is 0.12 s) was observed to be rapid. The self-powered device is a promising candidate for application in high-sensitivity and high-speed blue light photodetectors. These results provided a simple way to fabricate low-cost, high spectrum selectivity hybrid photodetector with large area.
Phase field simulation of kinetic superheating and melting of aluminum nanolayer irradiated by pico- and femtosecond laser
Authors: Seok Hwang Yong , Levitas Valery I.
Published: December 2013

Two melting mechanisms are reproduced and quantified for superheating and melting of Al nanolayer irradiated by pico- and femtosecond laser using the advanced phase-field approach coupled with mechanics and a two-temperature model. At heating rates Q≤79.04 K/ps induced by picosecond laser, two-sided barrierless surface melting forms two solid-melt interfaces, which meet near the center of a sample. The temperature for surface melting is a linear function, and for complete melting it is a cubic function, of logQ. At Q≥300 K/ps induced by femtosecond laser, barrierless and homogeneous melting (without nucleation) at the sample center occurs faster than due to interface propagation. Good agreement with experimental melting time was achieved in a range of 0.95≤Q≤1290 K/ps without fitting of material parameters.
Poly(vinylidene fluoride-co-hexafluoropropylene)-graft-poly(dopamine methacrylamide) copolymers: A nonlinear dielectric material for high energy density storage
Authors: Rahimabady Mojtaba , Qun Xu Li , Arabnejad Saeid , Yao Kui , Lu Li , Shim Victor P. W. , Gee Neoh Koon , Kang En-Tang
Published: December 2013

A nonlinear dielectric poly(vinylidene fluoride-co-hexafluoropropylene)-graft-poly(dopamine methacrylamide) [P(VDF-HFP)-g-PDMA] graft copolymer with ultra-high energy density of 33 J/cm3 was obtained by thermally initiated radical graft polymerization. It was observed that the dielectric constant of the graft copolymer films was 63% higher than that of P(VDF-HFP), with a large dielectric breakdown strength (>850 MV/m). Theoretical analyses and experimental measurements showed that the significant improvement in the electric polarization was attributed to the introduction of the highly polarizable hydroxyl groups in the PDMA side chains, and the large breakdown strength arose from the strong adhesion bonding of the catechol-containing graft copolymer to the metal electrode.
Tomographic investigation of fermi level pinning at focused ion beam milled semiconductor surfaces
Authors: Wolf D. , Lubk A. , Lenk A. , Sturm S. , Lichte H.
Published: December 2013

Electron holography in the transmission electron microscope (TEM) offers the spatial and signal resolution for studying effects like Fermi level pinning or dopant concentration variations important for the design of modern electronic devices. To overcome the loss of information along the projection direction, surface effects, and surface damage due to TEM specimen preparation, we apply electron holographic tomography to analyze the 3D potential distribution of semiconductor samples prepared by focused-ion-beam. We observe mid-band gap pinning of the Fermi level at Si surfaces but valence band pinning at Ge surfaces. The pinning extends over tens of nanometers into the bulk.
Recombination dynamics and carrier lifetimes in highly mismatched ZnTeO alloys
Authors: Lin Yan-Cheng , Tasi Ming-Jui , Chou Wu-Ching , Chang Wen-Hao , Chen Wei-Kuo , Tanaka Tooru , Guo Qixin , Nishio Mitsuhiro
Published: December 2013

This study investigates the recombination dynamics in highly mismatched ZnTeO alloys using time-resolved photoluminescence (PL) spectroscopy. The large PL energy redshift with increasing O content and the disappearance of the ZnTe emission verify the O-induced conduction band anticrossing effect. The incorporation of O generates electron localization below the E− conduction subband tail, which provide additional optical transitions and cause complex recombination mechanisms. Photoexcited free electrons in both the E+ and the E− conduction subbands favor rapid relaxation to low energy states. Additionally, temperature-independent long carrier lifetimes (>130.0 ns) that are induced by localized electrons increase with O concentration.
Negative permittivity and permeability spectra of Cu/yttrium iron garnet hybrid granular composite materials in the microwave frequency range
Authors: Tsutaoka Takanori , Fukuyama Koki , Kinoshita Hideaki , Kasagi Teruhiro , Yamamoto Shinichiro , Hatakeyama Kenichi
Published: December 2013

The relative complex permittivity and permeability spectra of the coagulated copper and yttrium iron garnet (Cu/YIG) hybrid granular composite materials have been studied in the microwave range. The insulator to metal transition was observed at the percolation threshold of Cu particle content (φCu = 16.0 vol. %) in the electrical conductivity. In the percolation threshold, the low frequency plasmonic state caused by the metallic Cu particle networks was observed. The percolated Cu/YIG granular composites show simultaneous negative permittivity and permeability spectra under external magnetic fields.
Super-resolution with a positive epsilon multi-quantum-well super-lens
Authors: Bak A. O. , Giannini V. , Maier S. A. , Phillips C. C.
Published: December 2013

We design an anisotropic and dichroic quantum metamaterial that is able to achieve super-resolution without the need for a negative permittivity. When exploring the parameters of the structure, we take into account the limits of semiconductor fabrication technology based on quantum well stacks. By heavily doping the structure with free electrons, we infer an anisotropic effective medium with a prolate ellipsoid dispersion curve which allows for near-diffractionless propagation of light (similar to an epsilon-near-zero hyperbolic lens). This, coupled with low absorption, allows us to resolve images at the sub-wavelength scale at distances 6 times greater than equivalent natural materials.
Phylogeny-based classification of microbial communities
Authors: Tanaseichuk Olga , Borneman James , Jiang Tao
Published: December 2013

Motivation: Next-generation sequencing coupled with metagenomics has led to the rapid growth of sequence databases and enabled a new branch of microbiology called comparative metagenomics. Comparative metagenomic analysis studies compositional patterns within and between different environments providing a deep insight into the structure and function of complex microbial communities. It is a fast growing field that requires the development of novel supervised learning techniques for addressing challenges associated with metagenomic data, e.g. sensitivity to the choice of sequence similarity cutoff used to define operational taxonomic units (OTUs), high dimensionality and sparsity of the data and so forth. On the other hand, the natural properties of microbial community data may provide useful information about the structure of the data. For example, similarity between species encoded by a phylogenetic tree captures the relationship between OTUs and may be useful for the analysis of complex microbial datasets where the diversity patterns comprise features at multiple taxonomic levels. Even though some of the challenges have been addressed by learning algorithms in the literature, none of the available methods take advantage of the inherent properties of metagenomic data.

Results: We proposed a novel supervised classification method for microbial community samples, where each sample is represented as a set of OTU frequencies, which takes advantage of the natural structure in microbial community data encoded by a phylogenetic tree. This model allows us to take advantage of environment-specific compositional patterns that may contain features at multiple granularity levels. Our method is based on the multinomial logistic regression model with a tree-guided penalty function. Additionally, we proposed a new simulation framework for generating 16S ribosomal RNA gene read counts that may be useful in comparative metagenomics research. Our experimental results on simulated and real data show that the phylogenetic information used in our method improves the classification accuracy.

Availability and implementation:  http://www.cs.ucr.edu/∼tanaseio/metaphyl.htm.

Contact:  tanaseio@cs.ucr.edu or jiang@cs.ucr.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Improving computational efficiency and tractability of protein design using a piecemeal approach. A strategy for parallel and distributed protein design
Authors: Pitman Derek J. , Schenkelberg Christian D. , Huang Yao-Ming , Teets Frank D. , DiTursi Daniel , Bystroff Christopher
Published: December 2013

Motivation: Accuracy in protein design requires a fine-grained rotamer search, multiple backbone conformations, and a detailed energy function, creating a burden in runtime and memory requirements. A design task may be split into manageable pieces in both three-dimensional space and in the rotamer search space to produce small, fast jobs that are easily distributed. However, these jobs must overlap, presenting a problem in resolving conflicting solutions in the overlap regions.

Results: Piecemeal design, in which the design space is split into overlapping regions and rotamer search spaces, accelerates the design process whether jobs are run in series or in parallel. Large jobs that cannot fit in memory were made possible by splitting. Accepting the consensus amino acid selection in conflict regions led to non-optimal choices. Instead, conflicts were resolved using a second pass, in which the split regions were re-combined and designed as one, producing results that were closer to optimal with a minimal increase in runtime over the consensus strategy. Splitting the search space at the rotamer level instead of at the amino acid level further improved the efficiency by reducing the search space in the second pass.

Availability and implementation: Programs for splitting protein design expressions are available at www.bioinfo.rpi.edu/tools/piecemeal.html.

Contact:  bystrc@rpi.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
tasiRNAdb: a database of ta-siRNA regulatory pathways
Authors: Zhang Changqing , Li Guangping , Zhu Shinong , Zhang Shuo , Fang Jinggui
Published: December 2013

Summary: In plants, many trans-acting small interfering RNA (ta-siRNA) regulatory pathways have been identified as significant components of the gene networks involved in development, metabolism, responses to biotic and abiotic stresses and DNA methylation at the TAS locus. To obtain a more comprehensive understanding on the nature of ta-siRNA regulatory pathways, we developed a freely accessible resource, tasiRNAdb, to serve as a repository for the sequences of ta-siRNA regulatory pathway-related microRNAs, TASs, ta-siRNAs and ta-siRNA targets, and for the cascading relations among them. With 583 pathways from 18 species, tasiRNAdb is the largest resource for known ta-siRNA regulatory pathways currently available. tasiRNAdb also provides a tool named TasExpAnalysis that was developed to map user-submitted small RNA and degradome libraries to a stored/input TAS and to perform sRNA phasing analysis and TAS cleavage analysis.

Availability: The database of plant ta-siRNA regulatory pathways is available at http://bioinfo.jit.edu.cn/tasiRNADatabase/.

Contact:  zhang_chq2002@sohu.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Assimilating genome-scale metabolic reconstructions with modelBorgifier
Authors: Sauls John T. , Buescher Joerg M.
Published: December 2013

Motivation: Genome-scale reconstructions and models, as collections of genomic and metabolic information, provide a useful means to compare organisms. Comparison requires that models are similarly notated to pair shared components.

Result: Matching and comparison of genome-scale reconstructions and models are facilitated by modelBorgifier. It reconciles models in light of different annotation schemes, allowing diverse models to become useful for synchronous investigation.

Availability and implementation: The modelBorgifier toolbox is freely available at http://www.brain-biotech.de/downloads/modelBorgifier.zip.

Contact:  jrb@brain-biotech.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Seabed classification using surface backscattering strength versus acoustic frequency and incidence angle measured with vertical, split-beam echosounders
Authors: Cutter George R. , Demer David A.
Published: December 2013

The multifrequency biplanar interferometric imaging technique (MBI) is applied to data from vertical, split-beam echosounders to produce sub-beam estimates of seabed surface-backscattering strength (Ss), incidence angle (θ), and roughness (${\rm {\cal R}}$). A simple model is used to quantify the variation of Ss versus θ = {2–20°} and acoustic frequency, f = {18, 38, 70, 120 and 200 kHz}. The coefficients of the angle- and frequency-dependent terms of the model indicate seabed material properties, principally small- and large-scale roughness and hardness. These indices are combined with the estimates of θ and ${\rm {\cal R}}$ to classify the seabed using unsupervised cluster analysis. This technique is applied to data from the Forty-Three-Fathom Bank, a seamount in the Southern California Bight. The resulting seabed classifications are consistent with the surficial lithology and the spatial distribution of known rockfish (Sebastes spp.) habitat. The method should be generally applicable to seabed classification.
The effects of polymorphisms on human gene targeting
Authors: Deyle David R. , Li Li B. , Ren Gaoying , Russell David W.
Published: December 2013

DNA mismatches that occur between vector homology arms and chromosomal target sequences reduce gene targeting frequencies in several species; however, this has not been reported in human cells. Here we demonstrate that even a single mismatched base pair can significantly decrease human gene targeting frequencies. In addition, we show that homology arm polymorphisms can be used to direct allele-specific targeting or to improve unfavorable vector designs that introduce deletions.
Sugar-modified G-quadruplexes: effects of LNA-, 2′F-RNA– and 2′F-ANA-guanosine chemistries on G-quadruplex structure and stability
Authors: Li Zhe , Lech Christopher Jacques , Phan Anh Tuân
Published: December 2013

G-quadruplex-forming oligonucleotides containing modified nucleotide chemistries have demonstrated promising pharmaceutical potential. In this work, we systematically investigate the effects of sugar-modified guanosines on the structure and stability of a (4+0) parallel and a (3+1) hybrid G-quadruplex using over 60 modified sequences containing a single-position substitution of 2′-O-4′-C-methylene-guanosine (LNAG), 2′-deoxy-2′-fluoro-riboguanosine (FG) or 2′-deoxy-2′-fluoro-arabinoguanosine (FANAG). Our results are summarized in two parts: (I) Generally, LNAG substitutions into ‘anti’ position guanines within a guanine-tetrad lead to a more stable G-quadruplex, while substitutions into ‘syn’ positions disrupt the native G-quadruplex conformation. However, some interesting exceptions to this trend are observed. We discover that a LNAG modification upstream of a short propeller loop hinders G-quadruplex formation. (II) A single substitution of either FG or FANAG into a ‘syn’ position is powerful enough to perturb the (3+1) G-quadruplex. Substitution of either FG or FANAG into any ‘anti’ position is well tolerated in the two G-quadruplex scaffolds. FANAG substitutions to ‘anti’ positions are better tolerated than their FG counterparts. In both scaffolds, FANAG substitutions to the central tetrad layer are observed to be the most stabilizing. The observations reported herein on the effects of LNAG, FG and FANAG modifications on G-quadruplex structure and stability will enable the future design of pharmaceutically relevant oligonucleotides.
A phylogenetic model for understanding the effect of gene duplication on cancer progression
Authors: Ma Qin , Reeves Jaxk H. , Liberles David A. , Yu Lili , Chang Zheng , Zhao Jing , Cui Juan , Xu Ying , Liu Liang
Published: December 2013

As biotechnology advances rapidly, a tremendous amount of cancer genetic data has become available, providing an unprecedented opportunity for understanding the genetic mechanisms of cancer. To understand the effects of duplications and deletions on cancer progression, two genomes (normal and tumor) were sequenced from each of five stomach cancer patients in different stages (I, II, III and IV). We developed a phylogenetic model for analyzing stomach cancer data. The model assumes that duplication and deletion occur in accordance with a continuous time Markov Chain along the branches of a phylogenetic tree attached with five extended branches leading to the tumor genomes. Moreover, coalescence times of the phylogenetic tree follow a coalescence process. The simulation study suggests that the maximum likelihood approach can accurately estimate parameters in the phylogenetic model. The phylogenetic model was applied to the stomach cancer data. We found that the expected number of changes (duplication and deletion) per gene for the tumor genomes is significantly higher than that for the normal genomes. The goodness-of-fit test suggests that the phylogenetic model with constant duplication and deletion rates can adequately fit the duplication data for the normal genomes. The analysis found nine duplicated genes that are significantly associated with stomach cancer.