bluuebunny/crossref_metadata_2025 huggingface dataset:
PTOMSM: A modified version of Topological Overlap Measure used for predicting Protein-Protein Interaction Network
Authors: Huang Xun
Published: December 2009

A variety of methods are developed to integrating diverse biological data to predict novel interaction relationship between proteins. However, traditional integration can only generate protein interaction pairs within existing relationships. Therefore, we propose a modified version of Topological Overlap Measure to identify not only extant direct PPIs links, but also novel protein interactions that can be indirectly inferred from various relationships between proteins. Our method is more powerful than a naïve Bayesian-network-based integration in PPI prediction, and could generate more reliable candidate PPIs. Furthermore, we examined the influence of the sizes of training and test datasets on prediction, and further demonstrated the effectiveness of PTOMSM in predicting PPI. More importantly, this method can be extended naturally to predict other types of biological networks, and may be combined with Bayesian method to further improve the prediction.
Recent Advancements in Understanding the Ecology of Soil Extracellular Enzymes
Authors: Wallenstein Matthew , Steinweg J. Megan , McMahon Shawna
Published: December 2009

Extracellular enzymes are the agents of detritus decomposition, and are critical for biogeochemical cycling in soils. Despite decades of research, we have only a rudimentary understanding of the controls on enzyme production, stabilization, turnover, and in-situ activity. This limits our ability to interpret measured enzyme activities in an ecological framework. We will present several recent innovations that are advancing our understanding of how soil microbial community interactions with their abiotic environment affect in-situ enzyme activity. In Arctic tundra soils, we developed a model for in-situ Β-glucosidase activity by extrapolating from enzyme activities measured in the lab at a range of temperatures to actual field temperatures. The results of this model suggest that enzyme activity is limited by temperature in the winter and by nitrogen limitation to enzyme production in the summer. In a climate warming and precipitation manipulation experiment in a Boston old field, we found increased enzyme activities in drought plots despite a decrease in microbial biomass. Evidence from the temperature sensitivity of enzyme activity suggests that drought decreased the degradation rate of enzymes, resulting in larger enzyme pools. We will also discuss the importance of tannin inhibition of enzymes, which an often overlooked control on in-situ enzyme activities. We have found that different enzymes are not equivalently affected by increasing tannin concentrations, suggesting that changes in plant litter tannin chemistry in response to climate change could alter soil nutrient stoichiometry. By focusing on controls on in-situ enzyme activity, we hope to advance our understanding of the ecology of soil extracellular enzymes.
NaSb
3
F
10
: A new second-order nonlinear optical crystal to be used in the IR region with very high laser damage threshod
Authors: Zhang Gang , Qin Jingui , Liu Tao , Li Yanjun , Wu Yicheng , Chen Chuangtian
Published: December 2009

This paper reports the second-order nonlinear optical (NLO) property of NaSb3F10, a potential new NLO material in the infrared region. The compound exhibits a phase-matchable second harmonic generation (SHG) efficiency of about 3.2 times that of KH2PO4 based on the powder SHG measurement. A measurement indicates that its laser damage threshold is as high as about 1.3 GW/cm2, which is much higher than all those IR NLO crystals reported in the literature. It also shows excellent transparency in the range of 0.25–7.8 μm with relativity high thermal stability. Single crystal of the size 12×10×8 mm3 has been grown in aqueous solution by a slow evaporation technique.
Tensor generalizations of affine symmetry vectors
Authors: Cook Samuel A. , Dray Tevian
Published: December 2009

A definition is suggested for affine symmetry tensors, which generalize the notion of affine vectors in the same way that (conformal) Killing tensors generalize (conformal) Killing vectors. An identity for these tensors is proven, which gives the second derivative of the tensor in terms of the curvature tensor, generalizing a well-known identity for affine vectors. Additionally, the definition leads to a good definition of homothetic tensors. The inclusion relations between these types of tensors are exhibited. The relationship between affine symmetry tensors and solutions to the equation of geodesic deviation is clarified, again extending known results about Killing tensors.
Creating desired potentials by embedding small inhomogeneities
Authors: Ramm A. G.
Published: December 2009

The governing equation is [∇2+k2−q(x)]u=0 in R3. It is shown that any desired potential q(x), vanishing outside a bounded domain D, bounded in D, Riemann integrable, can be obtained if one embeds into D many small scatterers qm(x), vanishing outside balls Bm≔{x:|x−xm|<a}, such that qm=Am in Bm, qm=0 outside Bm, 1≤m≤M, M=M(a). It is proven that if the number of small scatterers in any subdomain Δ is defined as N(Δ)≔∑xm∊Δ1 and is given by the formula N(Δ)=|V(a)|−1∫Δn(x)dx[1+o(1)] as a→0, where V(a)=4πa3/3, then the limit of the function uM(x), lima→0 uM=ue(x), does exist and solves the equation [∇2+k2−q(x)]u=0 in R3, where q(x)=n(x)A(x), A(xm)=Am, and uM(x) is a solution to the equation [∇2+k2−p(x)]u=0, where p(x)≔pM(x) is some piecewise-constant potential. The total number M of small inhomogeneities is equal to N(D) and is of the order O(a−3) as a→0. A similar result is derived in the one-dimensional case.
Foldy–Wouthuysen wave functions and conditions of transformation between Dirac and Foldy–Wouthuysen representations
Authors: Neznamov V. P. , Silenko A. J.
Published: December 2009

The block diagonalization of the Hamiltonian is not sufficient for the transformation to the Foldy–Wouthuysen (FW) representation. The conditions enabling the transition from the Dirac representation to the FW one are formulated and proven. The connection between wave functions in the two representations is derived. The results obtained allow calculating expectation values of operators corresponding to main classical quantities.
Band tailing effects in neon-implanted GaN
Authors: Majid Abdul , Ali Akbar
Published: December 2009

High resolution x-ray diffraction and optical transmission measurements were performed on neon-implanted metal-organic chemical-vapor deposition-grown GaN thin films, successively annealed at 800 and 1000 °C, to study the effect of implantation. Several subsidiary peaks on lower angle side of the main GaN peak were observed in high resolution x-ray diffraction pattern recorded after implantation. The peaks are ascribed to the expansion of the lattice in the implanted part of the samples. Optical transmission measurements revealed a consistent increase in band tailing and redshift in optical band gap of the implanted samples with increasing dose. The band tailing is proposed to be due to expansion of the lattice caused by the production of point defects in the implanted samples. A correlation between optical and structural properties of the implanted samples was studied using results obtained from dose-dependent variation in interplanar lattice spacing, optical band gap, and Urbach energy measurements.
Analysis of quantum walks with time-varying coin on d-dimensional lattices
Authors: Albertini Francesca , D’Alessandro Domenico
Published: December 2009

In this paper, we present a study of discrete time quantum walks whose underlying graph is a d-dimensional lattice. The dynamical behavior of these systems is of current interest because of their applications in quantum information theory as tools to design quantum algorithms. We assume that, at each step of the walk evolution, the coin transformation is allowed to change so that we can use it as a control variable to drive the evolution in a desired manner. We give an exact description of the possible evolutions and of the set of possible states that can be achieved with such a system. In particular, we show that it is possible to go from a state where there is probability 1 for the walker to be found in a vertex to a state where all the vertices have equal probability. We also prove a number of properties of the set of admissible states in terms of the number of steps needed to obtain them. We provide explicit algorithms for state transfer in low dimensional cases as well as results that allow to reduce algorithms on two-dimensional lattices to algorithms on the one-dimensional lattice, the cycle.
Merging bond-order potentials with charge equilibration
Authors: Mikulski Paul T. , Knippenberg M. Todd , Harrison Judith A.
Published: December 2009

A method is presented for extending any bond-order potential (BOP) to include charge transfer between atoms through a modification of the split-charge equilibration (SQE) formalism. Variable limits on the maximum allowed charge transfer between atomic pairs are defined by mapping bond order to an amount of shared charge in each bond. Charge transfer is interpreted as an asymmetry in how the shared charge is distributed between the atoms of the bond. Charge equilibration (QE) assesses the asymmetry of the shared charge, while the BOP converts this asymmetry to the actual amount of charge transferred. When applied to large molecules, this BOP/SQE method does not exhibit the unrealistic growth of charges that is often associated with QE models.
Conduction in graphenes
Authors: Fowler P. W. , Pickup B. T. , Todorova T. Z. , Myrvold W.
Published: December 2009

It is shown that, within the tight-binding approximation, Fermi-level ballistic conduction for a perimeter-connected graphene fragment follows a simple selection rule: the zero eigenvalues of the molecular graph and of its subgraph minus both contact vertices must be equal in number, as must those of the two subgraphs with single contact vertices deleted. In chemical terms, the new rule therefore involves counting nonbonding orbitals of four molecules. The rule is initially derived within the source and sink potential scattering framework, but has equivalent forms that unify the molecular-orbital and valence-bond approaches to conduction. It is shown that the new selection rule can be cast in terms of Kekulé counts, bond orders, and frontier-orbital coefficients. In particular, for a Kekulean graphene, conduction pathways are shown to be ranked in efficiency by a (nonmonotonic) function of Pauling bond order between the contact vertices. Frontier-orbital analysis of conduction approximates this function. For a monoradical graphene, the analogous function is shown to depend on Pauling spin densities at contact vertices.
Standing-wave excited photoemission experiments on Si/MoSi2 multilayer mirrors in the soft x-ray regime: An analytical modeling approach
Authors: Döring Sven , Schönbohm Frank , Weier Daniel , Lehmkühler Felix , Berges Ulf , Tolan Metin , Fadley Charles S. , Westphal Carsten
Published: December 2009

Photoemission experiments were performed on Si/MoSi2 multilayers using soft x-ray standing waves for excitation. The combination of photoemission spectroscopy and standing-wave excitation results in a depth profile of the sample that is also sensitive to chemical states. The experimental data were analyzed using an approximate analytical, rather than a full numerical, method in order to more quickly yield results, as well as to calibrate and better understand the method. The important parameters in the resulting equations are discussed in detail. Thus, we quickly obtain access to the key parameters modulating the photoelectron intensity excited by x-ray standing waves. We demonstrate the analytical approach on a simple experimental test data set.
Determination of Co spin state in rutile Co:TiO2
Authors: Yan Wensheng , Sun Zhihu , Yao Tao , Pan Zhiyun , Li Zhongrui , Liu Qinghua , Wei Shiqiang
Published: December 2009

X-ray absorption near-edge structure (XANES) and first-principles calculations are employed to determine the Co spin state in the Co-doped TiO2 thin films. Based on the experiments and the theoretical calculations, we find that the transition of Co 1s electron to the unoccupied Co 3d eg states is clarified from the pre-edge single-peak in the Co K-edge XANES spectrum of the Co-doped TiO2 thin film, and that the Co 3d t2g states are occupied while the eg states are partially unoccupied. This suggests a low-spin configuration of the substitutional Co2+ in the Co-doped TiO2 thin film. The studies demonstrate the ability of Co K-edge XANES to provide information on spin state of Co ions in the Co-doped TiO2.
Sn
O
2
thick films for room temperature gas sensing applications
Authors: Khun Khun Kamalpreet , Mahajan Aman , Bedi R. K.
Published: December 2009

Porous nanosized SnO2 powder has been synthesized by a simple nonaqueous sol gel method using SnCl2⋅2H2O and C2H5OH as precursors. Thermal stabilization of the gel is investigated by thermogravimetric/differential thermal analysis. SnO2 powder has been obtained by calcining the gel at 500°C for 3h and studied for its structural properties using x-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), and transmission electron microscopy (TEM). XRD observations confirm the formation of rutile structured SnO2. On an average, 35nm size particles have been found in TEM micrographs of SnO2 powder. FESEM of the powder reveals the formation of a porous network formed by weak aggregation of nanoparticles. An attempt has been made to fabricate gas sensor by depositing thick SnO2 films on glass substrate. Gas sensing studies show that the sensing response of SnO2 sensor toward ammonia is comparatively higher at room temperature as compared to that toward acetone and ethanol.
Switching mechanism transition induced by annealing treatment in nonvolatile Cu/ZnO/Cu/ZnO/Pt resistive memory: From carrier trapping/detrapping to electrochemical metallization
Authors: Yang Y. C. , Pan F. , Zeng F. , Liu M.
Published: December 2009

ZnO/Cu/ZnO trilayer films sandwiched between Cu and Pt electrodes were prepared for nonvolatile resistive memory applications. These structures show resistance switching under electrical bias both before and after a rapid thermal annealing (RTA) treatment, while it is found that the resistive switching effects in the two cases exhibit distinct characteristics. Compared with the as-fabricated device, the memory cell after RTA demonstrates remarkable device parameter improvements including lower threshold voltages, lower write current, and higher Roff/Ron ratio. A high-voltage forming process is avoided in the annealed device as well. Furthermore, the RTA treatment has triggered a switching mechanism transition from a carrier trapping/detrapping type to an electrochemical-redox-reaction-controlled conductive filament formation/rupture process, as indicated by different features in current-voltage characteristics. Both scanning electron microscopy observations and Auger electron spectroscopy depth profiles reveal that the Cu charge trapping layer in ZnO/Cu/ZnO disperses uniformly into the storage medium after RTA, while x-ray diffraction and x-ray photoelectron spectroscopy analyses demonstrate that the Cu atoms have lost electrons to become Cu2+ ions after dispersion. The above experimental facts indicate that the altered status of Cu in the ZnO/Cu/ZnO trilayer films during RTA treatment should be responsible for the switching mechanism transition. This study is envisioned to open the door for understanding the interrelation between different mechanisms that currently exist in the field of resistive memories.
Growth and characterization of aligned ultralong and diameter-controlled silicon nanotubes by hot wire chemical vapor deposition using electrospun poly(vinyl pyrrolidone) nanofiber template
Authors: Zhou Ming , Li Ruishan , Zhou Jinyuan , Guo Xiaosong , Liu Bin , Zhang Zhenxing , Xie Erqing
Published: December 2009

Using aligned suspended polyvinyl pyrrolidone nanofibers array as template, aligned ultralong (about 4 mm) silicon nanotubes have been prepared by a hot wire chemical vapor deposition process. Scanning electron microscopy and transmission electron microscopy demonstrate that the inner diameter (35–200 nm) and wall thickness (20–400 nm) of Si tubes are controlled, respectively, by baking the electrospun nanofibers and by coating time. The tube wall is composed of nanoparticle or nanopillar, and the inner surface of the wall is smoother than the outer surface of the wall. The microphotoluminescence spectra of the thinner Si nanotubes show three light emission bands in the red, green, and blue regions. And the luminescence mechanism is explained according to the quantum-confinement-luminescence center process and radiative recombination from the defect centers.
Evaluation of first crystallization in amorphous Ag-added Ag5.5In6.5Sb59Te29 thin films
Authors: Song Ki-Ho , Seo Jae-Hee , Kim Jun-Hyong , Lee Hyun-Yong
Published: December 2009

In this article, several experimental results were reported for the evaluation of the first crystallization speed (v1st) on the nanosecond time scale as well as the material characteristics of the Ag-added Ag–In–Sb–Te films. The (Ag)x(Ag5.5In6.5Sb59Te29)1−x (x=0, 0.1, and 0.2) films were prepared by thermal evaporation and their phase transformation from an amorphous state to a hexagonal structure via a stable fcc structure was confirmed using x-ray diffraction. Some differences were measured in the optical transmittance (TOP) and absorption between the amorphous and crystalline films in the wavelength (λ) range of 800–3000 nm using an UV-visible-IR spectrophotometer. The v1st values, evaluated using nanopulse reflection response, slightly improved with an increase in the Ag content. For example, the nucleation time/average growth time ratio for the Ag5.5In6.5Sb59Te29 and Ag0.2(Ag5.5In6.5Sb59Te29)0.8 films were approximately 170 ns/70 ns and 110 ns/60 ns, respectively, for an illumination power of 7 mW.
Manipulation of Faraday rotation in Bi-substituted yttrium-iron garnet film using electromagnetic interaction between Au nanoparticles in two-dimensional array
Authors: Ozaki Shinsuke , Kura Hiroaki , Maki Hideyuki , Sato Tetsuya
Published: December 2009

The Faraday rotation in Bi-substituted yttrium-iron garnet thin films, in which an artificially fabricated Au nanoparticle array is embedded, is studied as a function of lattice spacing compared with the extinction spectra. With decreasing lattice spacing in the Au array, the wavelengths corresponding to the enhanced Faraday rotation and the extinction peak showed blueshifts in the same manner. This indicates that Faraday rotation can be manipulated by means of the wavelength shift of localized surface plasmon resonance that originates from the change in electromagnetic interaction between Au nanoparticles.
Effects of doping and grading slope on surface and structure of metamorphic InGaAs buffers on GaAs substrates
Authors: Song Yuxin , Wang Shumin , Tångring Ivar , Lai Zonghe , Sadeghi Mahdad
Published: December 2009

We investigate the effects of doping and grading slope on the surface and structure of linearly alloy graded InGaAs buffers. It is found that the Be doping can improve material properties, resulting in smaller surface roughness and a lower threading dislocation density, while the Si doping has an opposite effect. The effect is strongly dependent on the grading slope. A moderate In grading slope is preferable for the strain relaxation and the minimization of the negative effect of Si doping. Physical mechanisms are proposed to explain the experimental observations. Since doping is essential for many types of optoelectronic devices, these results are valuable for improving the material properties and performance of metamorphic devices.
Dipolar electrostatic energy effect on relaxation process of monolayers at air-water interface: Analysis of thermodynamics and kinetics
Authors: Ou-Yang Wei , Weis Martin , Lee Keanchuan , Manaka Takaaki , Iwamoto Mitsumasa
Published: December 2009

In order to understand the effect of electrostatic energy on phase transition from monolayer to multilayer, isobaric relaxation process of Langmuir monolayers composed of stearic acid or ferroelectric polyvinylidene fluoride and trifluoroethylene copolymer with various vinylidene fluoride (VDF) ratios is investigated in terms of thermodynamic and kinetic analysis. A monotonous decreasing tendency of material loss with respect to temperature is observed for stearic acid monolayer, which is due to thermal activation effect on phase transition from monolayer to multilayer. In contrast, for the ferroelectric monolayer it presents a nonmonotonous behavior of losing materials with a peak position near the Curie temperature, which is not only owing to thermal activation but also dipole moment change. This observation is confirmed for the copolymer monolayers with other VDF content ratios. Amazingly, for the ferroelectric monolayers a good correspondence is found for critical temperatures evaluated from several independent methods including the analysis on slow collapse. This finding again tells the fact that the relaxation process, namely phase transition from monolayer to multilayer, is greatly influenced by dipolar electrostatic energy. Moreover, the study of time dependent relaxation process reveals a diffusionlike behavior of multilayer structure formation, which cannot be interpreted by classical models. Hence a new model based on diffusion-driven material transfer is proposed and diffusivity of the copolymer molecules is estimated with a value of 0.4×10−5 cm2/s. As a whole, this research reflects the importance of dipolar electrostatic energy for phase transition of monolayers at air-water interface.
Comparative study of electroabsorption spectra of polar and nonpolar organic molecules in solution and in a polymer film
Authors: Tayama Jumpei , Iimori Toshifumi , Ohta Nobuhiro
Published: December 2009

Electroabsorption (EA) spectra of polar and nonpolar molecules of coumarin 153 (C153) and pyrene in solution and in a polymer film of polymethylmethacrylate (PMMA) have been measured in the UV-visible region at room temperature. The shape of the EA spectra of C153 in benzene, 1,4-dioxane, or monochlorobenzene remarkably depends on the angle between the polarization direction of the absorption light and the applied electric field, whereas the EA spectra of C153 doped in PMMA show only the Stark shift and the field-induced change in spectral shape is negligible. These results demonstrate that C153 is reoriented by application of electric fields in solution, but the molecules are immobilized in a PMMA film. Based on the EA spectra, electric dipole moments both in the ground state and in the excited state have been evaluated for C153 in different solvents. In the EA spectra of pyrene, only the Stark shift is observed both in solution and in PMMA, indicating that the field-induced molecular reorientation does not occur both in solution and in PMMA. The change in dipole moment of C153 as well as the change in molecular polarizability of pyrene following absorption is much larger in solution than that in PMMA.
Translational energy and state resolved observations of D and D2 thermally desorbing from D clusters chemisorbed on graphite
Authors: Baouche S. , Hornekær L. , Baurichter A. , Luntz A. C. , Petrunin V. V. , Šljivančanin Ž.
Published: December 2009

Direct D atom desorption, as well as associative desorption of D2 molecules are observed in thermal desorption from D atoms chemisorbed on a C(0001) surface by combining laser induced T-jumps with resonance enhanced multiphoton ionization detection. Bleaching curves suggest that different classes of chemisorbed D atom clusters are present on the initial surface. The energy resolved atomic desorption flux, obtained via time of flight techniques, compares favorably (via detailed balance) with theoretical calculations of atomic sticking. Density functional theory calculations of chemical processes (atomic desorption, atomic diffusion/cluster annealing, and associative desorption) on an extensive set of four atom H(D) clusters chemisorbed on C(0001) provide a good interpretation of the experiments. State and energy resolved D2 desorption fluxes are compared with previous state averaged results. In combination with density functional theory calculations these measurements reveal a substantial energy loss (>1 eV) to the surface in the associative desorption.
Magnetomotive drive and detection of clamped-clamped mechanical resonators in water
Authors: Venstra W. J. , Westra H. J. R. , Gavan K. Babaei , van der Zant H. S. J.
Published: December 2009

We demonstrate magnetomotive drive and detection of doubly clamped string resonators in water. A compact 1.9 T permanent magnet is used to detect the fundamental and higher flexural modes of 200 μm long resonators. Good agreement is found between the magnetomotive measurements and optical measurements performed on the same resonator. The magnetomotive detection scheme can be used to simultaneously drive and detect multiple sensors or scanning probes in viscous fluids without alignment of detector beams.
Reynolds number effect on the wake of two staggered cylinders
Authors: Zhou Y. , Feng S. X. , Alam Md. Mahbub , Bai H. L.
Published: December 2009

This work aims to investigate, based on the measured/reported Strouhal number (St) and the flow structure, the Reynolds number (Re) effect on the wake of two identical cylinders with a diameter of d over P∗=P/d=1.2–4.0 and α=0°–90°, where P is the center-to-center spacing between the two cylinders and α is the angle of incident flow with respect to the line through the two cylinder centers. The Re range examined is from 1.5×103 to 2.0×104. Two hotwires were used to measure St simultaneously behind each of the two cylinders. The St-Re relationship is classified into four distinct types, i.e., types 1–4. Each is linked to distinct initial conditions, viz., interactions between the four shear layers around the cylinders. Type 1 occurs at small P∗, not exceeding 1.25. The two cylinders act like a single body, producing a single St across the wake throughout the range of Re examined. On the other hand, type 2 occurs at small α (<10°). Although single valued, the St in type 2 displays a sudden jump with increasing Re due to a switch in the shear layer, separated from the upstream cylinder, from overshooting to reattachment on the downstream cylinder (type 2A) or from reattachment to coshedding vortices (type 2B), depending on P∗. Type 3 is in the region of intermediate P∗ [(1.2–1.5)–2.2] and α (10°–75°). Two distinct St occur at low Re. The lower and the higher ranges of St are associated with the downstream and upstream cylinders, respectively. With increasing Re, the higher St collapses to the lower, which is attributed to a change in the inner shear layer, separated from the upstream cylinder, from squeezing through the gap between cylinders to reattachment on the downstream cylinder. Type 4 occurs at large P∗ (>1.2–2.2) and again exhibits at low Re two St, above and below the Strouhal number St0 in the wake of an isolated cylinder, both changing suddenly or progressively to St0 with increasing Re, which results from a change in the inner shear layer, separated from the upstream cylinder, from reattachment on the downstream cylinder to forming vortices between the cylinders. These types of Re-St relationships are also connected to the flow structure modes reported in literature. The dependence of the St and St-Re relationships on P∗ and α is provided, which may be used for the prediction of St in related problems.
Buoyant formation number of a starting buoyant jet
Authors: Wang Ruo-Qian , Law Adrian Wing-Keung , Adams E. Eric , Fringer Oliver B.
Published: December 2009

Understanding the influence of buoyancy on the formation number is important for analyzing the development of a starting buoyant jet and the interactions between its vortex ring and trailing stem. Numerical simulations with a large-eddy simulation model are performed to reproduce the starting buoyant jet in conditions ranging from pure jet to lazy plume. From the results, an improved method to determine the formation number is proposed based on the occurrence of a step jump in the vortex ring circulation. A comparison of the numerical results with the experimental data for a starting pure jet is first performed. The widely accepted formation number (≈4.0) is obtained, which implies that the method is satisfactory. The effect of buoyancy on the formation number is then investigated for two turbulent discharge conditions of Re=2000 and 2500 and with a wide range of buoyancy flux. Best-fit results are obtained that correlate the formation number with the Richardson number. Finally, a slug model that incorporates buoyancy is developed to allow prediction of the “buoyant formation number” for the starting buoyant jet using a limiting value of 0.33 for the dimensionless energy, which is the same value for a pure jet.
Characteristics of coherent vortical structures in turbulent flows over progressive surface waves
Authors: Yang Di , Shen Lian
Published: December 2009

Vortical structures in turbulence over progressive surface waves are studied using the data from direct numerical simulation of a stress-driven turbulent Couette flow above a waving surface. Instantaneous flow field and its evolution, vorticity statistics, and conditionally averaged flow field with various sampling methods are examined. Unique vortical structures are identified, which are found to be strongly dependent on the wave motion. For a slow wave (with a small value of wave age c/u∗=2; here c is the phase speed of the wave and u∗ is the friction velocity), the vortical structures are characterized by reversed horseshoe vortices and quasistreamwise vortices. The former is concentrated above the wave trough and is associated with sweep events there; the latter has high intensity over the windward face of the wave and is associated with ejection events. Relative to the waveform, the coherent vortical structures propagate in the downstream direction. Vortex turning and vortex stretching play an important role in the vortex transformation and evolution processes. For an intermediate wave (c/u∗=14) and a fast wave (c/u∗=25), the dominant vortical structure is bent quasistreamwise vortices, which are predominantly horizontal but have a distinctive downward bending in their upstream ends near the wave trough. The vortices are found to propagate in the upstream direction with respect to the waveform. The above-wave coherent vortices identified in this study are found to play an important role in the turbulent transport process.
Role of ionization in orientation dependence of molecular high-order harmonic generation
Authors: Chen Y. J. , Hu Bambi
Published: December 2009

We investigate the orientation dependence of high-order harmonic generation (HHG) from O2 and CO2 molecules using the strong-field approximation (SFA). Our simulations reveal the important modulation of the ionization to the HHG orientation dependence, especially at larger orientation angles. By virtue of a simplified model arising from the SFA, we show that this modulation can be read from the harmonic order where the HHG spectra at different orientation angles intersect. These results give suggestions on probing the molecular structure and dynamics using HHG.
Accurate description of phase diagram of clathrate hydrates at the molecular level
Authors: Belosludov Rodion V. , Subbotin Oleg S. , Mizuseki Hiroshi , Kawazoe Yoshiyuki , Belosludov Vladimir R.
Published: December 2009

In order to accurately estimate the thermodynamic properties of hydrogen clathrate hydrates, we developed a method based on the solid solution theory of van der Waals and Platteeuw. This model allows one to take into account the influence of guest molecules on the host lattice and guest-guest interactions—especially when more than one guest molecule occupies a cage. The free energies, equations of state, and chemical potentials of hydrogen and mixed propane-hydrogen clathrate hydrates of cubic structure II with different cage fillings have been estimated using this approach. Moreover, the proposed theory has been used for construction p−T phase diagrams of hydrogen hydrate and mixed hydrogen-propane hydrates in a wide range of pressures and temperatures. For the systems with well defined interactions the calculated curves of “guest gas-hydrate-ice Ih” equilibrium agree with the available experimental data. We also believe that the present model allows one not only to calculate the hydrogen storage ability of known hydrogen hydrate but also predict this value for structures that have not yet been realized by experiment.
The competition between quadratic and integral invariants in inviscid truncated two-dimensional and quasigeostrophic shallow-water turbulence
Authors: Fox S. , Davidson P. A.
Published: December 2009

We investigate the behavior of spectrally truncated simulations of inviscid two-dimensional and quasigeostrophic shallow-water (QGSW) turbulence. Under the assumption that the only conserved quantities are the energy and enstrophy (the total energy and the potential enstrophy in the case of QGSW turbulence), it is possible to use arguments from statistical mechanics to predict an absolute equilibrium form for the (total) energy spectrum E(k)=ak/(k2+b), where a and b are constants. However, other robust integral invariants exist in these systems. In strictly two-dimensional turbulence the low-wavenumber spectrum has the expansion E∼Jk−1+Lk+Ik3+O(k5), where J, L, and I are various integral moments of the two-point vorticity correlation function ⟨ωω′⟩. J and L are invariants, while I is generally time dependent. In the case of QGSW turbulence, the equivalent expansion for the total energy spectrum is Et∼LkR2k−1+ÎkR2k+M̂kR2k3+N̂kR2k5+O(k7), where kR is the Rossby deformation wavenumber and Î, M̂, and N̂ are related to further integral moments of the two-point vorticity correlation function. In this system it is found that Î and M̂ are additional invariants. There must, therefore, be competition at the low-wavenumber end of the spectrum between the developing equilibrium spectrum and the region controlled by the integral invariants. We find that while the equilibrium spectrum comes to dominate an increasing range of wavenumbers, it is always blocked from the region k→0 by the presence of the integral invariants. Furthermore, the rate at which the region occupied by the equilibrium spectrum expands is almost independent of the form of both the equilibrium and low-wavenumber spectra. This can be interpreted as the inverse energy cascade, which carries the equilibrium spectrum to low k, being insensitive to the very high and very low k form of the spectrum.
The number of degrees of freedom of three-dimensional Navier–Stokes turbulence
Authors: Tran Chuong V.
Published: December 2009

In Kolmogorov’s phenomenological theory of turbulence, the energy spectrum in the inertial range scales with the wave number k as k−5/3 and extends up to a dissipation wave number kν, which is given in terms of the energy dissipation rate ϵ and viscosity ν by kν∝(ϵ/ν3)1/4. This result leads to Landau’s heuristic estimate for the number of degrees of freedom that scales as Re9/4, where Re is the Reynolds number. Here we consider the possibility of establishing a quantitative basis for these results from first principles. In particular, we examine the extent to which they can be derived from the three-dimensional Navier–Stokes system, making use of Kolmogorov’s hypothesis of finite and viscosity-independent energy dissipation only. It is found that the Taylor microscale wave number kT (a close cousin of kν) can be expressed in the form kT≤CU/ν=(CU/‖u‖)1/2(ϵ/ν3)1/4. Here U and ‖u‖ are a “microscale” velocity and the root mean square velocity, respectively, and C≤1 is a dynamical parameter. This result can be seen to be in line with Kolmogorov’s prediction for kν. Furthermore, it is shown that the minimum number of greatest Lyapunov exponents whose sum becomes negative does not exceed Re9/4, where Re is defined in terms of an average energy dissipation rate, the system length scale, and ν. This result is in a remarkable agreement with the Landau estimate, up to a presumably slight discrepancy between the conventional and the present energy dissipation rates used in the definition of Re.
Spectral shapes of surface-enhanced resonance Raman scattering sensitive to the refractive index of media around single Ag nanoaggregates
Authors: Yoshida Ken-ichi , Itoh Tamitake , Biju Vasudevanpillai , Ishikawa Mitsuru , Ozaki Yukihiro
Published: December 2009

We found large spectral changes in surface-enhanced resonance Raman scattering (SERRS) with increasing refractive index of media around single Ag nanoaggregates. We analyzed relationship between the spectral changes in SERRS and those in plasma (plasmon) resonance based on the twofold electromagnetic (EM) enhancement theory. The analysis revealed that the changes in SERRS spectra are induced by changes in spectral shapes of twofold EM enhancement factors, which arise from coupling of plasma resonance with both incident and Raman scattering light.
The origin of 2.78 eV emission and yellow coloration in bulk AlN substrates
Authors: Sedhain A. , Du L. , Edgar J. H. , Lin J. Y. , Jiang H. X.
Published: December 2009

The yellow color of bulk AlN crystals was found to be caused by the optical absorption of light with wavelengths shorter than that of yellow. This yellow impurity limits UV transparency and hence restricts the applications of AlN substrates for deep UV optoelectronic devices. Here, the optical properties of AlN epilayers, polycrystalline AlN, and bulk AlN single crystals have been investigated using photoluminescence (PL) spectroscopy to address the origin of this yellow appearance. An emission band with a linewidth of ∼0.3 eV (at 10 K) was observed at ∼2.78 eV. We propose that the origin of the yellow color in bulk AlN is due to a band-to-impurity absorption involving the excitation of electrons from the valence band to the doubly negative charged state, (VAl2−), of isolated aluminum vacancies, (VAl)3−/2− described by VAl2−+hν=VAl3−+h+. In such a context, the reverse process is responsible for the 2.78 eV PL emission.
Dissolution dynamics of thin films measured by optical reflectance
Authors: Punckt Christian , Aksay Ilhan A.
Published: December 2009

Measuring the dissolution dynamics of thin films in situ both with spatial and temporal resolution can be a challenging task. Available methods such as scanning electrochemical microscopy rely on scanning the specimen and are intrinsically slow. We developed a characterization technique employing only an optical microscope, a digital charge coupled device camera, and a computer for image processing. It is capable of detecting dissolution rates of the order of nm/min and has a spatial and temporal resolution which is limited by the imaging and recording setup. We demonstrate the capabilities of our method by analyzing the electrochemical dissolution of copper thin films on gold substrates in a mild hydrochloric acid solution. Due to its simplicity, our technique can be implemented in any laboratory and can be applied to a variety of systems such as thin film sensors or passive coatings.
Accurate thermodynamics for short-ranged truncations of Coulomb interactions in site-site molecular models
Authors: Rodgers Jocelyn M. , Weeks John D.
Published: December 2009

Coulomb interactions are present in a wide variety of all-atom force fields. Spherical truncations of these interactions permit fast simulations but are problematic due to their incorrect thermodynamics. Herein we demonstrate that simple analytical corrections for the thermodynamics of uniform truncated systems are possible. In particular, results for the simple point charge/extended (SPC/E) water model treated with spherically truncated Coulomb interactions suggested by local molecular field theory [J. M. Rodgers and J. D. Weeks, Proc. Natl. Acad. Sci. U.S.A. 105, 19136 (2008)] are presented. We extend the results developed by Chandler [J. Chem. Phys. 65, 2925 (1976)] so that we may treat the thermodynamics of mixtures of flexible charged and uncharged molecules simulated with spherical truncations. We show that the energy and pressure of spherically truncated bulk SPC/E water are easily corrected using exact second-moment-like conditions on long-ranged structure. Furthermore, applying the pressure correction as an external pressure removes the density errors observed by other research groups in NPT simulations of spherically truncated bulk species.
Plasma-assisted molecular beam epitaxy of high quality In2O3(001) thin films on Y-stabilized ZrO2(001) using In as an auto surfactant
Authors: Bierwagen Oliver , White Mark E. , Tsai Min-Ying , Speck James S.
Published: December 2009

The surface roughness of In2O3(001) films is a roadblock to potential semiconductor applications of this material. Using plasma-assisted molecular beam epitaxy we found that In2O3(001) films grow rough by the formation of {111} facets and In2O3(111) films grow smooth without facetting due to the conventionally used (oxygen-rich) conditions. This behavior indicates that the (111) surface is thermodynamically prefered over the (001) surface. We demonstrate that under indium-rich growth conditions these thermodynamics are changed allowing In2O3(001) films to grow smoothly without facetting. Surface indium plays a key role by acting as an auto surfactant that lowers the surface free energy difference between the (001) and the (111) surface.
Role of reversal incoherency in reducing switching field and switching field distribution of exchange coupled composite bit patterned media
Authors: Hauet T. , Dobisz E. , Florez S. , Park J. , Lengsfield B. , Terris B. D. , Hellwig O.
Published: December 2009

Model exchange coupled composite media, namely [Co/Pd]5/Pd(t)/[Co/Ni]3/Co multilayers, deposited onto prepatterned substrates have been investigated for potential use in bit patterned recording. Optimizing the thickness of the Pd interlayer allows decreasing the switching field (HC) and switching field distribution (σSFD) while maintaining thermal stability. The dependence of the remanent coercivity on the external field angle indicates that the gain in HC and σSFD originates from the incoherent magnetization reversal introduced by slightly decoupling the hard and soft multilayer stacks. This tendency is confirmed by further reductions in HC and σSFD, when inserting another Pd interlayer within the hard [Co/Pd]5 stack.
Bio-organic field effect transistors based on crosslinked deoxyribonucleic acid (DNA) gate dielectric
Authors: Yumusak C. , Singh Th. B. , Sariciftci N. S. , Grote J. G.
Published: December 2009

Using DNA-based biopolymers purified from salmon waste, as an insulating layer, bio-organic field effect transistor (BiOFET) devices were fabricated. Such devices exhibit current-voltage characteristics with low operational voltages as compared with using other organic dielectrics. The observed hysteresis in transfer characteristics of such BiOFETs can be reduced using a crosslinking process. Such crosslinked DNA complex is used as a gate dielectric in n-type C60 as well as p-type α-sexithiophene (T6) based BiOFETs.
Phase-locking and frustration in an array of nonlinear spin-torque nano-oscillators
Authors: Tiberkevich Vasil , Slavin Andrei , Bankowski Elena , Gerhart Grant
Published: December 2009

We demonstrate that the cooperative dynamics of an array of coupled spin-torque nano-oscillators (STNO) can be controlled by introduction of an additional external phase shift βc between microwave current, which couples STNOs, and microwave voltage on the array. When this external phase shift βc compensates the intrinsic phase shift β0, caused by the STNO nonlinearity, a phase-locking regime with increased output power and vanishing inhomogeneous linewidth broadening is achieved. In the opposite case, when external and intrinsic phase shifts are added, the STNO array demonstrates a frustration regime with low output power and wide and noisy frequency spectrum.
Cluster sizes in direct and indirect molecular dynamics simulations of nucleation
Authors: Napari Ismo , Julin Jan , Vehkamäki Hanna
Published: December 2009

We performed molecular dynamics simulations of a Lennard-Jones fluid, and compared the sizes of critical clusters in direct simulations of a nucleation event in vapor phase with the sizes of clusters in stable equilibrium with the surrounding vapor. By applying different cluster criteria it is shown that both the critical clusters and the equilibrium clusters have dense cores of similar size but the critical clusters have more outlying cluster atoms surrounding this core. The cluster definition introduced by ten Wolde and Frenkel [J. Chem. Phys. 109, 9901 (1998)], where each cluster atom must have at least five neighboring atoms within the distance of 1.5 times the Lennard-Jones length parameter, agrees well with the cluster size obtained from classical nucleation theory, and we find this agreement to be independent of temperature. The cluster size obtained from the observed nucleation rates by the first nucleation theorem is larger than the classical estimate and much smaller than the size given by the density profile of the equilibrium cluster.
High-speed Ge photodetector monolithically integrated with large cross-section silicon-on-insulator waveguide
Authors: Feng Dazeng , Liao Shirong , Dong Po , Feng Ning-Ning , Liang Hong , Zheng Dawei , Kung Cheng-Chih , Fong Joan , Shafiiha Roshanak , Cunningham Jack , Krishnamoorthy Ashok V. , Asghari Mehdi
Published: December 2009

We demonstrate a compact, high speed Ge photodetector efficiently butt-coupled with a large cross-section silicon-on-insulate (SOI) waveguide in which the Ge p-i-n junction is placed in the horizontal direction to enable very high speed operation. The demonstrated photodetector has an active area of only 0.8×10 μm2, greater than 32 GHz optical bandwidth, and a responsivity of 1.1 A/W at a wavelength of 1550 nm. Very importantly the device can readily be integrated with high performance wavelength-division-multiplexing filters based on large cross-section SOI waveguide to form monolithic integrated silicon photonics receivers for multichannel terabit data transmission applications.
Imbalanced charge mobility in oxygen treated polythiophene/fullerene based bulk heterojunction solar cells
Authors: Chellappan Vijila , Ng Ging Meng , Tan Mein Jin , Goh Wei-Peng , Zhu Furong
Published: December 2009

The effect of oxygen induced traps on charge mobility in bulk heterojunction solar cells using poly(3-hexylthiophene) (P3HT):l-(3-methoxycarbonyl)-propyl-l-phenyl-(6, 6) methanofullerene (PCBM) blend have been studied using photoinduced charge extraction by linearly increasing voltage (PhotoCELIV) technique. The solar cells exposed to oxygen exhibit dual PhotoCELIV peaks, whereas the solar cell without oxygen treatment show single PhotoCELIV peak with the charge mobility of the order of 10−4 cm2/V s. It is demonstrated that the oxygen treatment imbalance the charge mobility in the P3HT/PCBM photoactive layer, which affects the power conversion efficiency and lifetime of the solar cell. The single PhotoCELIV peak for the device without oxygen treatment indicates that the charge mobility is balanced, that causes the overlapping of electron and hole transients.
In situ measurement of the internal luminescence quantum efficiency in organic light-emitting diodes
Authors: Flämmich Michael , Gather Malte C. , Danz Norbert , Michaelis Dirk , Meerholz Klaus
Published: December 2009

The internal luminescence quantum efficiency q is one limiting factor for the performance of organic light-emitting diodes. Photoluminescence measurements are frequently used to estimate q but these neglect effects of the local environment of the emissive sites and the electrical excitation mechanism. We present a method for the in situ measurement of q under electrical operation. The current efficiency of several devices with different emitter-cathode distances is quantitatively compared. Precise optical simulation allows determining q without additional assumptions.