bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimization of collective enzyme activity via spatial localization
Authors: Buchner Alexander , Tostevin Filipe , Hinzpeter Florian , Gerland Ulrich
Published: October 2013

The spatial organization of enzymes often plays a crucial role in the functionality and efficiency of enzymatic pathways. To fully understand the design and operation of enzymatic pathways, it is therefore crucial to understand how the relative arrangement of enzymes affects pathway function. Here we investigate the effect of enzyme localization on the flux of a minimal two-enzyme pathway within a reaction-diffusion model. We consider different reaction kinetics, spatial dimensions, and loss mechanisms for intermediate substrate molecules. Our systematic analysis of the different regimes of this model reveals both universal features and distinct characteristics in the phenomenology of these different systems. In particular, the distribution of the second pathway enzyme that maximizes the reaction flux undergoes a generic transition from co-localization with the first enzyme when the catalytic efficiency of the second enzyme is low, to an extended profile when the catalytic efficiency is high. However, the critical transition point and the shape of the extended optimal profile is significantly affected by specific features of the model. We explain the behavior of these different systems in terms of the underlying stochastic reaction and diffusion processes of single substrate molecules.
Observation of out-of-plane unidirectional anisotropy in MgO-capped planar nanowire arrays of Fe
Authors: Arora S. K. , O'Dowd B. J. , Polishchuk D. M. , Tovstolytkin A. I. , Thakur P. , Brookes N. B. , Ballesteros B. , Gambardella P. , Shvets I. V.
Published: October 2013

We report on the effect of cap layer material on the magnetic properties and aging of the Fe-NW (nanowire) arrays grown on oxidized vicinal Si (111) templates using atomic terrace low angle shadowing technique. We find that the Fe-NW arrays capped with metallic (Ag) layers do not show any sign of degradation with aging, whereas NW arrays capped with insulating dielectric (MgO) layers show degradation of the saturation magnetization and an out-of-plane unidirectional anisotropy. We find that this out-of-plane unidirectional anisotropy competes with the shape anisotropy which is still the dominant anisotropy. The origin of this additional anisotropy is explained on the basis of oxidation of Fe due to the presence of MgO that leads to the formation of an oxide interlayer. This oxide interlayer forms at the expense of NW materials, leading to reduction in the thickness of some of the Fe-NWs within the array, and orients their magnetic moments out-of-plane. The reduction in NW thickness and the presence of Fe-O interlayer facilitates stabilization of this anisotropy. Our model is supported by x-ray absorption spectroscopy studies performed as a function of aging, which suggests that the oxide interlayer thickness increases with aging.
Underwater depth reconstruction by local water wave measurements
Authors: Przadka A. , Petitjeans P. , Pagneux V. , Maurel A. , Ing R. K.
Published: October 2013

We present an experimental study of underwater depth reconstruction obtained by a method based on the Bessel series expansion of the solutions of the 2D linear water wave equation. This is achieved by measuring capillary-gravity waves using a contactless space-time resolved Fourier Transform Profilometry method. The ability of the method is exemplified for several type of bathymetry in laboratory experiments.
Voltage-controllable terahertz radiation from coherent longitudinal optical phonons in a p-i-n diode structure of GaAs
Authors: Nakayama Masaaki , Asai Souta , Takeuchi Hideo , Ichikawa Osamu , Hata Masahiko
Published: October 2013

We propose and demonstrate the voltage-controllable terahertz radiation from coherent longitudinal optical (LO) phonons in a p-i-n diode of GaAs at room temperature under illumination of a femtosecond pulse laser. It was found that the intensity of the terahertz radiation is continuously and drastically enhanced by an increase in reverse bias voltage (electric field strength) from 0 (22) to 8.0 V (140 kV/cm). The analysis of the electric-field-strength dependence of the intensity indicates that the initial polarization of the LO phonon induced by the electric field dominates the enhancement and that the second-order electric susceptibility is considerable.
Generation of optical vortex based on computer-generated holographic gratings by photolithography
Authors: Li Shaoxiang , Wang Zhenwei
Published: October 2013

The Laguerre-Gaussian beam is a typical example of the optical vortices, which can be generated by computer-generated holograms (CGHs) with the topological charge controlled. Here, we fabricated transmission-amplitude CGH gratings (up to 100 lines per millimeter) on metal film by photolithography technique. Such CGH grating grooves feature high resolution and fine smoothness, so that the gratings can be used to generate Laguerre-Gaussian beam with perfect mode. They are also applicable for the generation of femtosecond optical vortices due to the high damage threshold of the metal film.
Properties of high-β microturbulence and the non-zonal transition
Authors: Pueschel M. J. , Hatch D. R. , Görler T. , Nevins W. M. , Jenko F. , Terry P. W. , Told D.
Published: October 2013

The physics underlying the non-zonal transition [M. J. Pueschel et al., Phys. Rev. Lett. 110, 155005 (2013)] are explored in detail, and various studies are presented which support the theory that critically weakened zonal flows are indeed responsible for the failure of ion-temperature-gradient-driven turbulence at high plasma β to saturate at typical transport values. Regarding flux-surface-breaking magnetic fluctuations and their impact on zonal flows, numerical approaches to obtaining zonal flow residuals are elaborated on, and simulation results are shown to agree with analytical predictions, corroborating the interpretation that flux-surface-breaking magnetic fluctuations cause the transition. Consistently, the zonal-flows-related energetics of the turbulence are found to change fundamentally when exceeding the threshold.
Experimental study on the evolution of traveling waves over an undulated incline
Authors: Reck Daniel , Aksel Nuri
Published: October 2013

We present experimental results on the evolution of traveling waves over a strongly undulated incline. In order to investigate the difference between waves in the linearly stable and unstable region, we set the Reynolds number near the neutral curve. That way, we were able to cross the neutral curve by increasing the frequency of excitation, without changing the velocity field of the basic flow. The amplitude of excitation was also varied, to analyze the evolution of both linear and nonlinear waves. We report on a rich variety of phenomena, including: (a) energy transfer from the excitation frequency to its higher harmonics, (b) the growth rate of the traveling waves, (c) the stability of traveling waves depending on its amplitude, and (d) the amplitude of saturation depending on the excitation frequency. We compare our results to those so far available in the literature. To our knowledge, this is the first experimental work on the development of traveling waves over strongly undulated substrate geometries.
Accuracy assessment of sheet-charge approximation for Fowler-Nordheim tunneling into charged insulators
Authors: Hiraiwa Atsushi , Saito Tatsuya , Daicho Akira , Kawarada Hiroshi
Published: October 2013

Various insulators are used as gate dielectrics and passivation layers in wide-bandgap (WBG) semiconductor devices as well as in advanced Si devices, and the understanding of their current conduction mechanism is essential to achieve their high performance and high reliability. Because these insulators are more or less charged, the conduction current is mostly caused by the Fowler-Nordheim (FN) tunneling into charged insulators, ruling out the conventional analytic FN formula. In order to facilitate the analysis of these currents, we focused on the method, named sheet-charge approximation (SCA), of approximating the charge distribution in the insulators by a charge sheet that has the same areal density and centroid as those of the original. Using, as references, the results obtained exactly calculating the tunneling current in the framework of the Wentzel-Kramers-Brillouin approximation, we confirmed the advantage of SCA over the previous method using a tunneling-endpoint field, the error of SCA-estimated areal charge densities being at most 30% for rectangular charge distributions of which charge centroids are known as in stacked films. In a more general case where the centroid is unknown, the SCA usually provides only a charge moment with reference to the insulator/anode interface, being unable to decompose the moment into the areal charge density and centroid. However, this demerit of SCA can be overcome through a reverse-biased current-voltage measurement using a capacitor formed on a heavily doped substrate or a capacitor with a diffusion layer attached, which measurement provides a charge moment with reference to the original cathode/insulator interface. Using these two kinds of charge moments, we can separately extract the areal charge density and centroid. Hence, the SCA has practical significance as a tool for analyzing conduction currents through charged insulators, especially through stacked films, and accordingly will play an important role in improving the performance and reliability of gate dielectrics and passivation layers for various WBG semiconductor devices as well as of high-k gate stacks for advanced Si devices.
Asymmetric transport property of fluorinated graphene
Authors: Tahara Kosuke , Iwasaki Takayuki , Furuyama Satoko , Matsutani Akihiro , Hatano Mutsuko
Published: October 2013

Carrier transport properties of fluorinated graphene with various fluorination rates are presented. Onset of transition from insulating to metallic conduction is observed in dilute fluorinated graphene. Highly fluorinated graphene shows electron-hole asymmetry in transport properties and local resistivity maximum at the hole conduction region, which are presumably caused by the existence of resonant fluorine impurities. Drastic change of the asymmetric feature occurs after removing fluorine atoms and creating structural defects by thermal annealing. These results suggest that the type of impurities or defects in graphene is detectable by examining asymmetry in transport properties.
Carrier concentration modulation by hot pressing pressure in n-type nanostructured Bi(Se)Te alloy
Authors: Chan Tsung-ta E. , LeBeau James M. , Venkatasubramanian Rama , Thomas Peter , Stuart Judy , Koch Carl C.
Published: October 2013

We demonstrate experimentally that an optimal hot pressing pressure is required for high thermoelectric power factor in different n-type Bi(Se)Te alloys for a given processing temperature. This phenomenon is attributed to the variations in carrier concentration, which changes the Seebeck coefficient and therefore the power factor. The variations could arise from the difference in the concentration of charged antisite defects as their formation energy changes with pressures. Furthermore, modifications of the energy gap resulting from the lattice distortions at high pressure also likely play a role.
Impact of the n+ emitter layer on the structural and electrical properties of p-type polycrystalline silicon thin-film solar cells
Authors: Kumar A. , Hidayat H. , Ke C. , Chakraborty S. , Dalapati G. K. , Widenborg P. I. , Tan C. C. , Dolmanan S. , Aberle A. G.
Published: October 2013

The effect of the phosphine (PH3) flow rate on the doping profile, in particular the peak doping concentration of the n+ emitter layer, of solid phase crystallised polycrystalline silicon thin-film solar cells on glass is investigated by electrochemical capacitance-voltage profiling. The peak n+ layer doping is found to increase with increasing PH3 gas flow, resulting in a shift of the p-n junction location towards the centre of the diode. The impact of the PH3 flow rate on the crystal quality of the poly-Si films is analysed using ultraviolet (UV) reflectance and UV/visible Raman spectroscopy. The impact of the PH3 flow rate on the efficiency of poly-Si thin-film solar cells is investigated using electrical measurements. An improvement in the efficiency by 46% and a pseudo energy conversion efficiency of 5% was obtained through precise control of the flow rate at an intermediate n+ emitter layer doping concentration of 1.0 × 1019 cm−3. The best fabricated poly-Si thin-film solar cell is also found to have the highest crystal quality factor, based on both Raman and UV reflectance measurements.
Single-frequency blue light generation by single-pass sum-frequency generation in a coupled ring cavity tapered laser
Authors: Bjarlin Jensen Ole , Michael Petersen Paul
Published: October 2013

A generic approach for generation of tunable single frequency light is presented. 340 mW of near diffraction limited, single-frequency, and tunable blue light around 459 nm is generated by sum-frequency generation (SFG) between two tunable tapered diode lasers. One diode laser is operated in a ring cavity and another tapered diode laser is single-passed through a nonlinear crystal which is contained in the coupled ring cavity. Using this method, the single-pass conversion efficiency is more than 25%. In contrast to SFG in an external cavity, the system is entirely self-stabilized with no electronic locking.
Nanoscale displacement sensing using microfabricated variable-inductance planar coils
Authors: Coskun M. Bulut , Thotahewa Kasun , Ying York-Sing , Yuce Mehmet , Neild Adrian , Alan Tuncay
Published: October 2013

Microfabricated spiral inductors were employed for nanoscale displacement detection, suitable for use in implantable pressure sensor applications. We developed a variable inductor sensor consisting of two coaxially positioned planar coils connected in series to a measurement circuit. The devices were characterized by varying the air gap between the coils hence changing the inductance, while a Colpitts oscillator readout was used to obtain corresponding frequencies. Our approach shows significant advantages over existing methodologies combining a displacement resolution of 17 nm and low hysteresis (0.15%) in a 1 × 1 mm2 device. We show that resolution could be further improved by shrinking the device's lateral dimensions.
Substrate effects on quasiparticles and excitons in graphene nanoflakes
Authors: Sheng Weidong , Sun Mengchao , Zhou Aiping , Xu S. J.
Published: October 2013

The effects of substrate on electronic and optical properties of triangular and hexagonal graphene nanoflakes with armchair edges are investigated by using a configuration interaction approach beyond double excitation scheme. The quasiparticle correction to the energy gap and exciton binding energy are found to be dominated by the long-range Coulomb interactions and exhibit similar dependence on the dielectric constant of the substrate, which leads to a cancellation of their contributions to the optical gap. As a result, the optical gaps are shown to be insensitive to the dielectric environment and unexpectedly close to the single-particle gaps.
Leakage current through the poly-crystalline HfO2: Trap densities at grains and grain boundaries
Authors: Pirrotta Onofrio , Larcher Luca , Lanza Mario , Padovani Andrea , Porti Marc , Nafría Montserrat , Bersuker Gennadi
Published: October 2013

We investigate the role of grains and grain boundaries (GBs) in the electron transport through poly-crystalline HfO2 by means of conductive atomic force microscopy (CAFM) measurements and trap-assisted tunneling simulations. CAFM experiments demonstrate that the leakage current through a thin dielectric film preferentially flows via the GBs. The current I-V characteristics measured on both types of sites, grains, and GBs are successfully simulated by utilizing the multiphonon trap-assisted tunneling model, which accounts for the inelastic charge transport via the electron traps. The extracted density of electrically active traps, whose energy parameters match those of the positively charged oxygen vacancies in hafnia, is ∼3 × 1019 cm−3 at the grains, whereas a much higher value of (0.9÷2.1) × 1021 cm−3 is required to reproduce the leakage current through the GBs.
Acoustic one-way frequency up-converter with high transmission efficiency
Authors: Kan Weiwei , Liang Bin , Zhu Xuefeng , Zou Xinye , Yang Jun , Cheng Jianchun
Published: October 2013

We have devised an acoustic one-way frequency up-converter comprising a nonlinear cavity and two different superlattices, for converting acoustic energy into the second harmonic wave with high transmission efficiency in only one particular direction. The resonance in the high-Q cavity significantly enhances the interaction between the acoustic waves and the nonlinear medium, leading to abnormal dependences of efficiency on the incident wave amplitude and the nonlinearity parameters. The performance of the proposed structure is verified by numerically solving the nonlinear acoustic partial-differential-equations for a full transient solution. The results show that the transmission efficiency can be promoted by three orders of magnitude as compared with previous devices of the same size and, moreover, reach its maximum when both the incident wave and the nonlinearity are comparatively weak. The parameter dependence of efficiency as well as the necessary condition under which the designed device works are also investigated. The proposed design helps to remarkably improve the sensitivity and reduce the size for similar acoustic one-way devices, which may benefit the potential application of the resulting devices.
Effect of trapped electron on the dust ion acoustic waves in dusty plasma using time fractional modified Korteweg-de Vries equation
Authors: Nazari-Golshan A. , Nourazar S. S.
Published: October 2013

The time fractional modified Korteweg-de Vries (TFMKdV) equation is solved to study the nonlinear propagation of small but finite amplitude dust ion-acoustic (DIA) solitary waves in un-magnetized dusty plasma with trapped electrons. The plasma is composed of a cold ion fluid, stationary dust grains, and hot electrons obeying a trapped electron distribution. The TFMKdV equation is derived by using the semi-inverse and Agrawal's methods and then solved by the Laplace Adomian decomposition method. Our results show that the amplitude of the DIA solitary waves increases with the increase of time fractional order β, the wave velocity v0, and the population of the background free electrons λ. However, it is vice-versa for the deviation from isothermality parameter b, which is in agreement with the result obtained previously.
Reduction of weakly nonlinear parabolic partial differential equations
Authors: Chiba Hayato
Published: October 2013

It is known that the Swift-Hohenberg equation \documentclass[12pt]{minimal}\begin{document}$\partial u/\partial t = -(\partial _x^2 + 1)^2u + \varepsilon (u-u^3)$\end{document}∂u/∂t=−(∂x2+1)2u+ɛ(u−u3) can be reduced to the Ginzburg-Landau equation (amplitude equation) \documentclass[12pt]{minimal}\begin{document}$\partial A/\partial t\break = 4\partial _x^2 A + \varepsilon (A-3A|A|^2)$\end{document}∂A/∂t=4∂x2A+ɛ(A−3A|A|2) by means of the singular perturbation method. This means that if ɛ > 0 is sufficiently small, a solution of the latter equation provides an approximate solution of the former one. In this paper, a reduction of a certain class of a system of nonlinear parabolic equations \documentclass[12pt]{minimal}\begin{document}$\partial u/\partial t = \mathcal {P}u + \varepsilon f(u)$\end{document}∂u/∂t=Pu+ɛf(u) is proposed. An amplitude equation of the system is defined and an error estimate of solutions is given. Further, it is proved under certain assumptions that if the amplitude equation has a stable steady state, then a given equation has a stable periodic solution. In particular, near the periodic solution, the error estimate of solutions holds uniformly in t > 0.
Bi nanowire-based thermal biosensor for the detection of salivary cortisol using the Thomson effect
Authors: Lee Seunghyun , Hyun Lee Jung , Kim MinGin , Kim Jeongmin , Song Min-Jung , Jung Hyo-Il , Lee Wooyoung
Published: October 2013

We present a study of a thermal biosensor based on bismuth nanowire that is fabricated for the detection of the human stress hormone cortisol using the Thomson effect. The Bi nanowire was grown using the On-Film Formation of Nanowires (OFF-ON) method. The thermal device was fabricated using photolithography, and the sensing area was modified with immobilized anti-cortisol antibodies conjugated with protein G for the detection of cortisol. The voltages were measured with two probe tips during surface modification to investigate the biochemical reactions in the fabricated thermal biosensor. The Bi nanowire-based thermal biosensor exhibited low detection limit and good selectivity for the detection of cortisol.
Monolithic hybrid tandem solar cells comprising copper indium gallium diselenide and organic subcells
Authors: Reinhard Manuel , Sonntag Paul , Eckstein Ralph , Bürkert Linda , Bauer Andreas , Dimmler Bernhard , Lemmer Uli , Colsmann Alexander
Published: October 2013

Combining wide and narrow band gap absorbers in tandem solar cells is a promising approach to improve the energy conversion of sun light. In this work, we present hybrid tandem devices comprising monolithically connected copper indium gallium diselenide (CIGS) bottom cells and polymer top cells. The thin polymer:fullerene bulk heterojunction absorber layers were transferred onto the rough CIGS surface by a soft-contact lamination technique. Sputtered or solution-deposited top cathodes complete the tandem devices with enhanced open circuit voltages.
Bandgap engineering in perovskite oxides: Al-doped SrTiO3
Authors: Posadas Agham B. , Lin Chungwei , Demkov Alexander A. , Zollner Stefan
Published: October 2013

The ability to modulate the bandgap of a material without altering its functional properties is crucial for fabricating heterojunctions for device applications. Here, we explore experimentally and theoretically the effect of the substitution of Ti with Al on the bandgap of perovskite oxide SrTiO3. We grow Al-doped SrTiO3 films directly on Si(100) and show from electron energy loss spectra that the bandgap is increased by approximately 0.3 eV over undoped SrTiO3. This bandgap increase is confirmed by spectroscopic ellipsometry measurements on identical films grown on LaAlO3 substrates, which show a 0.3 eV blue shift in the steep increase of the absorption edge. Current vs. voltage measurements show a reduction in leakage current by six orders of magnitude at a field of 1 MV/cm. We use density functional theory to explain how Al replacing Ti modifies the conduction band edge density of states resulting in the experimentally observed increase in the bandgap.
Broadband second harmonic generation in GaAs nanowires by femtosecond laser sources
Authors: He Hao , Zhang Xiaoqing , Yan Xin , Huang Lili , Gu Chenglin , Hu Ming-lie , Zhang Xia , Ren Xiao min , Wang Chingyue
Published: October 2013

Nonlinear optical property of semiconductor nanowires plays a key role in nanoscale optoelectronics. In this paper, we demonstrate an excellent frequency converter based on GaAs nanowires (NWs), in which second harmonic generation (SHG) is excited by femtosecond lasers from 800 nm to 1800 nm. Simultaneous SHG with a bandwidth of 300-nm is excited by a super-continuum source at 1000–1600 nm. Broadband SHG can also be acquired from an isolated single NW and the process is coherent. The experimental results suggest that GaAs NWs are potential broadband optical nonlinear converters in nanoscale optoelectronics.
Weak localization and Raman study of anisotropically etched graphene antidots
Authors: Oberhuber Florian , Blien Stefan , Heydrich Stefanie , Yaghobian Fatemeh , Korn Tobias , Schüller Christian , Strunk Christoph , Weiss Dieter , Eroms Jonathan
Published: October 2013

We study a crystallographic etching process of graphene nanostructures, where zigzag edges can be prepared selectively. The process involves heating exfoliated single-layer graphene samples with a predefined pattern of antidot arrays in an argon atmosphere at 820 ∘C, which selectively removes carbon atoms located on armchair sites. Atomic force microscopy and scanning electron microscopy cannot resolve the structure on the atomic scale. However, weak localization and Raman measurements, which both probe intervalley scattering at armchair edges, indicate that zigzag regions are enhanced compared to samples prepared with oxygen based reactive ion etching only.
Simultaneously increasing the magnetization and coercivity of bulk nanocomposite magnets via severe plastic deformation
Authors: Li Hailing , Lou Li , Hou Fuchen , Guo Defeng , Li Wei , Li Xiaohong , Gunderov Dmitry V. , Sato Kiminori , Zhang Xiangyi
Published: October 2013

In general, there is a trade-off between magnetization and coercivity in nanocomposite magnets. Here, we demonstrate a simultaneous enhancement of both the magnetization and coercivity in bulk α-Fe/Nd2Fe14B nanocomposite magnets prepared via a severe plastic deformation (SPD) compared with thermally annealed magnets. The enhanced magnetization results from a high fraction (>30%) of α-Fe phase induced by SPD, while the increase in coercivity from 4.6 to 7.2 kOe is attributed to an enhancement in domain wall pinning strength. This study shows an increase in energy product is possible in the nanocomposite magnets for a large inclusion of soft-magnetic phase.
Localization of charge carriers in layered crystals MexTiSe2 (Me = Cr, Mn, Cu) studied by the resonant photoemission
Authors: Yarmoshenko Y. M. , Shkvarin A. S. , Yablonskikh M. V. , Merentsov A. I. , Titov A. N.
Published: October 2013

The probability of charge transfer in layered titanium diselenide between monolayers containing Cr, Mn, and Cu with different concentrations and host lattice TiSe2 is estimated according to the resonant photoemission data. For this purpose, the Raman-Auger contributions and narrow bands just below the Fermi energy were separated in the valence band spectra. These contributions provide the information about charge transfer. It is shown that the localization of the 3d electrons is typical for Cr and Cu atoms and strongly depends on theirs concentration. In MnxTiSe2, Mn 3d electrons are delocalized and the probability of the charge transfer is the greatest as compared with other compounds under investigation.
Gate controlled spin pumping at a quantum spin Hall edge
Authors: Narayan Awadhesh , Hurley Aaron , Sanvito Stefano
Published: October 2013

We propose a four-terminal device designed to manipulate by all electrical means the spin of a magnetic adatom positioned at the edge of a quantum spin Hall insulator. We show that an electrical gate, able to tune the interface resistance between a quantum spin Hall insulator and the source and drain electrodes, can switch the device between two regimes: one where the system exhibits spin pumping and the other where the adatom remains in its ground state. This demonstrates an all-electrical route to control single spins by exploiting helical edge states of topological materials.
Growth and properties of GaSbBi alloys
Authors: Rajpalke M. K. , Linhart W. M. , Birkett M. , Yu K. M. , Scanlon D. O. , Buckeridge J. , Jones T. S. , Ashwin M. J. , Veal T. D.
Published: October 2013

Molecular-beam epitaxy has been used to grow GaSb1−xBix alloys with x up to 0.05. The Bi content, lattice expansion, and film thickness were determined by Rutherford backscattering and x-ray diffraction, which also indicate high crystallinity and that >98% of the Bi atoms are substitutional. The observed Bi-induced lattice dilation is consistent with density functional theory calculations. Optical absorption measurements and valence band anticrossing modeling indicate that the room temperature band gap varies from 720 meV for GaSb to 540 meV for GaSb0.95Bi0.05, corresponding to a reduction of 36 meV/%Bi or 210 meV per 0.01 Å change in lattice constant.
Band gap in hypersonic surface phononic lattice of nickel pillars
Authors: Trzaskowska A. , Mielcarek S. , Sarkar J.
Published: October 2013

Brillouin light scattering was applied for investigation of surface wave propagation in phononic materials made of a silicon surface loaded with a nanostructure of nickel pillars. The results revealed the presence of phononic energy gap in the GHz range. The presence of such an energy gap was theoretically confirmed by the finite element method. The width of the energy gap was found to be related to the height of the pillars and was shown to be limited by the frequencies of the modes localized in the pillars. The modes were thoroughly analysed.
Local lattice distortions in single Co-implanted ZnO nanowires
Authors: Chu M. H. , Martínez-Criado G. , Segura-Ruiz J. , Geburt S. , Ronning C.
Published: October 2013

This work reports on the local structure of as-implanted and thermally-treated single Co:ZnO nanowires studied using a hard X-ray nanoprobe. Although the Co ions are incorporated into the wurtzite ZnO lattice, X-ray absorption near edge structure data show high structural disorder in the as-implanted nanowires compared with the annealed ones. In particular, extended X-ray absorption fine structure from single wires reveals a lattice distortion around Zn sites of the as-implanted nanowires, which involves an expansion of the stable wurtzite lattice. The observed local lattice response confirms good recovery of the implantation-induced damage within the ZnO lattice through a thermal treatment.
Electron spin lifetime of a single antimony donor in silicon
Authors: Tracy L. A. , Lu T. M. , Bishop N. C. , Ten Eyck G. A. , Pluym T. , Wendt J. R. , Lilly M. P. , Carroll M. S.
Published: October 2013

We present measurements of the electron spin lifetime (T1) of a single Sb donor in Si. For a magnetic field (B) oriented along the [100] Si crystal direction and low temperature (T) such that kT≪gμB, we find T1−1=KB5, where K=1.7×10−3 Hz T−5. The T1−1∝B5 dependence is expected for donor electron spin relaxation due to g-factor dependence on crystal strain. The magnitude of T1 is within a factor of two of theoretical estimates and is in close agreement with values obtained for bulk donor ensembles.
Spatial profile of charge storage in organic field-effect transistor nonvolatile memory using polymer electret
Authors: She Xiao-Jian , Liu Jie , Zhang Jing-Yu , Gao Xu , Wang Sui-Dong
Published: October 2013

Spatial profile of the charge storage in the pentacene-based field-effect transistor nonvolatile memories using poly(2-vinyl naphthalene) electret is probed. The electron trapping into the electret after programming can be space dependent with more electron storage in the region closer to the contacts, and reducing the channel length is an effective approach to improve the memory performance. The deficient electron supply in pentacene is proposed to be responsible for the inhomogeneous electron storage in the electret. The hole trapping into the electret after erasing is spatially homogeneous, arising from the sufficient hole accumulation in the pentacene channel.
Directional spontaneous emission enhancement in hyperbolic metamaterials
Authors: Sreekanth K. V. , Biaglow T. , Strangi G.
Published: October 2013

In this paper, we experimentally demonstrate the control of spontaneous emission enhancement in multilayered Au/Al2O3 hyperbolic metamaterials (HMMs). The hyperbolic dispersion of the Au/Al2O3 multilayers at optical frequencies is confirmed by using effective medium theory, and then the results are validated by experiments performed through variable angle spectroscopic ellipsometry. The modification of spontaneous emission enhancement is observed when the emission wavelengths of different chromophores deposited on top of the multilayer are tuned from the elliptical to hyperbolic spectral region of the HMM. The simulation results further support the modification of spontaneous emission enhancement in designed HMM. This proposed concept and methodology promises potential applications in areas such as single photon sources and biosensing.
An analytical model for finite radius dual-beam mode-mismatched thermal lens spectroscopy
Authors: Sabaeian Mohammad , Nadgaran Hamid
Published: October 2013

In this work, a new model for dual-beam mode-mismatch thermal lens spectroscopy is presented. The model was based on a new analytical solution of time-dependent heat equation for finite radius cylindrical samples exposed to TEM00 excitation laser beams. The Fresnel diffraction integration method was used to calculate time-dependent on-axis probe beam intensity. All aberrations in thermal lens were taken into account. The model yields accurate values for absorption coefficient and thermal diffusivity of methylene blue aqueous solution. Furthermore, the optimized mode-mismatched version of this model when applied to pure water as a very low absorbent yields its absorption coefficient and thermal diffusivity values close to literature data. In contrast to traditional model, this model does not need to omit any term in its theory to fit the experimental data.
Doped zinc oxide window layers for dye sensitized solar cells
Authors: Kumar Vinod , Singh Neetu , Kumar Vijay , Purohit L. P. , Kapoor Avinashi , Ntwaeaborwa Odireleng M. , Swart Hendrik C.
Published: October 2013

The present paper reports the fabrication of dye sensitized solar cell (DSSC), where boron doped ZnO (BZO) and aluminum-boron co-doped ZnO (AZB) thin films were used as front window electrodes. The highly crystalline zinc oxide (ZnO) nanoparticles (NPs) synthesized by the sol-gel route were used as host material for the dye. The efficiencies of the DSSCs formed using the BZO and AZB as window layers were obtained to be 1.56 and 1.84%, respectively. The enhanced efficiency in the case of an AZB window layer based DSSC is attributed to the increase in conductivity induced by co-doping of Al and B and an increase in the number of conducting pathways between the window layer and NPs provided by the nanorods. This facilitates a new approach in the window layer (doped ZnO) for DSSC application.
Flexible, low-loss, large-area, wide-angle, wavelength-selective plasmonic multilayer metasurface
Authors: Li Ping-Chun , Yu Edward T.
Published: October 2013

Flexible, low-loss, large-area multilayer plasmonic optical metasurfaces are demonstrated and analyzed that provide wavelength-selective reflectance >95% and transmittance <1% with low absorption and robustness to variation in angle of incidence and polarization. These characteristics are shown to be insensitive to vertical misalignment between layers, and defects within individual layers. Analysis based on analytical modeling and numerical simulations provides physical insights into reflectance, loss, and bandwidth of these multilayer metasurface structures. Fabry-Perot resonances associated with phase shifts from each individual metasurface are also examined, and evidence of m = 0 resonance due to the nonzero, wavelength dependent phase shift from the metasurface cavity is demonstrated and explained. Finally, fabrication on flexible substrates via rapid, large-area nanosphere lithography, and the robustness of optical properties of interlayer misalignment together enable the demonstration of wavelength-selective focusing at optical frequencies.
Atomic-scale distortion of optically activated Sm dopants identified with site-selective X-ray absorption spectroscopy
Authors: Ishii Masashi , Crowe Iain F. , Halsall Matthew P. , Hamilton Bruce , Hu Yongfeng , Sham Tsun-Kong , Harako Susumu , Zhao Xin-Wei , Komuro Shuji
Published: October 2013

The local structure of luminescent Sm dopants was investigated using an X-ray absorption fine-structure technique with X-ray-excited optical luminescence. Because this technique evaluates X-ray absorption from luminescence, only optically active sites are analyzed. The Sm L3 near-edge spectrum contains split 5d states and a shake-up transition that are specific to luminescent Sm. Theoretical calculations using cluster models identified an atomic-scale distortion that can reproduce the split 5d states. The model with C4v local symmetry and compressive bond length of Sm–O of a six-fold oxygen (SmO6) cluster is most consistent with the experimental results.
A Series of Imidazolyl-Containing Bisphosphonates with Abundant Hydrogen-Bonding Interactions: Syntheses, Structures, and Bone-Binding Affinity
Authors: Qiu Ling , Lin Jianguo , Wang Liqing , Cheng Wen , Cao Yang , Liu Xuewen , Luo Shineng
Published: October 2013

A series of novel bisphosphonates (BPs) were designed and synthesised as longer-chain analogues of the clinically widely used BP–zoledronate (ZL). They were characterised by mass spectrometry, infrared spectroscopy, NMR spectroscopy, and single-crystal X-ray diffraction. All the crystals are zwitterions with one of the phosphonate oxygen atoms deprotonated and the hydrogen atom transferred to the nitrogen of the imidazole ring. A lot of strong hydrogen bonds are observed among the phosphonate oxygens, hydroxy groups, and protonated nitrogen atoms. An accurate, precise, and robust method was developed to determine the bone binding affinities of BPs based on high performance liquid chromatography. The results show that these five BPs have a strong affinity for hydroxyapatite and the binding capacity decreases when the substituted alkyl groups increase in size.
Synthesis, Characterisation, Interaction with DNA, Cytotoxicity, and Apoptotic Studies of Ruthenium(II) Polypyridyl Complexes
Authors: Devi C. Shobha , Nagababu Penumaka , Reddy V. Venkat , Sateesh V. , Srishailam A. , Satyanarayana S.
Published: October 2013

We report the synthesis and characterisation of two new ruthenium(ii) polypyridyl complexes containing monodentate ancillary ligands [Ru(L)4(4HEPIP)], where L = 4-aminopyridine (1) or pyridine (2) and 4HEPIP = 2-(4-hydroxy-3-ethoxyphenyl)-1H-imidazo[4,5-f][1,10](phenanthroline). These complexes were characterised by elemental analysis and ultraviolet-visible, infrared, and 1H NMR spectroscopy. The binding properties of the two complexes towards calf thymus (CT)-DNA were investigated with different spectrophotometric methods, viscosity measurements, and salt dependent studies. Experimental results indicated that the complexes interact with CT-DNA base pairs by intercalation. Upon irradiation at 365 nm, these complexes efficiently cleave pBR322 DNA from super coiled form I to nicked form II. Their cytotoxicity on different cancer cell lines such as A549, Du145, and HeLa was investigated. The IC50 values are 39.5, 28.3, and 27.3 μM for complex 1, and 55, 67.9, and 47.9 μM for complex 2 respectively. Cellular uptake and apoptosis induced by these complexes was also studied.
Spatial regulation dominates gene function in the ganglia chain
Authors: Hibsh Dror , Schori Hadas , Efroni Sol , Shefi Orit
Published: October 2013

Motivation: To understand the molecular mechanisms of neurons, it is imperative to identify genomic dissimilarities within the heterogeneity of the neural system. This is especially true for neuronal disorders in which spatial considerations are of critical nature. For this purpose, Hirudo medicinalis provides here an ideal system in which we are able to follow gene expression along the central nervous system, to affiliate location with gene behavior.

Results: In all, 221.1 million high-quality short reads were sequenced on the Illumina Hiseq2000 platform at the single ganglion level. Thereafter, a de novo assembly was performed using two state-of-the-art assemblers, Trinity and Trans-ABySS, to reconstruct a comprehensive de novo transcriptome. Classification of Trinity and Trans-ABySS transcripts produced a non-redundant set of 76 845 and 268 355 transcripts (>200 bp), respectively. Remarkably, using Trinity, 82% of the published medicinal leech messenger RNAs was identified. For the innexin family, all of the 21 recently reported genes were identified. Spatial regulation analysis across three ganglia throughout the entire central nervous system revealed distinct patterns of gene expression. These transcriptome data were combined with expression distribution to produce a spatio-transcripto map along the ganglia chain. This study provides a resource for gene discovery and gene regulation in future studies.

Contact:  orit.shefi@biu.ac.il or sol.efroni@biu.ac.il

Supplementary information:  Supplementary data are available at Bioinformatics online.
Biological Activity of thetzsGene of NopalineAgrobacterium tumefaciensGV3101 in Plant Regeneration and Genetic Transformation
Authors: Han Zhao-Fen , Hunter David M. , Sibbald Susan , Zhang Ji-Shu , Tian Lining
Published: October 2013

Agrobacterium tumefaciens has been widely used in plant genetic transformation. Hormone-encoding genes residing in the T-DNA region have been removed, resulting in disarmed Agrobacterium strains that are used in various transformation experiments. Nopaline Agrobacterium strains, however, carry another hormone gene, trans-zeatin synthesizing (tzs), that codes for trans-zeatin in the virulence region of the tumor-inducing plasmids. We investigated the activity and function of the tzs gene of a nopaline Agrobacterium sp. strain GV3101 in plant in vitro regeneration. Leaf explants of tobacco and Nicotiana benthamiana co-cultured with strain GV3101 exhibited active shoot regeneration in media without added plant growth regulators. On medium without plant growth regulators, transgenic shoots were also induced from explants co-cultured with GV3101 containing a binary vector. Enzyme-linked immunosorbent assay showed that cell-free extracts of Agrobacterium sp. strain GV3101 culture contained the trans-zeatin at 860 ng/liter. Polymerase chain reaction using tzs-specific primers showed that the tzs gene was present in strain GV3101 but not in other Agrobacterium strains. The study showed that the tzs gene in GV3101 was actively expressed, and that trans-zeatin produced in the Agrobacterium strain can promote plant shoot regeneration.
Fine Tuning of Reactive Oxygen Species Homeostasis Regulates Primed Immune Responses in Arabidopsis
Authors: Pastor Victoria , Luna Estrella , Ton Jurriaan , Cerezo Miguel , García-Agustín Pilar , Flors Victor
Published: October 2013

Selected stimuli can prime the plant immune system for a faster and stronger defense reaction to pathogen attack. Pretreatment of Arabidopsis with the chemical agent β-aminobutyric acid (BABA) augmented H2O2 and callose production after induction with the pathogen-associated molecular pattern (PAMP) chitosan, or inoculation with the necrotrophic fungus Plectosphaerella cucumerina. However, BABA failed to prime H2O2 and callose production after challenge with the bacterial PAMP Flg22. Analysis of Arabidopsis mutants in reactive oxygen species (ROS) production (rbohD) or ROS scavenging (pad2, vtc1, and cat2) suggested a regulatory role for ROS homeostasis in priming of chitosan- and P. cucumerina-inducible callose and ROS. Moreover, rbohD and pad2 were both impaired in BABA-induced resistance against P. cucumerina. Gene expression analysis revealed direct induction of NADPH/respiratory burst oxidase protein D (RBOHD), γ-glutamylcysteine synthetase 1 (GSH1), and vitamin C defective 1 (VTC1) genes after BABA treatment. Conversely, ascorbate peroxidase 1 (APX1) transcription was repressed by BABA after challenge with chitosan or P. cucumerina, probably to provide a more oxidized environment in the cell and facilitate augmented ROS accumulation. Measuring ratios between reduced and oxidized glutathione confirmed that augmented defense expression in primed plants is associated with a more oxidized cellular status. Together, our data indicate that an altered ROS equilibrium is required for augmented defense expression in primed plants.
Patterns of sperm damage in Chernobyl passerine birds suggest a trade-off between sperm length and integrity
Authors: Hermosell Ignacio G. , Laskemoen Terje , Rowe Melissah , Møller Anders P. , Mousseau Timothy A. , Albrecht Tomáš , Lifjeld Jan T.
Published: October 2013

Interspecific variation in sperm size is enigmatic, but generally assumed to reflect species-specific trade-offs in selection pressures. Among passerine birds, sperm length varies sevenfold, and sperm competition risk seems to drive the evolution of longer sperm. However, little is known about factors favouring short sperm or constraining the evolution of longer sperm. Here, we report a comparative analysis of sperm head abnormalities among 11 species of passerine bird in Chernobyl, presumably resulting from chronic irradiation following the 1986 accident. Frequencies of sperm abnormalities varied between 15.7 and 77.3% among species, more than fourfold higher than in uncontaminated areas. Nonetheless, species ranked similarly in sperm abnormalities in unpolluted areas as in Chernobyl, pointing to intrinsic factors underlying variation in sperm damage among species. Scanning electron microscopy of abnormal spermatozoa revealed patterns of acrosome damage consistent with premature acrosome reaction. Sperm length, but not sperm competition risk explained variation in sperm damage among species. This suggests that longer spermatozoa are more susceptible to premature acrosome reaction. Therefore, we hypothesize a trade-off between sperm length and sperm integrity affecting sperm evolution in passerine birds.
Diet alters species recognition in juvenile toads
Authors: Pfennig Karin S. , Rodriguez Moncalvo Verónica G. , Burmeister Sabrina S.
Published: October 2013

Whether environmental effects during juvenile development can alter the ontogeny of adult mating behaviour remains largely unexplored. We evaluated the effect of diet on the early expression of conspecific recognition in spadefoot toads,
Spea bombifrons
. We found that juvenile toads display phonotaxis behaviour six weeks post-metamorphosis. However, preference for conspecifics versus heterospecifics emerged later and was diet dependent. Thus, the environment can affect the early development of species recognition in a way that might alter adult behaviour. Evaluating such effects is important for understanding variation in hybridization between species and the nature of species boundaries.
Dynamic compaction of granular materials
Authors: Favrie N. , Gavrilyuk S.
Published: October 2013

An Eulerian hyperbolic multiphase flow model for dynamic and irreversible compaction of granular materials is constructed. The reversible model is first constructed on the basis of the classical Hertz theory. The irreversible model is then derived in accordance with the following two basic principles. First, the entropy inequality is satisfied by the model. Second, the corresponding ‘intergranular stress’ coming from elastic energy owing to contact between grains decreases in time (the granular media behave as Maxwell-type materials). The irreversible model admits an equilibrium state corresponding to von Mises-type yield limit. The yield limit depends on the volume fraction of the solid. The sound velocity at the yield surface is smaller than that in the reversible model. The last one is smaller than the sound velocity in the irreversible model. Such an embedded model structure assures a thermodynamically correct formulation of the model of granular materials. The model is validated on quasi-static experiments on loading–unloading cycles. The experimentally observed hysteresis phenomena were numerically confirmed with a good accuracy by the proposed model.