bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification and Characterisation of a Bryophyte Polyphenol Oxidase Encoding Gene from Physcomitrella patens
Authors: Richter H. , Lieberei R. , von Schwartzenberg K.
Published: May 2005

Abstract: Polyphenol oxidases (PPO) are enzymes of secondary plant metabolism that catalyse the oxidation of polyphenols to quinones. Because of their ubiquitous appearance in the plant kingdom, an important role is assumed; however, the exact physiological function of PPOs remains unclear. In this work, the identification, cloning, and characterisation of a bryophyte PPO from the moss Physcomitrella patens is presented. PPO activity from protein extracts was determined polarographically after activation by SDS. Four Physcomitrella ESTs with homologies to known plant PPOs were selected from publicly accessible databases, and PCR experiments demonstrated that they belong to the same gene, named Pp_ppo1. The identified cDNA was found to be 2402 bp long, containing a single open reading frame of 1611 bp encoding for a 536 amino acid protein with a molecular mass of 60.1 kDa. Cloning and sequencing of a genomic part of Pp_ppo1 revealed the presence of a 94‐bp intron. The time course of Pp_ppo1 gene expression in liquid culture was monitored by real time RT‐PCR, revealing increasing transcription levels until the 4th day, a maximum between the 4th and the 8th day, and decreasing transcription until the 12th day. A comparison of the deduced amino acid sequence of Pp_ppo1 with seed plant PPOs revealed similarities such as the presence of two highly conserved copper‐binding domains and a similar pattern of hydrophobic regions, but also differences such as a stronger membrane association and a shorter signal sequence, thus reflecting the phylogenetic distance of Physcomitrella from seed plants.
Glyco‐Engineering of Moss Lacking Plant‐Specific Sugar Residues
Authors: Huether C. M. , Lienhart O. , Baur A. , Stemmer C. , Gorr G. , Reski R. , Decker E. L.
Published: May 2005

Abstract: The commercial production of complex pharmaceutical proteins from human origin in plants is currently limited through differences in protein N‐glycosylation pattern between plants and humans. On the one hand, plant‐specific α(1,3)‐fucose and β(1,2)‐xylose residues were shown to bear strong immunogenic potential. On the other hand, terminal β(1,4)‐galactose, a sugar common on N‐glycans of pharmaceutically relevant proteins, e.g., antibodies, is missing in plant N‐glycan structures. For safe and flexible production of pharmaceutical proteins, the humanisation of plant protein N‐glycosylation is essential. Here, we present an approach that combines avoidance of plant‐specific and introduction of human glycan structures. Transgenic strains of the moss Physcomitrella patens were created in which the α(1,3)‐fucosyltransferase and β(1,2)‐xylosyltransferase genes were knocked out by targeted insertion of the human β(1,4)‐galactosyltransferase coding sequence in both of the plant genes (knockin). The transgenics lacked α(1,3)‐fucose and β(1,2)‐xylose residues, whereas β(1,4)‐galactose residues appeared on protein N‐glycans. Despite these significant biochemical changes, the plants did not differ from wild type with regard to overall morphology under standard cultivation conditions. Furthermore, the glyco‐engineered plants secreted a transiently expressed recombinant human protein, the vascular endothelial growth factor, in the same concentration as unmodified moss, indicating that the performed changes in glycosylation did not impair the secretory pathway of the moss. The combined knockout/knockin approach presented here, leads to a new generation of engineered moss and towards the safe and flexible production of correctly processed pharmaceutical proteins with humanised N‐glycosylation profiles.
Large‐Scale Analysis of 73 329 Physcomitrella Plants Transformed with Different Gene Disruption Libraries: Production Parameters and Mutant Phenotypes
Authors: Schween G. , Egener T. , Fritzowsky D. , Granado J. , Guitton M.‐C. , Hartmann N. , Hohe A. , Holtorf H. , Lang D. , Lucht J. M. , Reinhard C. , Rensing S. A. , Schlink K. , Schulte J. , Reski R.
Published: May 2005

Abstract: Gene targeting in the moss Physcomitrella patens has created a new platform for plant functional genomics. We produced a mutant collection of 73 329 Physcomitrella plants and evaluated the phenotype of each transformant in comparison to wild type Physcomitrella. Production parameters and morphological changes in 16 categories, such as plant structure, colour, coverage with gametophores, cell shape, etc., were listed and all data were compiled in a database (mossDB). Our mutant collection consists of at least 1804 auxotrophic mutants which showed growth defects on minimal Knop medium but were rescued on supplemented medium. 8129 haploid and 11 068 polyploid transformants had morphological alterations. 9 % of the haploid transformants had deviations in the leaf shape, 7 % developed less gametophores or had a different leaf cell shape. Other morphological deviations in plant structure, colour, and uniformity of leaves on a moss colony were less frequently observed. Preculture conditions of the plant material and the cDNA library (representing genes from either protonema, gametophore or sporophyte tissue) used to transform Physcomitrella had an effect on the number of transformants per transformation. We found correlations between ploidy level and plant morphology and growth rate on Knop medium. In haploid transformants correlations between the percentage of plants with specific phenotypes and the cDNA library used for transformation were detected. The number of different cDNAs present during transformation had no effect on the number of transformants per transformation, but it had an effect on the overall percentage of plants with phenotypic deviations. We conclude that by linking incoming molecular, proteome, and metabolome data of the transformants in the future, the database mossDB will be a valuable biological resource for systems biology.
The Family of CONSTANS‐Like Genes inPhyscomitrella patens
Authors: Zobell O. , Coupland G. , Reiss B.
Published: May 2005

Abstract:TheCONSTANS (CO)gene plays a central role in the regulation of flowering time inArabidopsis,and is a member of a family of 17CO‐likegenes.COandCO‐likegenes have been found in all flowering plants, but not in yeast and animals. To address the question of the origin ofCO,we analysed this gene family in the mossPhyscomitrella patens,a phylogenetically distant organism. Database searches in EST libraries that almost completely covered thePhyscomitrellatranscriptome, and Southern blotting, identified only three genes that had all of the hallmarks ofCO.Further analysis demonstrated that these are most similar toCO‐likegenesAtCOL3/AtCOL4/AtCOL5,a group ofArabidopsisgenes closely related to, but distinct fromCO,suggesting that theCObranch of theAtCOLphylogeny does not exist in thePhyscomitrellagenome. Since 17COLgenes occur inArabidopsisand only three closely related and two distantly related genes were found inPhyscomitrella,the family of CO‐like proteins appears to be smaller inPhyscomitrellathan inArabidopsis,in agreement with observations made with other gene families. The data also indicate thatCO‐likegenes must have existed in the common ancestor of bryophytes and flowering plants, and thatCOoriginated in the group ofCO‐likegenes represented byAtCOL3/AtCOL4/AtCOL5.Furthermore, expression of the three closely relatedPhyscomitrellahomologues is regulated by light, suggesting that the role of CO in flowering time control was probably derived from an ancestral function in light signal transduction.
Image Analysis Supported Moss Cell Disruption in Photo‐Bioreactors
Authors: Lucumi A. , Posten C. , Pons M.‐N.
Published: May 2005

Abstract: Diverse methods for the disruption of cell entanglements and pellets of the moss Physcomitrella patens were tested in order to improve the homogeneity of suspension cultures. The morphological characterization of the moss was carried out by means of image analysis. Selected morphological parameters were defined and compared to the reduction of the carbon dioxide fixation, and the released pigments after cell disruption. The size control of the moss entanglements based on the rotor stator principle allowed a focused shear stress, avoiding a severe reduction in the photosynthesis. Batch cultures of P. patens in a 30.0‐l pilot tubular photo‐bioreactor with cell disruption showed no significant variation in growth rate and a delayed cell differentiation, when compared to undisrupted cultures. A highly controlled photoautotrophic culture of P. patens in a scalable photo‐bioreactor was established, contributing to the development required for the future use of mosses as producers of relevant heterologous proteins.
Molecular Tools to StudyPhyscomitrella patens
Authors: Frank W. , Decker E. L. , Reski R.
Published: May 2005

Abstract:The mossPhyscomitrella patenshas become a suitable model plant system for the analysis of diverse aspects of modern plant biology. The research strategies have been influenced by the implementation of state‐of‐the‐art cell culture and molecular biology techniques. The forthcoming completion of thePhyscomitrellagenome sequencing project will generate many open questions, the examination of which will rely on a diverse set of molecular tools. Within this article, we intend to introduce the essential cell culture and molecular biology techniques which have been adopted in recent years to makePhyscomitrellaamenable to a wide range of genetic analyses. Many research groups have made valuable contributions to improve the methodology for the study ofPhyscomitrella.We would like to apologise to all colleagues whose important contributions could not be cited within this manuscript.
Is the Rehydrin TrDr3 from Tortula ruralis Associated with Tolerance to Cold, Salinity, and Reduced pH? Physiological Evaluation of the TrDr3‐Orthologue, HdeD from Escherichia coli in Response to Abiotic Stress
Authors: Peng C. A. , Oliver M. J. , Wood A. J.
Published: May 2005

Abstract: We have employed EST analysis in the resurrection moss Tortula ruralis to discover genes that control vegetative desiccation tolerance and describe the characterization of the EST‐derived cDNA TrDr3 (Tortula ruralis desiccation‐stress related). The deduced polypeptide TRDR3 has a predicted molecular mass of 25.5 kDa, predicted pI of 6.7, and six transmembrane helical domains. Preliminary expression analyses demonstrate that the TrDr3 transcript ratio increases in response to slow desiccation relative to the hydrated control in both total and polysomal mRNA (mRNP fraction), which classifies TrDr3 as a rehydrin. Bioinformatic searches of the electronic databases reveal that Tortula TRDR3 shares significant similarities to the hdeD gene product (HNS‐dependent expression) from Escherichia coli. The function of the HdeD protein in E. coli is unknown, but it is postulated to be involved in a mechanism of acid stress defence. To establish the role of E. coli HdeD in abiotic stress tolerance, we determined the log survival percentage from shaking cultures of wild‐type bacteria and the isogenic hdeD deletion strain (ΔhdeD) in the presence of low temperature (28 °C), elevated NaCl (5 % (w/v)), or decreased pH (4.5), or all treatments simultaneously. The ΔhdeD deletion strain was less sensitive, as compared to wild‐type E. coli, in response to decreased pH (p > 0.009), and the combination of all three stresses (p > 0.0001).
A nested sequence of projectors and corresponding braid matrices R̂(θ). 1. Odd dimensions
Authors: Chakrabarti A.
Published: May 2005

A basis of N2 projectors, each an N2×N2 matrix with constant elements, is implemented to construct a class of braid matrices R̂(θ), θ being the spectral parameter. Only odd values of N are considered here. Our ansatz for the projectors Pα appearing in the spectral decomposition of R̂(θ) leads to exponentials exp(mαθ) as the coefficient of Pα. The sums and differences of such exponentials on the diagonal and the antidiagonal, respectively, provide the (2N2−1) nonzero elements of R̂(θ). One element at the center is normalized to unity. A class of supplementary constraints imposed by the braid equation leaves 12(N+3)(N−1) free parameters mα. The diagonalizer of R̂(θ) is presented for all N. Transfer matrices t(θ) and L(θ) operators corresponding to our R̂(θ) are studied. Our diagonalizer signals specific combinations of the components of the operators that lead to a quadratic algebra of N2 constant N×N matrices. The θ dependence factors out for such combinations. R̂(θ) is developed in a power series in θ. The basic difference arising for even dimensions is made explicit. Some special features of our R̂(θ) are discussed in a concluding section.
Origin of methyl torsional barrier in 1-methyl-2-(1H)-pyridone
Authors: Pradhan B. , Singh Bhanu P. , Nandi Chayan K. , Chakraborty T. , Kundu T.
Published: May 2005

The laser induced fluorescence excitation and single vibronic excitation dispersed fluorescence spectra have been studied for supersonic jet cooled 1-methyl-2(1h)-pyridone. The methyl torsional bands and some low frequency vibrational transitions were assigned for both ground and excited states. The torsional parameters V3=244cm−1 and V6=15cm−1 for the ground state and V3=164cm−1 and V6=40cm−1 for the excited state were obtained. To get the insight into the methyl torsional barrier, ab initio calculations were performed and compared with the experimental results. Origin of potential barrier was traced by partitioning the barrier energy into changes in bond–antibond interaction, structural, and steric energies accompanying methyl rotation using natural bond orbital analysis. The role of local interactions in ascertaining the barrier potential reveals that its nature cannot be understood without considering the molecular flexing. The hyperconjugation between CHσ* and ring π* observed in lowest unoccupied molecular orbital (LUMO) stabilizes the methyl group conformer that undergoes a 60° rotation in the excited state with respect to that of the ground state, and it is the change in LUMO that plays important role in the excited state barrier formation.
C
2
H
+
H
2
C
O
: A new route for formaldehyde removal
Authors: Dong Hao , Ding Yi-hong , Sun Chia-chung
Published: May 2005

The title unknown reaction is theoretically studied at various levels to probe the interaction mechanism between the ethynyl radical (HCC∙) and formaldehyde (H2CO). The most feasible pathway is a barrier-free direct H-abstraction process leading to acetylene and formyl radical (C2H2+HCO) via a weakly bound complex, and then the product can take secondary dissociation to the final product C2H2+CO+H. The C-addition channel leading to propynal plus H-atom (HCCCHO+H) has the barrier of only 3.6, 2.9, and 2.1kcal∕mol at the CCSD(T)∕6-311+G(3df,2p)∕∕MP2∕6-311G(d,p)+ZPVE, CCSD(T)∕6-311+G(3df,2p)∕∕QCISD∕6-311G(d,p)+ZPVE, and G3//MP2 levels, respectively [CCSD(T)—coupled cluster with single, double, and triple excitations; ZPVE—zero-point vibrational energy; QCISD—quadratic configuration interaction with single and double excitations; G3//MP2—Gaussian-3 based on Moller–Plesset geometry]. The O addition also leading to propynal plus H atom needs to overcome a higher barrier of 5.3, 8.7, and 3.0kcal∕mol at the three corresponding levels. The title no-barrier reaction presents a new efficient route to remove the pollutant H2CO, and should be included in the combustion models of hydrocarbons. It may also represent the fastest radical-H2CO reaction among the available theoretical data. Moreover, it could play an important role in the interstellar chemistry where the zero- or minute-barrier reactions are generally favored. Discussions are also made on the possible formation of the intriguing propynal in space via the title reaction on ice surface.
Collision-induced nonadiabatic transitions in the second-tier ion-pair states of iodine molecule: Experimental and theoretical study of the I2(fg+) collisions with rare gas atoms
Authors: Akopyan M. E. , Novikova I. Yu. , Poretsky S. A. , Pravilov A. M. , Smolin A. G. , Tscherbul T. V. , Buchachenko A. A.
Published: May 2005

Nonadiabatic transitions induced by collisions with He, Ar, Kr, and Xe atoms in the I2 molecule excited to the f0g+ second-tier ion-pair state are investigated by means of the optical–optical double resonance spectroscopy. Fluorescence spectra reveal that the transition to the F0u+ state is a dominant nonradiative decay channel for f state in He, Ar, and Kr, whereas the reactive quenching is more efficient for collisions with Xe atom. Total rate constants and vibrational product state distributions for the f→F electronic energy transfer are determined and analyzed in terms of energy gaps and Franck–Condon factors for the combining vibronic levels at initial vibrational excitations vf=8, 10, 14, and 17. Quantum scattering calculations are performed for collisions with He and Ar atoms, implementing a combination of the diatomics-in-molecule and long-range perturbation theories to evaluate diabatic PESs and coupling matrix elements. Calculated rate constants and vibrational product state distributions agree well with the measured ones, especially in case of Ar. Qualitative comparison is made with the previous results for the second-tier f0g+→F0u+ transition in collisions with I2(X) molecule and the first-tier E0g+→D0u+ transition induced by collisions with the rare gas atoms.
Adiabatic squeezing of molecular wave packets by laser pulses
Authors: Chang Bo Y. , Lee Sungyul , Sola Ignacio R. , Santamaría Jesús
Published: May 2005

Strong pulse sequences can be used to control the position and width of the molecular wave packet. In this paper we propose a new scheme to maximally compress the wave packet in a quasistatic way by freezing it at a peculiar adiabatic potential shaped by two laser pulses. The dynamic principles of the scheme and the characteristic effect of the different control parameters are presented and analyzed. We use two different molecular models, electronic potentials modeled by harmonic oscillators, with the same force constants, and the Na2 dimer, to show the typical yield that can be obtained in compressing the initial (minimum width) molecular wave function.
Higher order (A+E)⊗e pseudo-Jahn–Teller coupling
Authors: Eisfeld Wolfgang , Viel Alexandra
Published: May 2005

The pseudo-Jahn–Teller (PJT) coupling of a nondegenerate state A with a twofold degenerate state E by a degenerate vibrational mode e is studied for a general system with a C3 main rotational axis. The PJT coupling terms up to sixth order are derived by symmetry considerations for this general (A+E)⊗e case. The obtained expression for the 3×3 diabatic potential energy matrix is found to be closely related to the expression recently developed for the higher order Jahn–Teller case [A. Viel and W. Eisfeld, J. Chem. Phys. 120, 4603 (2004)]. The dynamical PJT coupling, which can arise for states of appropriate symmetry if one of the vibrational modes induces a change of the nuclear point group between D3h, C3v, C3h, and C3, is discussed. The effect of the higher order PJT coupling is tested by a two-dimensional model study based on the e bending mode of NH3+. The models are analyzed by fitting the two-dimensional potential energy surfaces. The significance of the higher order terms on the nonadiabatic dynamics is demonstrated by quantum wave packet propagations.
On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level
Authors: Dąbkowska Iwona , Jurečka Petr , Hobza Pavel
Published: May 2005

The geometries and interaction energies of stacked and hydrogen-bonded uracil dimers and a stacked adenine⋯thymine pair were studied by means of high-level quantum chemical calculations. Specifically, standard as well as counterpoise-corrected optimizations were performed at second-order Møller–Plesset (MP2) and coupled cluster level of theory with single, double, and perturbative triple excitations [CCSD(T)] levels with various basis sets up to the complete basis set limit. The results can be summarized as follows: (i) standard geometry optimization with small basis set (e.g., 6-31G*) provides fairly reasonable intermolecular separation; (ii) geometry optimization with extended basis sets at the MP2 level underestimates the intermolecular distances compared to the reference CCSD(T) results, whereas the MP2/cc-pVTZ counterpoise-corrected optimization agrees well with the reference geometries and, therefore, is recommended as a next step for improving MP2/cc-pVTZ geometries; (iii) the stabilization energy of stacked nucleic acids base pairs depends considerably on the method used for geometry optimization, so the use of reliable geometries, such as counterpoise-corrected MP2/cc-pVTZ ones, is recommended; (iv) the density functional theory methods fail completely in locating the energy minima for stacked structures and when the geometries from MP2 calculations are used, the resulting stabilization energies are strongly underestimated; (v) the self-consistent charges–density functional tight binding method, with inclusion of the empirical dispersion energy, accurately reproduces interaction energies and geometries of dispersion-bonded (stacked) complexes; this method can thus be recommended for prescanning the potential energy surfaces of van der Waals complexes.
Time-resolved measurements of the structure of water at constant density
Authors: Lindenberg A. M. , Acremann Y. , Lowney D. P. , Heimann P. A. , Allison T. K. , Matthews T. , Falcone R. W.
Published: May 2005

Dynamical changes in the structure factor of liquid water, S(Q,t), are measured using time-resolved x-ray diffraction techniques with 100ps resolution. On short time scales following femtosecond optical excitation, we observe temperature-induced changes associated with rearrangements of the hydrogen-bonded structure at constant volume, before the system has had time to expand. We invert this data to extract transient changes in the pair correlation function associated with isochoric heating effects, and interpret these in terms of a decrease in the local tetrahedral ordering.
Condensation and relaxation/transformation of dense t-ZrO2 nanoparticles
Authors: Tsai Meng-Hsiu , Chen Shuei-Yuan , Shen Pouyan
Published: May 2005

Dense tetragonal (t)-ZrO2 nanocondensates were synthesized under very rapid heating and cooling by pulsed Nd-YAG (YAG—yttrium aluminum garnet) laser ablation with oxygen background gas and characterized by electron diffraction. The t-ZrO2 nanoparticles with a residual stress up to about 5GPa tended to form deformation twins/faults upon local electron dosage. By contrast, the t-ZrO2 nanoparticles formed at an-order-of-magnitude higher power have a residual stress above 6GPa and tended to transform into a metastable cubic (c) phase vulnerable to amorphization. The relaxation/transformation of the self-constrained t-ZrO2 nanoparticles can be rationalized by a lowering of internal energy under the influence of resolved shear stress and local electron heating.
Polymer-centered theory in comparison with surfactant-centered theory: A lattice Monte Carlo study
Authors: Behjatmanesh-Ardakani Reza
Published: May 2005

Lattice Monte Carlo simulation is used to study micellization of both pure and surfactant-polymer mixture, with an emphasis on cluster size distribution. The amphiphile molecule is of the type H4T4 where the H (head) monomers like the solvent molecules and the T (tail) monomers are solvophobic. To compare polymer- and surfactant-centered theories, copolymers with the structure of (H4T4)5 are used instead of homopolymers. Since above copolymer molecules have the structural unit like the structure of surfactant molecules, it is possible to study the competition between the binding of surfactant molecules to the copolymer and the micellization in a copolymer-free solution. Results show that, first, surfactant molecules bind to the copolymer molecules, and not until copolymers are saturated do micelles form. Furthermore, it is shown that for the model used in this paper, the polymer-centered theory is more appropriate than the surfactant-centered theory, and finally the cooperative nature of cluster formation on copolymers is also discussed.
Modeling of configurations and third-order nonlinear optical properties of methyl silsesquioxanes
Authors: Shen J. , Cheng W.-D. , Wu D.-S. , Li X.-D. , Lan Y.-Z. , Zhang H. , Gong Y.-J. , Li F.-F. , Huang S.-P.
Published: May 2005

Configuration optimizations, excited state properties, and the frequency-dependent third-order nonlinear optical polarizabilities have been investigated on a series of methyl-silsesquioxane (MeT) cages [CH3SiO1.5]n (n=4, 6, 8, and 10) using ab initio quantum mechanical methods coupled with the sum-over-states methods. The obtained electronic absorption spectra show a redshift as the cage size increases, and the absorption spectra are assigned as charge transfers from oxygen p type to silicon s type atomic orbitals. The calculated average third-order polarizabilities of ⟨γ⟩ in the three optical physical processes (third-harmonic generation, the electric-field-induced second-harmonic generation, and degenerate four-wave mixing) have wide nonresonance regions. For all the considered species, the values of γ decrease in the order of [MeT]4>[MeT]8(C2v)=[MeT]10>[MeT]6>[MeT]8(Oh).
Negative ions of ethylene sulfite
Authors: Robertson W. D. , Hammer N. I. , Bartmess J. E. , Compton R. N. , Diri K. , Jordan K. D.
Published: May 2005

The formation of negative ions in molecular beams of ethylene sulfite (ES, alternately called glycol sulfite or ethylene glycol, C2H4SO3) molecules has been studied using both Rydberg electron transfer (RET) and free electron attachment methods. RET experiments with jet-cooled ES show an unexpected broad profile of anion formation as a function of the effective quantum number (n*) of the excited rubidium atoms, with peaks at nmax*∼13.5 and 16.8. The peak at nmax*∼16.8 corresponds to an expected dipole-bound anion with an electron binding energy of 8.5 meV. It is speculated that the peak at nmax*∼13.5 derives from the formation of a distorted C2H4SO3− ion. We suggest that quasifree electron attachment promotes the breaking of one ring bond giving a long-lived acyclic anion and term this process incomplete dissociative electron attachment. Theoretical calculations of plausible ionic structures are presented and discussed. Electron beam studies of ES reveal the presence of multiple dissociative attachment channels, with the dominant fragment, SO2−, peaking at 1.3 eV and much weaker signals due to SO3−, SO−, and (ES-H)− peaking at 1.5, 1.7, and 0.9 eV, respectively. All of these products appear to originate from a broad temporary negative ion resonance centered at ∼1.4eV.
Critical thickness for ferroelectricity of BaTiO3 by first-principles calculations
Authors: Nakao Ryo , Ishizumi Keisuke , Takahashi Isao , Terauchi Hikaru , Hayafuji Yoshinori , Miura Kaoru
Published: May 2005

The critical thickness for ferroelectricity of a BaTiO3 film was determined by the first-principles discrete variational-Xα molecular orbital method and population analysis. Under the assumption that most ferroelectric perovskite oxides are predominantly ionic, a series of model clusters were developed for a BaTiO3 particle consisting of a Ba8Ti7O6 cluster constructed on the basis of the crystal structure of BaTiO3 phase and point charges surrounding the Ba8Ti7O6 cluster. The size of the model cluster was exactly defined by the size of a three-dimensional point-charge array. By comparing the dependence of the net charge of Ba, Ti, and O ions and of the overlap population between Ti3d and O2p orbitals on particle thickness in tetragonal and cubic BaTiO3 particles, the critical thickness for ferroelectricity was calculated to be about 12 nm for a BaTiO3 particle with a basal area of 20×20nm.
Effect of structural disorder on some physical properties of the Cu2MnAl Heusler alloy films
Authors: Kudryavtsev Y. V. , Oksenenko V. A. , Lee N. N. , Lee Y. P. , Rhee J. Y. , Dubowik J.
Published: May 2005

The structural dependence of the magnetic, transport, optical, and magneto-optical (MO) properties of Cu2MnAl Heusler alloy (HA) thin-film samples was investigated. Disordered thin films of Cu2MnAl HA fabricated by vapor-quenching deposition onto substrates cooled by liquid nitrogen behave as highly resistive Pauli paramagnets down to 5 K, while an annealing of the disordered films at 580 K for 1 h restores the L21-type ordered structure, as well as the ferromagnetic order and other physical properties typical for the ordered Cu2MnAl HA film. The film deposition onto substrates held at T⩾690K leads to the formation of a multiphase crystalline structure. A significant influence of the structural disorder on the optical and MO properties of Cu2MnAl was experimentally observed and discussed in terms of the electronic structure of the alloy.
Negative thermal expansion and spontaneous magnetostriction of Tb2Fe16.5Cr0.5 compound
Authors: Hao Yanming , Zhou Yan , Zhao Miao
Published: May 2005

The structure and magnetic properties of Tb2Fe16.5Cr0.5 compound have been investigated by means of x-ray diffraction and magnetization measurements. The Tb2Fe16.5Cr0.5 compound has a hexagonal Th2Ni17-type structure. Negative thermal expansion was found in Tb2Fe16.5Cr0.5 compound from 293 to 522 K by x-ray dilatometry. The coefficient of the average thermal expansion is α¯=−1.53×10−6K−1 from 293 to 500 K, and α¯=−1.53×10−4K−1 from 500 to 522 K, respectively. The magnetostrictive deformations from 293 to 522 K have been calculated by means of the differences between the experimental values of the lattice parameters and the corresponding values extrapolated from the paramagnetic range. The magnetization measurement shows that small amount of Cr atoms substitute for Fe atoms can increase obviously the Curie temperature of the Tb2Fe17 compound.
Nonuniformities of electrical resistivity in undoped 6H-SiC wafers
Authors: Li Q. , Polyakov A. Y. , Skowronski M. , Sanchez E. K. , Loboda M. J. , Fanton M. A. , Bogart T. , Gamble R. D.
Published: May 2005

Chemical elemental analysis, temperature-dependent Hall measurements, deep-level transient spectroscopy, and contactless resistivity mapping were performed on undoped semi-insulating (SI) and lightly nitrogen-doped conducting 6H-SiC crystals grown by physical vapor transport (PVT). Resistivity maps of commercial semi-insulating SiC wafers revealed resistivity variations across the wafers between one and two orders of magnitude. Two major types of variations were identified. First is the U-shape distribution with low resistivity in the center and high in the periphery of the wafer. The second type had an inverted U-shape distribution. Secondary-ion-mass spectrometry measurements of the distribution of nitrogen concentration along the growth axis and across the wafers sliced from different locations of lightly nitrogen-doped 6H–SiC boules were conducted. The measured nitrogen concentration gradually decreased along the growth direction and from the center to the periphery of the wafers. This change gives rise to the U-like distribution of resistivity in wafers of undoped SI-SiC. The concentrations of deep electron traps exhibited similar dependence. Compensation of nitrogen donors by these traps can result in the inverted U-like distribution of resistivity. Possible reasons for the observed nonuniformities include formation of a (0001) facet in PVT growth coupled with orientation-dependent nitrogen incorporation, systematic changes of the gas phase composition, and increase of the deposition temperature during boule growth.
Writing self-assembled monolayers with Cs: Optimization of atomic nanolithography imaging using self-assembled monolayers on gold substrates
Authors: O’Dwyer C. , Gay G. , Viaris de Lesegno B. , Weiner J. , Ludolph K. , Albert D. , Oesterschulze E.
Published: May 2005

We report the results of a study into the factors controlling the quality of nanolithographic imaging. Self-assembled monolayer (SAM) coverage, subsequent postetch pattern definition, and minimum feature size all depend on the quality of the Au substrate used in material mask atomic nanolithographic experiments. We find that sputtered Au substrates yield much smoother surfaces and a higher density of {111}-oriented grains than evaporated Au surfaces. Phase imaging with an atomic force microscope shows that the quality and percentage coverage of SAM adsorption are much greater for sputtered Au surfaces. Exposure of the self-assembled monolayer to an optically cooled atomic Cs beam traversing a two-dimensional array of submicron material masks mounted a few microns above the self-assembled monolayer surface allowed determination of the minimum average Cs dose (2 Cs atoms per self-assembled monolayer molecule) to write the monolayer. Suitable wet etching, with etch rates of 2.2nmmin−1, results in optimized pattern definition. Utilizing these optimizations, material mask features as small as 230 nm in diameter with a fractional depth gradient of 0.8∕20nm were realized.
High-electric-field current–voltage characteristics and low-frequency oscillations in a low-dislocation-density semi-insulating GaAs
Authors: Kiyama M. , Tatsumi M. , Yamada M.
Published: May 2005

High-electric-field current–voltage (I–V) characteristics and low-frequency oscillations (LFO) have been measured in a low-dislocation-density semi-insulating GaAs. At the electrodes where several dislocations exist, the sublinear I–V behavior is weaker and more scattered, and the onset voltage of LFO is lower and its waveform is more complicated than those at the electrodes where no dislocations exist. The high-electric-field properties are discussed by the electrical inhomogeneities induced by the dislocations.
Isotope effects in the photofragmentation of symmetric molecules: The branching ratio of OD∕OH in water
Authors: Henriksen Niels E. , Møller Klaus B. , Engel Volker
Published: May 2005

With HOD initially in its vibrational ground state, we present a new detailed interpretation of the OD∕OH branching ratio (∼3) in the photoinduced process D+OH←HOD→H+OD, in the first absorption band. Using semiclassical arguments, we show that the branching ratio has little to do with the initial distribution of configurations, but the initial momentum distribution plays a key role in determination of the branching ratio. The formation of D+OH arises from initial situations where OD is stretching, and it stretches faster than OH, whereas all other motions lead to H+OD. This picture is confirmed by quantum wave-packet calculations.
Aspects of a new class of braid matrices: Roots of unity and hyperelliptic q for triangularity, L-algebra, link-invariants, noncommutative spaces
Authors: Chakrabarti A.
Published: May 2005

Various properties of a class of braid matrices, presented before, are studied considering N2×N2(N=3,4,…) vector representations for two subclasses. For q=1 the matrices are nontrivial. Triangularity (R̂2=I) corresponds to polynomial equations for q, the solutions ranging from roots of unity to hyperelliptic functions. The algebras of L operators are studied. As a crucial feature one obtains 2N central, grouplike, homogenous quadratic functions of Lij constrained to equality among themselves by the RLL equations. They are studied in detail for N=3 and are proportional to I for the fundamental 3×3 representation and hence for all iterated coproducts. The implications are analyzed through a detailed study of the 9×9 representation for N=3. The Turaev construction for link invariants is adapted to our class. A skein relation is obtained. Noncommutative spaces associated to our class of R̂ are constructed. The transfer matrix map is implemented, with the N=3 case as example, for an iterated construction of noncommutative coordinates starting from an (N−1) dimensional commutative base space. Further possibilities, such as multistate statistical models, are indicated.
High-temperature stability of ion-implanted zirconia and spinel
Authors: Gentils A. , Enescu S. E. , Thomé L. , Khodja H. , Blaise G. , Thomé T.
Published: May 2005

This paper reports a study of the high-temperature stability of ion-implanted yttria-stabilized zirconia and magnesium aluminate spinel, which are foreseen as matrices for the transmutation of nuclear waste. Stable analogs of radiotoxic fission products (Cs) were implanted into both materials and the stability of the implanted systems was studied upon annealing at a high temperature. Rutherford backscattering spectrometry experiments with a macro- and a micro-ion-beam, scanning electron microscopy, and atomic force microscopy observations show that the annealing behavior strongly depends on the material. In zirconia Cs begins to desorb out of the crystal at 550°C in samples which remain homogeneous. On the contrary, the desorption of Cs is observed at 850°C in spinel by the exfoliation of the surface of the samples.
Experimental investigation of hybrid-evaporation-glow discharge plasma immersion ion implantation
Authors: Li L. H. , Wu Y. Q. , Zhang Y. H. , Fu Ricky K. Y. , Chu Paul K.
Published: May 2005

High-voltage pulsed glow discharge is applied to plasma immersion ion implantation (PIII). In the glow discharge, the target constitutes the cathode and the gas tube forms the anode under a relatively high working gas pressure of 0.15–0.2Pa. The characteristics of the glow discharge and ion density are measured experimentally. Our results show resemblance to hollow-anode glow discharge and the anode fall is faster than that of general glow discharge. Because of electron focusing in the anode tube orifice, ions are ionized efficiently and most of them impact the negatively biased samples. The resulting ion current density is higher than that in other PIII modes and possible mechanisms of the glow discharge PIII are proposed and discussed.
Derivation of particle, string, and membrane motions from the Born–Infeld electromagnetism
Authors: Brenier Yann , Yong Wen-An
Published: May 2005

We derive classical particle, string, and membrane motion equations from a rigorous asymptotic analysis of the Born–Infeld nonlinear electromagnetic theory. We first add to the Born–Infeld equations the corresponding energy-momentum conservation laws and write the resulting system as a nonconservative symmetric 10×10 system of first-order PDEs. Then we show that four rescaled versions of the system have smooth solutions existing in the (finite) time interval where the corresponding limit problems have smooth solutions. Our analysis is based on a continuation principle previously formulated by Yong for (singular) limit problems.
Domain switching in ferroelectric ceramic materials under combined loads
Authors: Achuthan A. , Sun C. T.
Published: May 2005

An experimental study to investigate the various characteristics of the nonlinear behavior of a ferroelectric ceramic material under different electrical and mechanical loading conditions is reported. The nonlinear strain behavior under different loading conditions is obtained and used for studying the effect of residual stress, developed in the ferroelectric ceramic material during manufacture, on domain switching under applied loads. First, the behavior at low electric field and mechanical stress are studied by comparing the linear piezoelectric properties measured from the strain responses under mechanical and electrical loading with those measured by resonance method. This is followed by an investigation on the mechanism of polarization reversal due to cyclic electric field. Based on the observed large magnitude of strain and the comparison of the magnitude of the sum of transverse strains with the magnitude of strain in the poling direction it is concluded that polarization reversal due to cyclic electric field in the ferroelectric material at morphotropic phase boundary is the result of two successive 90° domain switchings of the individual domains rather than a direct 180° domain switching. Finally, two types of combined loading experiments were conducted to investigate the residual stress effect on the mechanism of domain switching. The behavior under combined loading shows many interesting characteristics. An attempt is made to explain the characteristics of the nonlinear ferroelectric behavior observed in the present experimental study based on the effect of residual stress on domain switching.
Time-resolved optical emission studies on the laser ablation of a graphite target: The effects of ambient gases
Authors: Park Hye Sun , Nam Sang Hwan , Park Seung Min
Published: May 2005

Time-resolved optical emission spectroscopy was employed to examine the temporal properties of a plume formed by laser ablation of a graphite target in He, N2, and Ar background gases. Time-dependent spectroscopic temperatures of electronically excited C2 and CN molecules generated in the plume at different background gases and pressures were derived by simulation of the emission spectra. The rotational temperature of CN molecules was significantly higher than the vibrational temperature. This indicates that they are formed in the gas phase by the chemical reaction C2+N2→CN. At pressure above 0.5Torr, the temperature in each background gas was apparently in the order of Ar>N2>He while there was no such gas dependence at 0.1Torr. The expansion dynamics and cooling rate of the plume turned out to be highly dependent on the background gas and its pressure.
Impact of reductive N2∕H2 plasma on porous low-dielectric constant SiCOH thin films
Authors: Cui Hao , Carter Richard J. , Moore Darren L. , Peng Hua-Gen , Gidley David W. , Burke Peter A.
Published: May 2005

Porous low-dielectric constant (low-κ) SiCOH thin films deposited using a plasma-enhanced chemical-vapor deposition have been comprehensively characterized before and after exposure to a reactive-ion-etch-type plasma of N2 and H2 chemistry. The low-κ film studied in this work is a carbon-doped silicon oxide film with a dielectric constant (κ) of 2.5. Studies show that a top dense layer is formed as a result of significant surface film densification after exposure to N2∕H2 plasma while the underlying bulk layer remains largely unchanged. The top dense layer is found to seal the porous bulk SiCOH film. SiCOH films experienced significant thickness reduction, κ increase, and leakage current degradation after plasma exposure, accompanied by density increase, pore collapse, carbon depletion, and moisture content increase in the top dense layer. Both film densification and removal processes during N2∕H2 plasma treatment were found to play important roles in the thickness reduction and κ increase of this porous low-κ SiCOH film. A model based upon mutually limiting film densification and removal processes is proposed for the continuous thickness reduction during plasma exposure. A combination of surface film densification, thickness ratio increase of top dense layer to bulk layer, and moisture content increase results in the increase in κ value of this SiCOH film.
Improved optical quality of GaNAsSb in the dilute Sb limit
Authors: Yuen Homan B. , Bank Seth R. , Wistey Mark A. , Harris James S. , Seong Maeng-Je , Yoon Seokhyun , Kudrawiec Robert , Misiewicz Jan
Published: May 2005

GaNAs(Sb) layers were grown by solid-source molecular-beam epitaxy utilizing a radio frequency (rf) nitrogen plasma source. The samples contained less nitrogen and antimony (0.5%–0.8% N and ⩽2% Sb) than in previous studies and were examined for their optical and electronic properties and any interactions between the elements. Secondary-ion-mass spectrometry, high-resolution x-ray diffraction, electroreflectance (ER) spectroscopy, and photoluminescence (PL) measurements were used to study those properties. We found that the addition of small amounts of antimony enhanced nitrogen incorporation into GaAs, similar to other studies that used 5–15× the mole fraction of antimony. The nitrogen concentration increased with increasing antimony flux. PL measurements indicated an improvement in optical quality with increasing nitrogen and antimony concentrations—contrary to the belief that adding more nitrogen necessarily degrades material quality. We collected and simulated ER spectra to examine the general band properties of the layers. Isoelectronic codoping can explain the improved quality when antimony is added to GaNAs. The improvement in GaNAs with small amounts of antimony holds great promise for improving strain-compensated GaInNAs(Sb)∕GaNAs devices.
General model and segregation coefficient measurement for ultrashallow doping by excimer laser annealing
Authors: Gillet Jean-Numa , Degorce Jean-Yves , Meunier Michel
Published: May 2005

A general model of ultrashallow doping by excimer laser annealing is derived from only one diffusion-segregation equation. In our model, the relative dopant profile after some laser shots reaches a stationary distribution, which only depends on the segregation and liquid-phase diffusion coefficients of the dopant but not on the laser-process parameters. From this result, a one-point method is proposed to experimentally determine the out-of-equilibrium segregation coefficient k. Only the relative dopant concentration at the material surface has to be measured prior to determine the k value. Experimental dopant profiles are compared to simulations generated with experimental k values.
Spark plasma sintering and thermal conductivity of carbon nanotube bulk materials
Authors: Zhang H. L. , Li J.-F. , Yao K. F. , Chen L. D.
Published: May 2005

Carbon nanotube (CNT) bulk samples were fabricated by spark plasma sintering (SPS), which, as a rapid consolidation technique, preserved the phase structure and diameter of cylindrical tubules of the CNTs even at high temperatures of up to 2000°C. The thermal conductivity of the resultant bulk samples was measured by the conventional laser-flash method, and the corresponding thermal conductivity was found to be as low as 4.2W∕m∕K at room temperature. This low thermal conductivity of the CNT bulk materials was explained on the basis of multiple physical elements including intensive tube–tube interactions. CNT bulk materials may find potential applications as thermoelectric materials that require low thermal conductivity, but high electrical conductivity.
Effect of ozone treatment on the electrical properties of (Ba0.7Sr0.3)TiO3 thin films
Authors: Halder Sandip , Schneller Theodor , Meyer Rene , Waser Rainer
Published: May 2005

Thin films of (BaxSr1−x)TiO3 were deposited on Pt-coated Si substrates by chemical solution deposition. The films were postannealed under ozone atmosphere at various temperatures. Although there was no change observed in the microstructure after the anneal in ozone, the dielectric dispersion and the loss tangents were reduced for the films. It was also noticed that the leakage current reduced by almost two orders of magnitude after treatment with ozone. The ozone treatment was done at various temperatures between 250 and 450°C to find an optimum temperature with regard to the electrical properties. Films postannealed in ozone at 350°C for 30min showed a leakage reduction by almost three orders of magnitude. The leakage dependence on ozone postannealing is discussed on the basis of an interface-dominated (Schottky injection) and a bulk-dominated (point defect approach) charge transport process as the two limiting conduction mechanisms across thin films.