bluuebunny/crossref_metadata_2025 huggingface dataset:
HEAT CONDUCTION IN ONE-DIMENSIONAL LATTICE WITH DOUBLE-WELL INTERACTION
Authors: LI HAIBIN
Published: April 2011

Heat conduction in one-dimensional lattice with double-well interaction potential is studied numerically in different temperature regions. In the low temperature case, different structures such as order, period-2, and disorder structure phases, lead to different anomalous heat conduction. In a shallow intermediate temperature region, the heat conductivity is finite in a large system size. When temperature increases high enough, the heat conduction is anomalous, as well as FPU-β model.
CHARACTERIZATION OF THE SINTERED Nd15Fe77B8 ALLOY
Authors: HADJADJ L.
Published: April 2011

In this work the purpose is, in addition to the determination of microhardness, to get some information about the effect of heat treatment on the microstructure of the magnetic Nd 15 Fe 77 B 8 alloy. For this study we have used an optical microscope and an electronic microprobe. The results show that the structure of the Nd 2 Fe 14 B phase, which confers good mechanical and magnetic properties on the alloy, is well tetragonal, as mentioned in several works. The morphology, the concentration and the quantity of this phase depend on the temperature of annealing. The microhardness of the phase has an average value between those of the other involved phases.
A VISUAL ATTENTION MODEL FOR NATURAL SCENES BASED ON DYNAMIC FEATURE COMBINATION
Authors: TIAN MINGHUI , WAN SHOUHONG , YUE LIHUA
Published: April 2011

In recent years, many research works indicate that human's visual attention is very helpful in some research areas that are related to computer vision, such as object recognition, scene understanding and object-based image/video retrieval or annotation. This paper presents a visual attention model for natural scenes based on a dynamic feature combination strategy. The model can be divided into three parts, which are feature extraction, dynamic feature combination and salient objects detection. First, the saliency features of color, information entropy and salient boundary are extracted from an original colored image. After that, two different evaluation measurements are proposed for two different categories of feature maps defined in this dynamic combination strategy, which measures the contribution of each feature map to saliency and carries out a dynamic weighting of individual feature maps. Finally, salient objects are located from an integrated saliency map and a computational method is given to simulate the location shift of the real human visual attention. Experimental results show that this model is effective and robust for saliency detection in natural scenes, also similar to the real human visual attention mechanism.
AUTOMATIC IMAGE COMPLETION WITH STRUCTURE PROPAGATION AND TEXTURE SYNTHESIS
Authors: CHEN XIAOWU , ZHOU BIN , XU FANG , ZHAO QINPING
Published: April 2011

In this paper, we present a novel automatic image completion solution in a greedy manner inspired by a primal sketch representation model. Firstly, an image is divided into structure (sketchable) components and texture (non-sketchable) components, and the missing structures, such as curves and corners, are predicted by tensor voting. Secondly, the textures along structural sketches are synthesized with the sampled patches of some known structure components. Then, using the texture completion priorities decided by the confidence term, data term and distance term, the similar image patches of some known texture components are found by selecting a point with the maximum priority on the boundary of hole region. Finally, these image patches inpaint the missing textures of hole region seamlessly through graph cuts. The characteristics of this solution include: (1) introducing the primal sketch representation model to guide completion for visual consistency; (2) achieving fully automatic completion. The experiments on natural images illustrate satisfying image completion results.
EXPLORATION AND OPTIMIZATION OF USER EXPERIENCE IN VIEWING VIDEOS ON A MOBILE PHONE
Authors: SONG WEI , TJONDRONEGORO DIAN , DOCHERTY MICHAEL
Published: April 2011

Compared with viewing videos on PCs or TVs, mobile users have different experiences in viewing videos on a mobile phone due to different device features such as screen size and distinct usage contexts. To understand how mobile user's viewing experience is impacted, we conducted a field user study with 42 participants in two typical usage contexts using a custom-designed iPhone application. With user's acceptance of mobile video quality as the index, the study addresses four influence aspects of user experiences, including context, content type, encoding parameters and user profiles. Accompanying the quantitative method (acceptance assessment), we used a qualitative interview method to obtain a deeper understanding of a user's assessment criteria and to support the quantitative results from a user's perspective. Based on the results from data analysis, we advocate two user-driven strategies to adaptively provide an acceptable quality and to predict a good user experience, respectively. There are two main contributions from this paper. Firstly, the field user study allows a consideration of more influencing factors into the research on user experience of mobile video. And these influences are further demonstrated by user's opinions. Secondly, the proposed strategies — user-driven acceptance threshold adaptation and user experience prediction — will be valuable in mobile video delivery for optimizing user experience.
INTEGRATING MECHANICAL CONTROL THEORY INTO MODELS OF BIOLOGICAL DEVELOPMENT — ANALYTICAL REVIEW
Authors: PETROV VALKO , AEGERTER CHRISTOF
Published: April 2011

This paper presents both a general review on developmental biomechanics and a concrete proposition for the computation of a symmetry breaking instability of a model of biological development in terms of self-organization theory. The necessary biological and physical facts taken from the literature are described and discussed in the context of a unified statement of the problems for mathematical modeling of pattern formation. This is then applied to planar cell polarization (PCP) of the Drosophila wing. In this way, the process is modeled by an elastopolarization equation. In terms of this statement, the mechanical specificity (interaction with basal plate) of wing PCP is characterized. Some aspects of modeling somite formation as well as other developmental processes are also concerned.
CONSTRUCTION OF ANATOMICALLY ACCURATE FINITE ELEMENT MODELS OF THE HUMAN HAND AND A RAT KIDNEY
Authors: MU LI ZHONG , SHAO HONG WEI , HE YING , ODA TOSHIAKI , JIA XUE MEI
Published: April 2011

The aim of the paper is to develop a method for generating three-dimensional (3D) models of organs from medical images (computerized tomography (CT) images, magnetic resonance imaging (MRI), etc.). There were three main steps in the development of the model: the first step was image processing. Different image-processing operators including blurring, sharpening, edge detection, region segmentation, mathematical morphology transformation, rotation, and movement of the kidney slices were performed to automatically construct the accurate boundary information. The second step was mesh generation of each slice based on the boundary information by using the transfinite interpolation (TFI) technique. In this paper, the TFI method was improved to create grids from images directly. The last step was reconstructing the models by stacking the 2D grid models and visualizing the result in the Advanced Visual System (AVS) software. In order to verify the effectiveness of this method, the finite element (FE) models of a rat kidney, human hand, and blood vessels were reconstructed and good results were obtained.
MATERIAL PROPERTIES OF ADULT RAT SKULL
Authors: MAO HAOJIE , WAGNER CHRISTINA , GUAN FENGJIAO , YENI YENER N. , YANG KING H.
Published: April 2011

Development of advanced computational rat head models requires accurate material properties of the rat brain, meninges, skull, and other soft tissues. This study investigated adult rat skull material properties, which are very limited in the current literature. A total of 20 skull specimens were harvested from 10 adult rats. High resolution (16 μm) microcomputed tomography scans were performed for each specimen to observe dimensional changes within each specimen and internal porosities through the cross sections. The specimens were tested in three-point bending at loading velocities of 0.02 and 200 mm/s. The elastic modulus, energy absorbed to failure, energy density, and bending stress were calculated using classical beam theory. Results demonstrated that bending velocity (strain rate) had significant effect on elastic modulus and bending stress, but not on energy and energy density. The Young's moduli of rat skull measured in this study were comparable to those measured from the adult human skull.
WALL SHEAR AND CIRCUMFERENTIAL STRESS CHANGES IN A PORCINE DOUBLE-LAYER VEIN GRAFT
Authors: JI Q. , MEI Y. Q. , WANG X. S. , WUSHA D. W.
Published: April 2011

This study aimed to evaluate short-term changes of wall shear stress and circumferential stress in a self-designed double-layer vein graft in a porcine vein graft model. In this study, left and right hind femoral arteries of 40 white pigs were randomly divided into an experimental group (double-layer vein graft) and a control group (single-layer vein graft). At one hour and then at one, two and four weeks after venous bypass grafting, sets of ten animals underwent Doppler-ultrasonic and electromagnetic flowmeter examinations to calculate wall shear stress in middle sections of the vein grafts. Then, the vein grafts were excised and subjected to mechanical tests to assess the circumferential stress. As a result, the double-layer vein grafts showed an increase in wall shear stress by 43.5% compared with the control group at one hour after venous bypass grafting. With time wall shear stress gradually increased, the intimal circumferential stress gradually decreased in the two groups. Intimal circumferential stress in the experimental group was significantly lower than that in the control group at each observational time-point. Hence, the double-layer support of the vein graft may have contributed towards a rise in wall shear stress and reduction in circumferential stress in the true vein graft over the four-week period after venous bypass grafting, and thus conferring some protection to the true vein graft.
INSIGHTS INTO A 3D HOMOLOGY MODEL OF ARYLESTERASE: THE KEY RESIDUES UPON PROTEIN-LIGAND DOCKING AND MM-PBSA CALCULATIONS
Authors: HAN WEIWEI , WANG YE , LUO QUAN , FENG YAN , NIU XIAODI
Published: April 2011

Arylesterases (E.C. 3.1.1.2) play an important role in nature, which show high enantioselectivity toward chemically and pharmaceutically important compound in addition to being environmentally friendly. The docking results indicate that Tyr34, Leu98, Ile64, Met36, and Ile38 have important contributions to the substrate binding and the side chains of these residues can provide a rather vdW interaction with the substrate. The molecular dynamics calculation of the free energy by MM-PBSA method implies that the S31A and S31G mutant enzymes show more stability as compared with the wild type, which is in harmony with the kinetic experiment that the 2-fold and 2.5-fold increase in the Km for S31A and S31G enzymes. From these results, we can conjecture that mutations of Ser31 make the active site more spacious than that of arylerases', and it can lead to the enzyme active. The new structural insights obtained from this computational study are expected to stimulate further biochemical studies on the structures and mechanisms of other members of the SGNH-hydrolases.
A THEORETICAL STUDY ON ADSORPTION OF THIOPHENE, BENZENE, AND HEXANE IN Na-, Ag-, AND Cu-EXCHANGED MORDENITE
Authors: LIU JIEXIANG , ZHANG XIAOGUANG , DONG MEI , WANG JIANGUO
Published: April 2011

Density functional theory method was applied to investigate adsorption of thiophene, benzene, and hexane in Na- , Ag- , and Cu -exchanged mordenite (MOR). A cluster model containing 16 tetrahedral atoms was constructed as structure model of MOR. The charge-balancing metallic ions ( Na+ , Ag+ , and Cu+ ) were introduced to produce the Lewis acid site (LAS). The acidic strength was estimated by calculating adsorption energy of NH3 in the model. The equilibrium configurations, Mulliken charge populations, and adsorption energies of thiophene, benzene, and hexane in models were calculated and analyzed. For the adsorbates investigated, interaction strengths followed the decreasing order of Cu –MOR > Ag –MOR > Na –MOR that agreed well with their Lewis acidic strengths. The interaction strengths followed the order of thiophene ≈ benzene > hexane in Na –MOR, and thiophene > benzene > hexane in Cu –MOR and Ag –MOR. Moreover, the interaction mechanisms of thiophene and benzene in Cu –MOR and Ag –MOR were investigated by the natural bond orbital (NBO) analysis. Furthermore, similar calculations were carried out for the adsorption of thiophene, benzene, and hexane in the naked Na+ , Cu+ , and Ag+ for comparison.
STUDY OF THE S1 AND S2 EXCITED STATES OF GAS-PHASE PROTONATED SCHIFF BASE RETINAL CHROMOPHORES IN ONE AND TWO PHOTON ABSORPTION
Authors: LI YUANZUO , SONG PENG , SHI YING , DING YONG , ZHOU FENGJIE , ZHAO MEIYU , CHEN MAODU
Published: April 2011

The S1 and S2 excited states of gas-phase protonated Schiff base retinal chromophores in the one- and two-photon absorptions (TPAs) are investigated with time-dependent density functional theory. In one-photon absorption, the two-dimensional (2D) site and three-dimensional (3D) cube representations reveal that S1 and S2 excited states of gas-phase protonated Schiff base retinal chromophores are all charge transfer excited states. To better study the weak S2 excited states of gas-phase protonated Schiff base retinal chromophores, we investigated theoretically excited state properties of them in TPA. For 11-cis dimethyl retinal, it is found that the cross section of S2 excited state is 51.04 GM in PTA, which is only slightly smaller than that of S1 (77.04 GM) in TPA. Therefore, the S2 excited state of 11-cis dimethyl retinal can be clearly observed in TPA experiment. The 2D site and 3D cube representations reveal that electronic transition from S1 to S2 excited state of gas-phase protonated Schiff base retinal chromophores in TPA are also of charge transfer character.
EFFECT OF pH ON STRUCTURE AND STABILITY OF COLLAGEN-LIKE PEPTIDE: INSIGHT FROM MOLECULAR DYNAMICS SIMULATION
Authors: PU SHANG-ZHI , ZHANG WEN-HUA , SHI BI
Published: April 2011

Molecular dynamics simulations were carried out to investigate the effect of pH on structure and stability of collagen-like peptide. All simulations were performed using the consistent valence force field (CVFF) molecular mechanical force field and isothermal-isobaric ensemble (NPT). The initial geometries of the collagen-like peptide were from an X-ray crystallographic structure. Some analyses from the molecular dynamics trajectories have been completed. The results show that the diameter of collagen-like peptide increases and the volume swells obviously in basic environment; however, the size of peptide changes slightly in acidic environment. The stability of collagen-like peptide decreases in acid and basic environment comparing to neutral environment based on root mean square deviation (RMSD). The number of hydrogen bond formed by peptide has a tendency to decrease in both acidic and basic environment. The average of intra-molecular H-bond is minimal under basic condition, and the average of inter-molecular H-bond between amino acid residues and water molecules is minimal under acid condition. The radial distribution function (RDF) shows that side-chain oxygen atoms are easier to form hydrogen bonds with water than side-chain nitrogen atoms. The interaction of various amino acid residues with water is position dependent. Distance between two triple helices increases markedly under highly basic condition, but changes slightly under highly acidic condition.
DIRECT DENSITY FUNCTIONAL THEORY DYNAMICS STUDY FOR THE CH3OCF2CF2OCH3 + OH REACTION
Authors: YU HONG-BO , CUI FENG-CHAO , WANG YONG-XIA , LIU HONG-XIA , LIU JING-YAO
Published: April 2011

The mechanism and kinetics of the reaction of CH3OCF2CF2OCH3 with OH radicals have been studied theoretically by a direct density functional theory dynamics method. All possible H -abstraction channels and displacement processes taking place on two different conformers of CH3OCF2CF2OCH3 have been taken into consideration. The potential energy surface information including the optimized geometries and harmonic vibrational frequencies of all the stationary points and barrier heights involved in these channels were obtained at the BB1K/6-31+G(d,p) level of theory. The rate constants were calculated using improved canonical variational transition state theory (ICVT) with the small-curvature tunneling correction (SCT) over the temperature range of 200–2000 K. The overall rate constant for the title reaction, which was obtained by considering the weight factor of each conformer from the Boltzman distribution function, is in reasonable agreement with the available experimental value. Three-term Arrhenius expression is fitted to be k T = 1.56 × 10-20 T 2.47 exp (-124.64/ T ) cm 3 molecule-1 s-1 (200–2000 K). Also, the enthalpies of formation of the reactant CH3OCF2CF2OCH3 and product radicals CH3OCF2CF2OCH2 and CH3OCF2CF2O , which lack experimental or theoretical data, were evaluated via applying isodesmic reactions.
THE CARRIER-ENVELOPE PHASE DEPENDENCE OF HIGH-ORDER HARMONIC EMISSION AND ISOLATED ATTOSECOND PULSE GENERATION
Authors: YANG DI , CONG SHU-LIN
Published: April 2011

We study theoretically the high-order harmonic generation from neon atoms in a two-color laser field, which is synthesized by a 5-fs/800-nm fundamental driving pulse and a 12-fs/1600-nm subharmonic controlling pulse. Numerical simulations show that the harmonic emission is strongly sensitive to the carrier-envelope phase (CEP) of either the fundamental driving pulse or the subharmonic controlling pulse. When neon atoms are driven by such laser pulses with optimal CEP, the generated high-order harmonic spectrum is a supercontinuum that corresponds to single attosecond pulse. The calculation results are explained in terms of the semiclassical "recollison" model and the time-frequency analysis.
A QUASICLASSICAL TRAJECTORY STUDY OF REACTIVE SCATTERING ON AN ANALYTICAL POTENTIAL ENERGY SURFACE FOR GeH2 SYSTEM
Authors: ZHANG LI , ZHU CHAO-YONG , JIANG GANG , ZHU CHAOYUAN , ZHU Z. H.
Published: April 2011

A quasiclassical trajectory method was employed to study reaction Ge+H 2 (v=0, j=0) and reverse reaction H+GeH (v=0, j=0) on an analytical potential energy surface obtained from simplified many-body expansion method with fitting to B3P86/CC-pVTZ calculations around a global minimum and a long-range van de Waals well plus spectroscopy data for diatomic molecules GeH and H2 . Reaction probabilities from both reaction and reverse reaction were calculated. Dominant reaction is complex-forming reaction Ge+H2 (v=0, j=0) → GeH2 , and its cross section is 10 times bigger than that of complex-forming reaction from the reverse reaction. There is no threshold effect for complex-forming reaction and the cross sections for both complex-forming reactions decrease with the increase of collision energy. Life time of complex is shown to be decreasing with increase of collision energy. Dominant reverse reaction is reaction H + GeH (v=0,j=0) → Ge+H2 ; the reaction probability decreases with the increase of collision energy and differential cross section shows that this reverse reaction has almost equal angular distribution at low collision energy and mostly forward scattering at high collision energy.
CLASSIFICATION OF LARGE MICROARRAY DATASETS USING FAST RANDOM FOREST CONSTRUCTION
Authors: MANILICH ELENA A. , ÖZSOYOǦLU Z. MERAL , TRUBACHEV VALERIY , RADIVOYEVITCH TOMAS
Published: April 2011

Random forest is an ensemble classification algorithm. It performs well when most predictive variables are noisy and can be used when the number of variables is much larger than the number of observations. The use of bootstrap samples and restricted subsets of attributes makes it more powerful than simple ensembles of trees. The main advantage of a random forest classifier is its explanatory power: it measures variable importance or impact of each factor on a predicted class label. These characteristics make the algorithm ideal for microarray data. It was shown to build models with high accuracy when tested on high-dimensional microarray datasets. Current implementations of random forest in the machine learning and statistics community, however, limit its usability for mining over large datasets, as they require that the entire dataset remains permanently in memory. We propose a new framework, an optimized implementation of a random forest classifier, which addresses specific properties of microarray data, takes computational complexity of a decision tree algorithm into consideration, and shows excellent computing performance while preserving predictive accuracy. The implementation is based on reducing overlapping computations and eliminating dependency on the size of main memory. The implementation's excellent computational performance makes the algorithm useful for interactive data analyses and data mining.
COMPARING MULTIPLE ChIP-SEQUENCING EXPERIMENTS
Authors: OZER HATICE GULCIN , HUANG YI-WEN , WU JIEJUN , PARVIN JEFFREY D. , HUANG TIM HUI-MING , HUANG KUN
Published: April 2011

New high-throughput sequencing technologies can generate millions of short sequences in a single experiment. As the size of the data increases, comparison of multiple experiments on different cell lines under different experimental conditions becomes a big challenge. In this paper, we investigate ways to compare multiple ChIP-sequencing experiments. We specifically studied epigenetic regulation of breast cancer and the effect of estrogen using 50 ChIP-sequencing data from Illumina Genome Analyzer II. First, we evaluate the correlation among different experiments focusing on the total number of reads in transcribed and promoter regions of the genome. Then, we adopt the method that is used to identify the most stable genes in RT-PCR experiments to understand background signal across all of the experiments and to identify the most variable transcribed and promoter regions of the genome. We observed that the most variable genes for transcribed regions and promoter regions are very distinct. Gene ontology and function enrichment analysis on these most variable genes demonstrate the biological relevance of the results. In this study, we present a method that can effectively select differential regions of the genome based on protein-binding profiles over multiple experiments using real data points without any normalization among the samples.
ANALYZING MODULAR RNA STRUCTURE REVEALS LOW GLOBAL STRUCTURAL ENTROPY IN MICRORNA SEQUENCE
Authors: SHAW TIMOTHY I. , MANZOUR AMIR , WANG YINGFENG , MALMBERG RUSSELL L. , CAI LIMING
Published: April 2011

Secondary structure remains the most exploitable feature for noncoding RNA (ncRNA) gene finding in genomes. However, methods based on secondary structure prediction may generate superfluous amount of candidates for validation and have yet to deliver the desired performance that can complement experimental efforts in ncRNA gene finding. This paper investigates a novel method, unpaired structural entropy (USE) as a measurement for the structure fold stability of ncRNAs. USE proves to be effective in identifying from the genome background a class of ncRNAs, such as precursor microRNAs (pre-miRNAs) that contains a long stem hairpin loop. USE correlates well and performs better than other measures on pre-miRNAs, including the previously formulated structural entropy. As an SVM classifier, USE outperforms existing pre-miRNA classifiers. A long stem hairpin loop is common for a number of other functional RNAs including introns splicing hairpins loops and intrinsic termination hairpin loops. We believe USE can be further applied in developing ab initio prediction programs for a larger class of ncRNAs.
LEX-SVM: EXPLORING THE POTENTIAL OF EXON EXPRESSION PROFILING FOR DISEASE CLASSIFICATION
Authors: YUAN XIONGYING , ZHAO YI , LIU CHANGNING , BU DONGBO
Published: April 2011

Exon expression profiling technologies, including exon arrays and RNA-Seq, measure the abundance of every exon in a gene. Compared with gene expression profiling technologies like 3′ array, exon expression profiling technologies could detect alterations in both transcription and alternative splicing, therefore they are expected to be more sensitive in diagnosis. However, exon expression profiling also brings higher dimension, more redundancy, and significant correlation among features. Ignoring the correlation structure among exons of a gene, a popular classification method like L1-SVM selects exons individually from each gene and thus is vulnerable to noise. To overcome this limitation, we present in this paper a new variant of SVM named Lex-SVM to incorporate correlation structure among exons and known splicing patterns to promote classification performance. Specifically, we construct a new norm, ex-norm, including our prior knowledge on exon correlation structure to regularize the coefficients of a linear SVM. Lex-SVM can be solved efficiently using standard linear programming techniques. The advantage of Lex-SVM is that it can select features group-wisely, force features in a subgroup to take equal weihts and exclude the features that contradict the majority in the subgroup. Experimental results suggest that on exon expression profile, Lex-SVM is more accurate than existing methods. Lex-SVM also generates a more compact model and selects genes more consistently in cross-validation. Unlike L1-SVM selecting only one exon in a gene, Lex-SVM assigns equal weights to as many exons in a gene as possible, lending itself easier for further interpretation.
TEMPORAL GRAPHICAL MODELS FOR CROSS-SPECIES GENE REGULATORY NETWORK DISCOVERY
Authors: LIU YAN , NICULESCU-MIZIL ALEXANDRU , LOZANO AURÉLIE , LU YONG
Published: April 2011

Many genes and biological processes function in similar ways across different species. Cross-species gene expression analysis, as a powerful tool to characterize the dynamical properties of the cell, has found a number of applications, such as identifying a conserved core set of cell cycle genes. However, to the best of our knowledge, there is limited effort on developing appropriate techniques to capture the causality relations between genes from time-series microarray data across species. In this paper, we present hidden Markov random field regression with L1penalty to uncover the regulatory network structure for different species. The algorithm provides a framework for sharing information across species via hidden component graphs and is able to incorporate domain knowledge across species easily. We demonstrate our method on two synthetic datasets and apply it to discover causal graphs from innate immune response data.
IN SEARCH OF THE PROTEIN NATIVE STATE WITH A PROBABILISTIC SAMPLING APPROACH
Authors: OLSON BRIAN , MOLLOY KEVIN , SHEHU AMARDA
Published: April 2011

The three-dimensional structure of a protein is a key determinant of its biological function. Given the cost and time required to acquire this structure through experimental means, computational models are necessary to complement wet-lab efforts. Many computational techniques exist for navigating the high-dimensional protein conformational search space, which is explored for low-energy conformations that comprise a protein's native states. This work proposes two strategies to enhance the sampling of conformations near the native state. An enhanced fragment library with greater structural diversity is used to expand the search space in the context of fragment-based assembly. To manage the increased complexity of the search space, only a representative subset of the sampled conformations is retained to further guide the search towards the native state. Our results make the case that these two strategies greatly enhance the sampling of the conformational space near the native state. A detailed comparative analysis shows that our approach performs as well as state-of-the-art ab initio structure prediction protocols.
Amphiphilic zinc phthalocyanine dendrimers by the Click Chemistry approach
Authors: Hahn Uwe , Torres Tomás
Published: April 2011

A series of new zinc phthalocyanine dendrimers with an increasing branched shell of oligoethylene glycol end groups has been synthesized. Owing to the presence of these hydrophilic termini at the dendrimer surface, all compounds are highly soluble in a wide range of solvents including water. The monodispersity of the amphiphilic dendrimers has been unambiguously evidenced by both NMR and MS techniques. UV-vis experiments point out that the tendency of the central phthalocyanine chromophore to aggregate in polar protic solvents is not significantly reduced regardless of the dendritic shell surrounding the macrocyclic chromophore.
PREPARATION OF CISPLATIN COMPOSITE MICRO/NANOFIBERS AND ANTITUMOR ACTIVITY IN VITRO AGAINST HUMAN TUMOR spc-a-1 CELLS
Authors: CHEN PING , WU QING-SHENG , DING YA-PING , ZHU ZI-CHUN
Published: April 2011

In this paper, the cisplatin composite micro/nanofibers were prepared by electrospinning. Average diameter of the typical products was about 700 nm, and cisplatins were incorporated in biodegradable poly (L-lactic acid) fibers. The controlled release of cisplatin can be gained for long time. The possible mechanisms of cisplatin release in the PBS and the PBS with proteinase K were discussed. 3-(4, 5)-dimethylthiahiazo-(-z-y1)-3, 5-di-phenytetrazoliumromide (MTT) method was used to test antitumor activities in vitro against human lung tumor spc-a-1 cells. When incubation time was 24 h, the same content of cisplatin from virgin cisplatin and the composite fibers has almost equal antitumor activity in vitro. However, when incubation time was 48 h, the composite fibers show much higher antitumor activity than the virgin cisplatin. The system may be useful in the postoperative local chemotherapy and have clinical applications as an implantable drug for tumor in the future.
SIMULATING DEFLECTION AND DETERMINING STABLE LENGTH OF FREESTANDING CARBON NANOTUBE PROBE/SENSOR IN THE VICINITY OF GRAPHENE LAYERS USING A NANOSCALE CONTINUUM MODEL
Authors: KOOCHI ALI , KAZEMI ASIEHSADAT , ABADYAN MOHAMADREZA
Published: April 2011

Herein, the deflection and instability of a freestanding carbon nanotube (CNT) probe/sensor in the vicinity of the graphene layers are investigated. A nanoscale continuum model is employed to obtain nonlinear constitutive equation of freestanding CNT. The van der Waals attraction is computed from the simplified Lennard-Jones potential for two common engineering cases including large and small number of graphene layers. Four approaches, i.e., approximated function, homotopy perturbation method, lumped parameter model and numerical analysis, are employed to solve the governing equation of CNT. The intermolecular force-induced deflection, minimum initial gap and stable length of freestanding CNT are determined. The analytical results agree well with the numerical solutions.
Interfacial Atomic Structure Between Pt-Added NiSi and Si(001)
Authors: Ikarashi Nobuyuki , Narihiro Mitsuru , Hase Takashi
Published: April 2011

A scanning transmission electron microscopy analysis of a Pt-added NiSi/Si(001) interfacial structure revealed that the interface is atomically abrupt and that Pt atoms segregate at the first NiSi interfacial atomic layer and occupy the Ni sites. In addition, the in-plane distribution of the Pt atoms is affected by the lattice stress distribution at the interface. Thus, we inferred that the Pt segregation lowered the interfacial stress to reduce the interface energy and that this interface energy reduction plays an important role in stabilizing the NiSi phase.
Quantitative Analysis of Stress Relaxation in Transmission Electron Microscopy Samples by Raman Spectroscopy with a High-Numerical Aperture Lens
Authors: Kosemura Daisuke , Ogura Atsushi
Published: April 2011

Transmission electron microscopy (TEM) has been used for the evaluation of strain in Si. In TEM measurements, stress relaxation is inevitable during the fabrication of TEM samples. It is important to know the extent of stress relaxation to obtain meaningful results in stress measurements by TEM. In this study, we demonstrate the quantitative analysis of stress relaxation in TEM samples using Raman spectroscopy with a high-numerical aperture (NA) oil-immersion lens. We consider that the z polarization of incident light can be accomplished using a high-NA lens, which allows us to excite the forbidden mode, i.e., the transverse optical (TO) phonon mode, in Si. We confirmed that the TO mode was surely excited in a strained Si on insulator (SSOI) substrate using a high-NA lens. Finally, stress relaxations in TEM samples of SSOI were obtained; the stress relaxations along the shorter and longer dimensions reach approximately 70 and 30%, respectively, in the TEM sample with a thickness of 240 nm (the length and depth of the TEM samples are 10 and 10 µm, respectively).
In situ Formation of HfN/HfSiON Gate Stacks with 0.5 nm Equivalent Oxide Thickness Utilizing Electron Cyclotron Resonance Plasma Sputtering on Three-Dimensional Si Structures
Authors: Sano Takahiro , Ohmi Shun-ichiro
Published: April 2011

In situ formation of HfN/HfSiON gate stacks on three-dimensional (3D) Si structures using electron cyclotron resonance (ECR) plasma sputtering method was investigated. The conditions of postdeposition annealing (PDA) of in situ formed HfN/HfSiON were optimized to suppress reactions occurring at the interfaces of the gate stack structures for realizing a small equivalent oxide thickness (EOT), low leakage current, and a low density of interface state (D
it). It was found that 600 °C/15 s was a suitable condition of PDA of the HfN/HfSiON/p-Si(100) structure to decrease D
it and hysteresis width in the capacitance–voltage (C–V) characteristic. The EOT and D
it of HfN/HfSiON/p-Si(100) annealed at 600 °C were 0.5 nm and an order of 1011 cm-2 eV-1, respectively. Furthermore, an excellent C–V characteristic of the HfN/HfSiON gate stack annealed at 600 °C was obtained even on 3D Si structures, and the EOT was as small as 0.53 nm.
Fabrication of Ge Metal–Oxide–Semiconductor Capacitors with High-Quality Interface by Ultrathin SiO2/GeO2 Bilayer Passivation and Postmetallization Annealing Effect of Al
Authors: Hirayama Kana , Ueno Ryuji , Iwamura Yoshiaki , Yoshino Keisuke , Wang Dong , Yang Haigui , Nakashima Hiroshi
Published: April 2011

A novel method of electrical passivation of a Ge surface by an ultrathin SiO2/GeO2 bilayer is proposed as an effective method for fabricating metal–oxide–semiconductor (MOS) structures, which can be processed through the thermal etching of GeO2 by vacuum annealing and subsequent SiO2 deposition. We demonstrated the feasibility of this passivation technique by performing interface state density (D
it) measurements of MOS capacitors, which were fabricated using several surface preparations and subsequent gate insulating film deposition. A D
it of 4×1011 cm-2 eV-1 was obtained at around midgap. We also investigated the effect of postmetallization annealing after Al deposition (Al-PMA). Al-PMA was found to be very effective for decreasing D
it, which was 9.4×1010 cm-2 eV-1 at around midgap for a capacitor with PMA at 400 °C. The role of Al as a defect terminator was discussed.
Native Oxidation Growth on Ge(111) and (100) Surfaces
Authors: Sahari Siti Kudnie , Murakami Hideki , Fujioka Tomohiro , Bando Tatsuya , Ohta Akio , Makihara Katsunori , Higashi Seiichiro , Miyazaki Seiichi
Published: April 2011

We studied the native oxide growth on Ge(100) and (111) surfaces treated by HCl and HF cleaning in clean room air by high-resolution X-ray photoelectron spectroscopy (XPS) and spectroscopic ellipsometry (SE). The native oxidation of both HCl- and HF-last Ge(100) surfaces exhibited likely layer-by-layer fashion. The native oxide growth of the n-Ge(100) was significantly faster than the p-Ge(100) at the early stage of native oxidation. This can be explained by the formation of an O2- ion through free electron transfer from the Ge to the adsorbed O2 molecules, which induces the surface electric field that can initiate the oxidation. In the case of different crystallographic orientations, the oxide rate of the Ge(100) surface was faster than that of the Ge(111) surface. This might be attributed to larger open space of the Ge(100) surface than that of the Ge(111) surface.
Annealing Effects on Ge/SiO2Interface Structure in Wafer-Bonded Germanium-on-Insulator Substrates
Authors: Yoshitake Osamu , Kikkawa Jun , Nakamura Yoshiaki , Toyoda Eiji , Isogai Hiromichi , Izunome Koji , Sakai Akira
Published: April 2011

We have investigated annealing effects on Ge/SiO2interfaces in wafer-bonded germanium-on-insulator substrates using transmission electron microscopy and electron energy loss spectroscopy. A number of nanometer-sized hollows were observed at the Ge/SiO2interfaces after annealing at 500 and 600 °C, while the density of these hollows was very small after annealing at 700 and 800 °C. The hollows are attributed to the formation of amorphous oxides of Si-rich Si1-xGexO2. The mechanism for the formation and disappearance of these amorphous hollows on the Ge substrates is discussed.
Electrical Characterization of Wafer-Bonded Germanium-on-Insulator Substrates Using a Four-Point-Probe Pseudo-Metal–Oxide–Semiconductor Field-Effect Transistor
Authors: Iwasaki Yuji , Nakamura Yoshiaki , Kikkawa Jun , Sato Motoki , Toyoda Eiji , Isogai Hiromichi , Izunome Koji , Sakai Akira
Published: April 2011

The electrical characteristics of wafer-bonded non-doped germanium-on-insulator (GOI) substrates were investigated using a four-point-probe pseudo-metal–oxide–semiconductor field-effect transistor. Annealing the wafer-bonded GOI substrates in vacuum strongly influenced their electrical characteristics. GOI samples annealed at temperatures below 500 °C exhibited n-channel depletion transistor operation, whereas GOI samples annealed at temperatures between 550 and 600 °C exhibited p-channel depletion transistor operation. The carrier mobility strongly depended on the sweep direction of the gate voltage; this characteristic disappeared after annealing at temperatures above 550 °C. The dependence of the electrical characteristics on the annealing temperature is explained in terms of the influence of the defect states on energy band bending near the interface.
Effect of Pr Valence State on Interfacial Structure and Electrical Properties of Pr Oxide/PrON/Ge Gate Stack Structure
Authors: Kato Kimihiko , Sakashita Mitsuo , Takeuchi Wakana , Kondo Hiroki , Nakatsuka Osamu , Zaima Shigeaki
Published: April 2011

In this study, we investigated the valence state and chemical bonding state of Pr in a Pr oxide/PrON/Ge structure. We clarified the relationship between the valence state of Pr and the Pr oxide/Ge interfacial reaction using Pr oxide/Ge and Pr oxide/PrON/Ge samples. We found the formation of three Pr oxide phases in Pr oxide films; hexagonal Pr2O3 (h-Pr2O3) (Pr3+), cubic Pr2O3 (c-Pr2O3) (Pr3+), and c-PrO2 (Pr4+). We also investigated the effect of a nitride interlayer on the interfacial reaction in Pr oxide/Ge gate stacks. In a sample with a nitride interlayer (Pr oxide/PrON/Ge), metallic Pr–Pr bonds are also formed in the c-Pr2O3 film. After annealing in H2 ambient, the diffusion of Ge into Pr oxide is not observed in this sample. Pr–Pr bonds probably prevent the interfacial reaction and Ge oxide formation, considering that the oxygen chemical potential of this film is lower than that of a GeO2/Ge system. On the other hand, the rapid thermal oxidation (RTO) treatment terminates the O vacancies and defects in c-Pr2O3. As a result, c-PrO2 with tetravalent Pr is formed in the Pr oxide/PrON/Ge sample with RTO. In this sample, the leakage current density is effectively decreased in comparison with the sample without RTO. Hydrogen termination works effectively in Pr oxide/PrON/Ge samples with and without RTO, and we can achieve an interface state density of as low as 4 ×1011 eV-1·cm-2.
Advanced Organic Polymer for the Aggressive Scaling of Low-k Materials
Authors: Pantouvaki Marianna , Huffman Craig , Zhao Larry , Heylen Nancy , Ono Yukiharu , Nakajima Michio , Nakatani Koji , Beyer Gerald P. , Baklanov Mikhail R.
Published: April 2011

An advanced organic polymer material of k = 2.2 has been successfully integrated in Cu lines with dielectric spacing from 80 to 20 nm. Cu lines with both TaN/Ta barrier and no barrier were fabricated. Current–voltage (I–V) and time dependent dielectric breakdown (TDDB) measurements were performed to study the scalability of this material. In the case of TaN/Ta barrier, no TDDB degradation was observed at 100 °C as the dielectric spacing changed from 80 to 30 nm. In the case of no barrier, TDDB performance at 100 °C was better than that of SiO2 without a barrier. However, TDDB at 200 °C showed a clear degradation. In contrast, no such degradation was present when TaN/Ta barrier was used.
Structure Analyses of Ti-Based Self-Formed Barrier Layers
Authors: Kohama Kazuyuki , Ito Kazuhiro , Sonobayashi Yutaka , Ohmori Kazuyuki , Mori Kenichi , Maekawa Kazuyoshi , Shirai Yasuharu , Murakami Masanori
Published: April 2011

Self-formed Ti-based barrier layer using Cu(Ti) alloy seed applied to 45-nm-node dual-damascene interconnects was reported to have sufficient barrier strength to prevent Cu diffusion into dielectrics. The constituent Ti compounds in the self-formed Ti-based barrier layers and the barrier structures in Cu(Ti)/dielectric samples were identified by X-ray photoelectron spectroscopy (XPS) analyses. Two types of SiOC with low dielectric constants, SiO2, and SiCN were used as dielectrics. The Ti-based barrier layers consisted mainly of amorphous Ti oxides such as TiO2, Ti2O3, and TiO, regardless of the dielectric. In addition to Ti oxides, barrier layers containing TiC, TiSi, and TiN were observed, depending on the dielectric. TiC and TiSi were in crystalline state. They were formed beneath the Cu(Ti) alloy films, and had orientation relationship with the crystalline Cu(Ti) alloy films. The amorphous Ti oxides were formed above the amorphous dielectric layers. The amorphous Ti oxides are believed to be formed continuously above the dielectric layers and prevent Cu diffusion into the dielectric layers.
Above-Complementary Metal–Oxide–Semiconductor Metal Pattern Technique for Postfabrication Tuning of On-Chip Inductor Characteristics
Authors: Kotani Koji , Sugimoto Atsuo , Omiya Yutaka , Ito Takashi
Published: April 2011

In the design of radio frequency (RF) circuits, modifying the characteristics of an inductor in efficient way is required to realize rapid prototyping of RF system-on-a-chip (SoC). We propose an above-complementary-metal–oxide–semiconductor (above-CMOS) metal pattern technique. In this technique, metal patterns are formed using a simple process on the passivation layer above the on-chip inductor. Since the metal pattern with different shapes has different effects, we can tune the characteristics of an on-chip inductor by forming various metal patterns in a chip-by-chip manner. This method can experimentally create various inductors from an identical on-chip inductor. Therefore, the optimization of inductor characteristics and related circuit performance can be carried out in a short period and at a low cost on a trial-and-error basis, which is very effective for rapid prototyping of RF SoCs. Adjustment of the oscillation frequency of the voltage-controlled oscillator using this technique and the technique of modeling the above-CMOS metal pattern are also described in this paper.
Double Dielectric Spacer for the Enhancement of Silicon p-Channel Tunnel Field Effect Transistor Performance
Authors: Virani Hasanali G. , Gundapaneni Suresh , Kottantharayil Anil
Published: April 2011

A double dielectric spacer concept is proposed for the enhancement of the performance of silicon p-channel tunnel field effect transistor. The double dielectric spacer consist of an inner layer made of a high-k material and an outer layer made of a low-k material. We show that the double dielectric spacer with high-k inner layer result in the concentration of the external fringe field near the source to channel junction, resulting in the improvement of ON state currents without degrading the OFF state current or the subthreshold swing. Further we have illustrated improved dynamic performance of the double dielectric spacer architecture using mixed mode simulations of unloaded and capacitively loaded inverter circuits for the first time. Performance improvements are illustrated and explained for silicon dioxide, aluminium oxide and hafnium oxide gate dielectrics.
Metal Schottky Source/Drain Technology for Ultrathin Silicon-on-Thin-Box Metal Oxide Semiconductor Field Effect Transistors
Authors: Shima Akio , Sugii Nobuyuki , Mise Nobuyuki , Hisamoto Digh , Takeda Ken-ichi , Torii Kazuyoshi
Published: April 2011

This paper reports novel, non-epitaxial raised source/drain (S/D) approaches to decrease the parasitic external resistance in complementary metal–oxide–semiconductor field-effect transistors (CMOSFETs) fabricated on ultrathin silicon on insulator (UTSOI). This technique utilizes a metal Schottky S/D process with dopant segregation. Selectively formed NiSi2 with dopant segregation fabricated by laser-spike annealing (LSA) significantly lowered effective Shottky-barrier height and, thereby, lowered contact resistance (ρc). Satisfying the requirements of UTSOI MOSFETs in the 32-nm node for low stand-by power (LSTP) application, external parasitic resistance was reduced to 140 (NMOS) and 350 (PMOS) Ω µm. Our results show that ρc is an important component of parasitic resistance in terms of improving device performance of UTSOI MOSFETs.
High-Temperature Properties of Drain Current Variability in Scaled Field-Effect Transistors Analyzed by Decomposition Method
Authors: Tsunomura Takaaki , Kumar Anil , Mizutani Tomoko , Nishida Akio , Takeuchi Kiyoshi , Inaba Satoshi , Kamohara Shiro , Terada Kazuo , Hiramoto Toshiro , Mogami Tohru
Published: April 2011

The properties of drain current variability in field-effect transistors (FETs) at high temperature are experimentally investigated. It is found that the on-state drain current (I
ON) at high temperature has a strong correlation with I
ON at room temperature and that there is no anomalous I
ON change from room temperature to high temperature. It is also found that I
ON variability at high temperature is smaller than that at room temperature. The origin of the decrease in I
ON variability with increasing temperature is analyzed by the decomposition method developed in our previous work. It is clarified that the decrease in the current–onset voltage component plays a dominant role, especially in the saturation region. Moreover, it is also clarified that thermal excitation of carriers suppresses current–onset voltage variability, and ultimately the current–onset voltage component of I
ON variability with increasing temperature.