bluuebunny/crossref_metadata_2025_split huggingface dataset:
Competitive absorption of epoxy monomers on carbon nanotube: A molecular simulation study
Authors: Wu Chaofu 
Published: May 2011

AbstractPosition restrained (PR) molecular dynamics (MD) simulations were carried out on the bulk models for the two composite systems including epoxy monomers and carbon nanotube (CNT). The pair energies and the radial distribution functions (RDFs) were computed to evaluate the relative strength of the epoxy monomers binding to the CNT. It is found that the aromatic amine binds more strongly to the CNT than does the aliphatic amine. A vivid view indicates the aromatic rings tend to form π‐stacking with the CNT, and the compounds with aromatic rings prefer to wrap the CNT. These simulated results are in good agreement with those obtained previously from the vacuum models. This work demonstrates that curing agents affect the interactions between epoxy resin and CNT. Other comparisons of relative binding strength of epoxy monomers also depend upon the temperature. Further analyses suggest that the aliphatic amine exhibits more strong interactions with epoxy resin than does the aromatic amine, mainly due to the presence of hydrogen bonds (HBs) between them. Thus, the ultimate performance of epoxy‐CNT polymer nanocomposites should be affected by the two reverse interactions. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2011.
Use of tumor dynamics to clarify the observed variability among biochemical recurrence nomograms for prostate cancer
Authors: Dimonte Guy , Bergstralh E.J. , Bolander M.E. , Karnes R.J. , Tindall D.J. 
Published: May 2011

AbstractBACKGROUNDNomograms for biochemical recurrence (BCR) of prostate cancer (PC) after radical prostatectomy can yield very different prognoses for individual patients. Since the nomograms are optimized on different cohorts, the variations may be due to differences in patient risk‐factor distributions. In addition, the nomograms assign different relative scores to the same PC risk factors and rarely stratify for tumor growth rate.METHODSWe compared BCR‐free probabilities from the GPSM model with a cell kinetics (CK) model that uses the individual's tumor state and growth rate. We first created a cohort of 143 patients that reproduced the GPSM patient distribution in Gleason score, Prostate specific antigen (PSA), Seminal vesicle involvement and Margin status since they form the GPSM score. We then performed 143 CK calculations to determine BCR‐free probabilities for comparison with the GPSM results for all scores and with four other prominent nomograms for a high‐risk patient.RESULTSThe BCR‐free probabilities from the CK model agree within 10% with those from the GPSM study for all scores once the CK model parameters are stratified in terms of the GPSM risk factors and the PSA doubling time (PSADT). However, the probabilities from widely used nomograms vary significantly.CONCLUSIONSThe CK model reproduces the observed GPSM BCR‐free probabilities with a broad stratification of model parameters for PC risk factors and can thus be used to describe PC progression for individual patients. The analysis suggests that nomograms should stratify for PSADT to be predictive. Prostate 72:280–290, 2012. © 2011 Wiley Periodicals, Inc.
Micro‐electroluminescence of cyan InGaN‐based multiple quantum well structures
Authors: Meyer Tobias , Peter Matthias , Danhof Julia , Schwarz Ulrich T. , Hahn Berthold 
Published: May 2011

AbstractMicro‐electroluminescence measurements were performed on multiple quantum well samples grown on sapphire and GaN substrates with emission wavelength 495 nm. Meandering structures were found both in intensity and peak energy. Areas with higher emission intensity had lower energy, which is a hint for carrier redistribution within the quantum wells. A comparison between atomic force microscopy and photoluminescence microscopy revealed that V‐shaped pits reside in regions with low intensity and are associated with higher emission energy. Small intensity and emission energy variations were also found in defect‐free areas and are probably caused by indium content or quantum well thickness fluctuations leading to higher carrier density in regions with low potential energy.
Different behavior of semipolar and polar InGaN/GaN quantum wells: Pressure studies of photoluminescence
Authors: Staszczak G. , Suski T. , Khachapuridze A. , Perlin P. , Funato M. , Kawakami Y. 
Published: May 2011

AbstractPhotoluminescence of (11–22) semipolar and (0001) polar InGaN/GaN quantum wells (QWs) was studied as a function of exciting laser intensity and hydrostatic pressure. A large photoluminescence energy shift with pressure (dEPL/dp) was observed in semipolar QWs comparing to polar ones. In addition, a negligible blue‐shift as a function of exciting laser intensity gives a strong argument for the absence of a built‐in electric field in the studied semipolar structures. These results suggest that In‐segregation effects play an important role in semipolar QWs.
Homoepitaxial growth of AlN on nitrided sapphire by LPE method using Ga–Al binary solution
Authors: Adachi Masayoshi , Maeda Kazuo , Tanaka Akikazu , Kobatake Hidekazu , Fukuyama Hiroyuki 
Published: May 2011

AbstractA novel liquid phase epitaxy method was proposed for growing an AlN layer using Ga–Al binary flux under normal pressure. In this method, nitrogen gas was injected into the flux. Then a nitrided sapphire substrate was used as a template to achieve homoepitaxial growth. Advantages of using a nitrided sapphire substrate were demonstrated; the optimum flux composition was investigated. We grew 1‐µm‐thick c‐axis oriented AlN layer for 5 h at 1573 K. The full width at half maximum values of X‐ray rocking curves for AlN (0002) and (10−12) were, respectively, 50 and 590 arcsec. Moreover, the surface morphology and interfacial structure were observed using a scanning electron microscope, laser microscope, and high‐resolution transmission electron microscope.
Low leakage current in AlGaN/GaN HFETs with preflow of Mg source before growth of u‐GaN buffer layer
Authors: Oshimura Yoshinori , Sugiyama Takayuki , Takeda Kenichiro , Iwaya Motoaki , Takeuchi Tetsuya , Kamiyama Satoshi , Akasaki Isamu , Amano Hiroshi 
Published: May 2011

AbstractAlGaN/GaN heterostructure field‐effect transistors were grown by metalorganic vapor phase epitaxy on Fe‐doped GaN substrates with a preflow of the Mg source. We realized a low drain leakage current, 1.05 µA/mm, at VDS = 20 V and VGS = −5 V with LGD = 3 µm. This leakage current was one order of magnitude lower than that obtained without a preflow of the Mg source. The breakdown voltage was over 250 V with LGD = 10 µm. The on resistance was estimated to be 3.6 mΩ cm2. No significant redistribution or memory effect of Mg was observed by secondary ion mass spectroscopy measurement.
Red emitting LEDs formed by indium rich quantum dots incorporated in MQWs
Authors: Soh C. B. , Liu W. , Chua S. J. , Tan Rayson J. N. , Ang S. S. , Chow S. Y. 
Published: May 2011

Abstractindium rich InGaN nanostructures grown by MOCVD were incorporated in InGaN/GaN quantum wells for long wavelength emission by optimizing the growth condition for the quantum dots (QDs) and InGaN quantum wells. The indium rich InGaN QDs were about 20 nm in diameter and 1.5 nm in height with a density of ∼1 × 1010 cm−2. The InGaN nanostructures in quantum wells capped by AlN were insensitive to In out‐diffusion due to formation of stable Al‐N bonds and lower mobility of Al adatoms on the film surface at 780 °C. The piezeoelectric field in the active layers of the light emitting diodes (LEDs) was reduced with the AlN capped layer and minimal blueshift of the electroluminescence was observed as compared to conventional InGaN/GaN LEDs was noted. The energy band profile of strained AlN/InGaN/QDs/InGaN/GaN quantum well system was analyzed.
Development of high efficiency 255–355 nm AlGaN‐based light‐emitting diodes
Authors: Pernot Cyril , Fukahori Shinya , Inazu Tetsuhiko , Fujita Takehiko , Kim Myunghee , Nagasawa Yosuke , Hirano Akira , Ippommatsu Masamichi , Iwaya Motoaki , Kamiyama Satoshi , Akasaki Isamu , Amano Hiroshi 
Published: May 2011

AbstractWe report on the fabrication and characterization of high efficiency ultraviolet (UV) light emitting diodes (LEDs) with emission wavelength ranging from 255 to 355 nm. Epi‐layers of UV LEDs were grown on AlGaN templates with sapphire substrates. Flip‐chip configuration without removing sapphire is used for characterization of the UV LEDs. External quantum efficiencies (EQEs) over 3% were obtained for all the investigated wavelengths with maximum value reaching 5.1% for 280 nm LED. Under RT DC operation at a current of 500 mA, output powers of 38, 77, and 64 mW were measured for 257, 280, and 354 nm, respectively. By using enhanced light extraction technologies, such as, moth‐eye structure on the back side of the sapphire substrate, we expect to improve these values by up to 50%.
DNA‐sensor based on AlGaN/GaN high electron mobility transistor
Authors: Schwarz Stefan U. , Linkohr Stefanie , Lorenz Pierre , Krischok Stefan , Nakamura Takako , Cimalla Volker , Nebel Christoph E. , Ambacher Oliver 
Published: May 2011

AbstractAlGaN/GaN high electron mobility transistors (HEMTs) show great promise for the realization of sensors for biomolecular, pharmaceutical and medical purposes. The high sensitivity and the stability in biological solutions are great advantages of this approach. Therefore, we created a novel HEMT‐based DNA hybridization sensor. In contrast to other comparable devices, this sensor uses a system of linker molecules to covalently bond the probe DNA to the semiconductor surface. This approach offers the possibility to adjust the density of the probe DNA and provides a highly stable connection. The device shows a clear signal when exposed to the target DNA sequence. Due to the robust attachment of the probe DNA, the double strand can be denatured without corrupting the device. Consequently, the detection of the hybridization event can be repeated several times.
Adaboosting‐based dynamic weighted combination of software reliability growth models
Authors: Li Haifeng , Zeng Min , Lu Minyan , Hu Xuan , Li Zhen 
Published: May 2011

AbstractSoftware reliability growth models (SRGMs) are very important for software reliability estimation and prediction and have been successfully applied in the critical airborne software. However, there is no general model which can perform well for different cases. Thus, some researchers proposed to obtain more accurate estimation and prediction than one single model by combining various individual SRGMs together. AdaBoosting is a commonly used machine learning algorithm for combining several weak predictors into a single strong predictor to significantly improve the estimating and forecasting accuracy, which may be very suitable for the combination of SRGMs. Hence, two novel AdaBoosting‐based combination approaches for improving the parametric SRGMs are presented in this paper. The first one selects several variations of one original SRGM for obtaining the self‐combination model (ASCM). The second selects several various candidate SRGMs for obtaining the multi‐combinational model (AMCM). Finally, two case studies are presented and the results show that: (1) the ASCM is fairly effective and applicable for improving the estimation and prediction performance of its corresponding original SRGM without adding any other factors and assumptions; (2) the AMCM is notably effective and applicable for combining SRGMs because it has well applicability and provides a significantly better reliability estimation and prediction power than the traditional SRGMs and also yields a better estimation and prediction power than the neural‐network‐based combinational model. Copyright © 2011 John Wiley & Sons, Ltd.
Quantum chemical modeling studies of ethylbenzene dehydrogenase activity
Authors: Szaleniec Maciej , Salwiński Aleksander , Borowski Tomasz , Heider Johann , Witko Malgorzata 
Published: May 2011

AbstractQuantum chemical modeling is used to predict the reactivity of ethylbenzene dehydrogenase (EBDH), a molybdenum enzyme that catalyzes the stereoselective oxidation of alkylaromatic and alkylheterocyclic hydrocarbons to the (S)‐enantiomers of secondary alcohols. The reaction mechanism is studied for four different substrates: ethylbenzene, 4‐ethylphenol, allylbenzene, and 4‐ethylpyridine with a cluster model of the active site. The modeling predicts radical CH activation followed by the formation of a radical intermediate product. Then another electron is transferred to form a carbocation species in TS2, followed by a tightly associated OH rebound step. The modeling study allows qualitative correlation of energy barriers with the results of kinetic assays and identifies factors influencing the chemical reactivity of EBDH with different substrates. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011.
CaCuO2 antiferromagnetism using shallow well added solely to atomic potential for generating O2− basis set of periodic molecular orbitals with consideration of coulomb potential in solid in an LDA
Authors: Fukushima Kimichika 
Published: May 2011

AbstractThe antiferromagnetism in an infinite‐layer copper oxide CaCuO2 was analyzed by adding a well potential solely to the atomic potential of an O2− ion in constructing a basis set for a Bloch‐type periodic linear combination of numerically calculated atomic orbitals. (The well is not added to the solid Hamiltonian.) In this method that solves a secular equation to find all electron states, the original Kohn−Sham local density approximation (LDA) was employed. (Magnetic properties calculated with generalized gradient approximation are more similar to those with the original Kohn−Sham LDA than Vosko−Wilk−Nusair results.) The Cu oxides contain the O2− ion, which is stable in a solid but emits an electron in a vacuum. This implies that the atomic wave equation of electrons for an isolated O2− in a vacuum lacks real solutions unless a well potential is added to the atomic potential. The well potential for the O2− basis set was calculated using the Coulomb potential generated by nuclei and electron clouds surrounding O2− in a solid. A relatively shallow well potential within an ion radius compared to the well depth usually used results in significant delocalization of electrons at the O2− site. This periodic molecular orbital method predicts insulating antiferromagnetic ordering in CaCuO2. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
Theoretical study on the reaction of butadiynyl radical (C4H) with ethylene (C2H4) to form C6H4 and H
Authors: Kim Joonghan , Ihee Hyotcherl 
Published: May 2011

AbstractThe reaction mechanisms of the butadiynyl radical (C4H) with ethylene (C2H4) to form H and C6H4 via hydrogen elimination are investigated using the density functional theory and high‐level ab initio methods. The calculated geometrical parameters and dipole moment of the 2Π state of C4H are in excellent agreement with previously reported values using CCSD(T) with large basis sets. The calculated reaction enthalpy is also in excellent agreement with that of previously reported value. These results indicate that theoretical level in this work is optimal and more expensive calculations may not be necessary for the systems studied in this work. Eight isomers of C6H4 are considered in this work, and we present the highly complex reaction pathways by grouping them into three categories; (i) pathways including only chain intermediates without any ring components, (ii) pathways including ring formations except the six‐membered ring, and (iii) pathways including the six‐membered ring. On the basis of the calculated results, the most favorable reaction pathway is simple and found in the first category; H elimination from the initial chain adduct of C4H with C2H4 yields H and one of C6H4 isomers (CH2CHCCCCH). This reaction is similar to that of the reaction of ethynyl (C2H) radical with C2H4. This result clarifies the assumption in the recent experimental kinetics study. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011.
A concentration result with application to subgraph count
Authors: Wolfovitz Guy 
Published: May 2011

AbstractLet H = (V,E) be a k ‐uniform hypergraph with a vertex set V and an edge set E. Let V
p be constructed by taking every vertex in V independently with probability p. Let X be the number of edges in E that are contained in V
p. We give a condition that guarantees the concentration of X within a small interval around its mean. The applicability of this result is demonstrated by deriving new sub‐Gaussian tail bounds for the number of copies of small complete and complete bipartite graphs in the binomial random graph. © 2011 Wiley Periodicals, Inc. Random Struct. Alg., 2012
Fast and reliable reconstruction of phylogenetic trees with indistinguishable edges
Authors: Gronau Ilan , Moran Shlomo , Snir Sagi 
Published: May 2011

AbstractPhylogenetic reconstruction methods attempt to reconstruct a tree describing the evolution of a given set of species using sequences of characters (e.g. DNA) extracted from these species as input. A central goal in this area is to design algorithms which guarantee reliable reconstruction of the tree from short input sequences, assuming common stochastic models of evolution. Thefast convergingreconstruction algorithms introduced in the last decade dramatically reduced the sequence length required to guarantee accurate reconstruction of the entire tree. However, if the tree in question contains even few edges which cannot be reliably reconstructed from the input sequences, then known fast converging algorithms may fail to reliably reconstruct all or most of the other edges. This calls for an adaptive approach suggested in this paper, calledadaptivefast convergence, in which the set of edges which can be reliably reconstructed gradually increases with the amount of information (length of input sequences) available to the algorithm.This paper presents an adaptive fast converging algorithm which returns a partially resolved topology containing no false edges: edges that cannot be reliably reconstructed are contracted into high degree vertices. We also present an upper bound on the weights of those contracted edges, which is determined by the length of input sequences and the depth of the tree. As such, the reconstruction guarantee provided by our algorithm for individual edges is significantly stronger than any previously published edge reconstruction guarantee. This fact, together with the optimal complexity of our algorithm (linear space and quadratic‐time), makes it appealing for practical use. © 2011 Wiley Periodicals, Inc. Random Struct. Alg., 40, 350–384, 2011
Long‐Term structural changes of plasmid DNA studied by atomic force microscopy
Authors: Kim Byung I. , Clark Reilly , Clark Tyler 
Published: May 2011

AbstractLong‐term stability of plasmid DNA (pDNA) conformations is critical in many research areas, especially those concerning future gene therapy. Despite its importance, the time‐evolution of pDNA structures has rarely been studied at a molecular resolution. Here, the time‐evolution of pDNA solutions spanning four years was observed with atomic force microscopy (AFM). The AFM data show that the pDNA molecules changed over time from isolated supercoiled structures, to aggregated supercoiled structures, to thin, branched network structures, and finally to wider, branched network structures. Additional topographical analysis of the AFM data suggests that the actions of residual proteins could be the main mechanism for the structural changes in our laboratory‐prepared pDNA. SCANNING 33:405–412, 2011. © 2011 Wiley Periodicals, Inc.
Random effects models for assessing diagnostic accuracy of traditional Chinese doctors in absence of a gold standard
Authors: Wang Zheyu , Zhou Xiao‐Hua 
Published: May 2011

AbstractTwo common problems in assessing the accuracy of traditional Chinese medicine (TCM) doctors in detecting a particular symptom are the unknown true symptom status and the ordinal‐scale of the symptom status. Wang et al. (Biostatistics 2011; DOI: 10.1093/biostatistics/kxq075) proposed a nonparametric maximum likelihood method for estimating the accuracy of different TCM doctors without a gold standard when the true symptom status is measured on an ordinal‐scale. A key assumption of their work is that the diagnosis results are independent conditional on the gold standard. This assumption can be violated in many practical situations. In this paper, we propose a random effects modeling approach that extends their method to incorporate dependence structure among different tests or doctors. The proposed method is illustrated on a real data set from TCM, which contains the diagnostic results from five doctors for the same patients regarding symptoms related to Chills disease. The same data set was analyzed by Wang et al. under the conditional independence assumption. In addition, we also discuss an ad hoc test for the model fitting and a likelihood ratio test on the random effects. Copyright © 2011 John Wiley & Sons, Ltd.
Separation of Chemical Reaction Intermediates by Metal–Organic Frameworks
Authors: Centrone Andrea , Santiso Erik E. , Hatton T. Alan 
Published: May 2011

AbstractHPLC columns custom‐packed with metal–organic framework (MOF) materials are used for the separation of four small intermediates and byproducts found in the commercial synthesis of an important active pharmaceutical ingredient in methanol. In particular, two closely related amines can be separated in the methanol reaction medium using MOFs, but not with traditional C18 columns using an optimized aqueous mobile phase. Infrared spectroscopy, UV–vis spectroscopy, X‐ray diffraction, and thermogravimetric analysis are used in combination with molecular dynamic simulations to study the separation mechanism for the best‐performing MOF materials. It is found that separation with ZIF‐8 is the result of an interplay between the thermodynamic driving force for solute adsorption within the framework pores and the kinetics of solute diffusion into the material pores, while the separation with Basolite F300 is achieved because of the specific interactions between the solutes and Fe3+ sites. This work, and the exceptional ability to tailor the porous properties of MOF materials, points to prospects for using MOF materials for the continuous separation and synthesis of pharmaceutical compounds.
Design and Application of Inorganic Nanoparticle Superstructures: Current Status and Future challenges
Authors: Gao Yan , Tang Zhiyong 
Published: May 2011

AbstractSelf‐assembly of inorganic nanoparticles (NPs) into superstructures, which is used as a general way to integrate functional inorganic NPs into macroscale devices, has attracted much research interest. This review will summarize the recent progress and discuss future challenges of the inorganic NP superstructures. Examples include both DNA‐based and polymer‐based NP assemblies with controlled positioning and geometries, and quasicrystalline ordered structures from the self‐assembly of binary or ternary NPs. Different from their individual NP counterparts, these self‐assembled superstructures possess unique properties, such as optical chirality and dynamic structural change under an external stimulus. Due to their diversified structures and functionalities, inorganic NP superstructures have shown a wide range of promise for applications in electronic and photonic devices, such as field‐effect transistors, magnetoresistive components, optical information recording, and solar cells.