bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling the internal mobility of the molecule of DNA
Authors: Yakushevich Ludmila V. 
Published: August 2002

AbstractRecent investigations of the DNA molecule showed that it has a rather moveable structure and that internal DNA mobility plays an important role in biologic activity of the molecule. We describe here one possible way of modeling the internal DNA mobility based on the Hamiltonian formalism and analytic methods of finding solutions of corresponding dynamic equations. The approach developed in this article permits us to model internal motions of both small and large amplitudes. To illustrate the algorithm, we consider in details modeling internal DNA motions associated with the process of unwinding of the DNA double helix. We discuss merits and demerits of the model obtained. Different ways to improve the model and approach by applying computer methods, databanks, and methods of visualizations are also discussed. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
On equilibrium intensive thermodynamic properties of composed p‐particles in many‐body systems
Authors: Bochicchio Roberto C. , Alcoba Diego R. 
Published: August 2002

AbstractEquilibrium intensive thermodynamic properties of p‐particles (p‐ons), i.e., composed particles formed by few particles of the same nature such as fermion or boson pairs (p=2), trios (p=3), etc., are investigated. The relation of the p‐particle correlation functions to its p‐hole counterparts and an existing covariant structure in the hierarchy of the p‐particle correlation functions allow these generalized intensive properties to be properly defined and characterized. The connection between these generalized properties of the composed objects and those of the components is also derived. An explicit derivation of the chemical potential for pairs and its generalization to p‐particles is performed. Such results are further extended to any intensive property. Finally, the present development allows some previous results to be clearly interpreted thus yielding an important support for our theory. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem 85: 63–71, 2001
Convergence of the orbital expansion in a correlated system: A test study on positronium
Authors: Bendazzoli Gian Luigi , Evangelisti Stefano , Leininger Thierry 
Published: August 2002

AbstractPositronium, the bound state of an electron and a positron, is an exactly soluble quantum system, similar to a light isotope of hydrogen. It can be studied using the finite basis quantum chemistry codes developed for atoms and molecules. In fact, positronium can be mimicked by two electrons with opposite spins, in the absence of any nucleus and having the sign of the Coulomb interaction reversed. The exact wave function has a cusp in the points of coalescence of the two particles (a “Coulomb peak”), and this fact makes the convergence of the total energy, as a function of the basis set size, extremely slow. For this reason, positronium can be used to test the convergence properties of the quantum chemistry methods used to describe the dynamic correlation. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001
An ab initio post‐Hartree–Fock study of vibrational infrared spectra of 5‐azacytosine and cytosine*
Authors: Yevgeniy Podolyan  , Yury V. Rubin  , Leszczyński Jerzy 
Published: August 2002

AbstractPost‐Hartree–Fock ab initio studies were performed to predict the infrared (IR) vibrational spectra of the two most stable tautomers of 5‐azacytosine and cytosine. All geometries were optimized without symmetry restrictions by the gradient procedure at the MP2 level of theory using the standard 6‐31G(d,p) basis set. IR spectra have been calculated at the MP2/6‐31G(d,p) approximation. We found similar patterns in the sequence of the modes of the harmonic frequencies for both cytosine and 5‐azacytosine in the 3400–900 cm−1 region and distinctive differences in the high‐frequency region. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 83: 203–212, 2001
Implementation and evaluation of MPI‐based parallel MD program
Authors: Trobec R. , Šterk M. , Praprotnik M. , Janežič D. 
Published: August 2002

AbstractThe message‐passing interface (MPI)‐based object‐oriented particle–particle interactions (PPI) library is implemented and evaluated. The library can be used in the n‐particle simulation algorithm designed for a ring of p interconnected processors. The parallel simulation is scalable with the number of processors, and has the time requirement proportional to n2/p if n/p is large enough, which guarantees optimal speedup. In a certain range of problem sizes, the speedup becomes superlinear because enough cache memory is available in the system. The library is used in a simple way by any potential user, even with no deep programming knowledge. Different simulations using particles can be implemented on a wide spectrum of different computer platforms. The main purpose of this article is to test the PPI library on well‐known methods, e.g., the parallel molecular dynamics (MD) simulation of the monoatomic system by the second‐order leapfrog Verlet algorithm. The performances of the parallel simulation program implemented with the proposed library are competitive with a custom‐designed simulation code. Also, the implementation of the split integration symplectic method, based on the analytical calculation of the harmonic part of the particle interactions, is shown, and its expected performances are predicted. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 84: 23–31, 2001
Potential energy surfaces in hybrid quantum mechanical/molecular mechanical methods
Authors: Tokmachev A. M. , Tchougréeff A. L. 
Published: August 2002

AbstractThe problem of conjunction between quantum and classical parts in hybrid quantum mechanical/molecular mechanical methods is considered. The form of the junction is deduced with use of the perturbation expansion on the assumption that the wave function underlying molecular mechanics is of the antisymmetrized product of strictly localized geminals type. The renormalization of the potential energy surfaces of the combined system due to interaction between quantum and classical subsystems is represented as a sum of contributions with transparent physical sense. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 84: 39–47, 2001
Effective Hamiltonian approach to catalytic activity of transition metal complexes
Authors: Tokmachev A. M. , Tchougréeff A. L. , Misurkin I. A. 
Published: August 2002

AbstractThe application of an effective electron Hamiltonian approach to the description of the electronic structure of transition metal complexes with chemically active ligands is analyzed. This approach is implemented in a computational code. The evolution of the electronic structure along a path of isomerization of quadricyclane to norbornadiene in the coordination sphere of Co‐tetraphenylporphyrin is considered. In addition, the electronic states of atomic oxygen coordinated to transition metal oxides and metal porphyrins are studied. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 84: 99–109, 2001
Theoretical study of MgO(001) surfaces: Pure, doped with Fe, Ca, and Al, and with and without adsorbed water
Authors: Almeida A. L. , Martins J. B. L. , Longo E. , Furtado N. C. , Taft C. A. , Sambrano J. R. , Lester W. A. 
Published: August 2002

AbstractAb initio calculations of large cluster models have been performed in order to study water adsorption at the five‐fold coordinated adsorption site on pure Mg(001) and MgO(001) surfaces doped with Fe, Ca, and Al. The geometric parameters of the adsorbed water molecule have been optimized preparatory to analysis of binding energies, charge transfer, preferential sites of interaction, and bonding distances. We have used Mulliken population analysis methods in order to analyze charge distributions and the direction of charge transfer. We have also investigated energy gaps, HOMO energies, and SCF orbital energies as well as the acid‐base properties of our cluster model. Numerical results are compared, where possible, with experiment and interpreted in the framework of various analytical models. © 2001 John Wiley & Sons, Inc. Int J Quant Chem, 2001
Theoretical studies on field‐induced superconductivity in molecular crystals
Authors: Nagao Hidemi , Kitagawa Yasutaka , Kawakami Takashi , Yoshimoto Takashi , Saito Hiroaki , Yamaguchi Kizashi 
Published: August 2002

AbstractWe investigate superconductivity of molecular crystals induced by charge injection by using a two‐band model based on the Green function techniques. Expressions of transition temperature for several phases derived from the model are summarized. The model is applied to a model of CuO2 plane for copper oxides, anthracene, oligothiophene, and C60 crystals and phase diagrams of the crystals are presented. It is important that the band structure of crystals is described by a two‐ or multiband model for realization of high‐Tc superconductivity. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001
Study of molecular orbitals in momentum space
Authors: Errea L. F. , Macías A. , Méndez L. , Riera A. , Pons B. , Sevila I. 
Published: August 2002

AbstractMolecular orbitals are presented in configuration and momentum representations. We propose to minimize large oscillations present in calculated momentum wavefunctions by cancelling position factor phases. We illustrate the distortion introduced by different electron translation factors and show continuum states and dynamical wavefunctions in momentum coordinates. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001
Determination of the disulfide bond pattern of a novel C‐type lectin from snake venom by mass spectrometry
Authors: Zeng Rong , Xu Qiang , Shao Xiao‐Xia , Wang Ke‐Yi , Xia Qi‐Chang 
Published: August 2002

AbstractThe disulfide bond pattern of Trimeresurus stejnegeri lectin (TSL), a new member of the C‐type lectin family, was determined by mass spectrometry. Four intrachain disulfide bonds of TSL, Cys3‐Cys14, Cys31‐Cys131, Cys38‐Cys133 and Cys106‐Cys123, and two interchain linkages, Cys2‐Cys2 and Cys86‐Cys86, were determined. Three strategies were used in this work. One intrachain (Cys106‐Cys123) and one interchain (Cys86‐Cys86) disulfide linkages were detected by standard MS methods. The disulfide bonds Cys2‐Cys2 and Cys3‐Cys14 were analyzed using a modified partial reduction procedure and MS/MS. The last two disulfide bonds were characterized by a MS/MS/MS technique. The strategies developed in this work could be applied more generally to detection of disulfide bond patterns. Copyright © 2001 John Wiley & Sons, Ltd.
Identification of substituted sites on MUC5AC mucin motif peptides after enzymatic O‐glycosylation combining β‐elimination and fixed‐charge derivatization
Authors: Czeszak X. , Ricart G. , Tetaert D. , Michalski J. C. , Lemoine J. 
Published: August 2002

AbstractA strategy for determination of O‐glycosylation site(s) in glycopeptides has been developed using model compounds obtained by enzymatic glycosylation (by human GaNTase‐T2 isoform) on peptides derived from the human MUC5AC mucin tandem repeat motif. The β‐elimination‐addition reaction (using dimethylamine and concomitantly ethanethiol) on the formerly glycosylated sites through a Michael‐type condensation produced efficient deglycosylation with appropriate chemical modification. After N‐terminal derivatization by a phosphonium group, peptide sequencing was then carried out by nanospray tandem mass spectrometry experiments. The highly predictable fragmentation pathways of these fixed‐charge phosphonium derivatives enable straightforward recognition of glycosylation site(s) based on the mass increment of +44 Da for originally glycosylated threonine compared to the mass of fragments containing nonglycosylated residues. Copyright © 2001 John Wiley & Sons, Ltd.
Evidence for an aryl migration during the electron impact induced fragmentation of substituted aryloxymethylquinoxalines
Authors: Starke I. , Sarodnick G. , Ovcharenko V. V. , Pihlaja K. , Kleinpeter E. 
Published: August 2002

AbstractThe electron impact (EI) mass spectra of 34 differently substituted 2‐phenoxymethyl‐, 2‐naphthyloxymethyl‐, 2‐pyridinyloxymethyl‐ and 2‐chinolinyloxymethylquinoxalines were recorded. The fragmentation patterns were examined by metastable ion analysis and exact mass measurements, employing finally also selective deuterium labelling. The inclusion of the substituted aryl ring moiety appears to be important for the fragmentation of the aryloxymethylquinoxalines. A molecular ion rearrangement is proposed for the observed loss of OH· and CHO· radicals. The influence of the different substituents on the aryl ring moiety on the rearrangement in the gas phase and on the resulting fragmentation was investigated. Copyright © 2001 John Wiley & Sons, Ltd.
Post‐source decay time‐of‐flight study of fragmentation mechanisms of protonated synthetic polymers under matrix‐assisted laser desorption/ionization conditions
Authors: Fournier I. , Marie A. , Lesage D. , Bolbach G. , Fournier F. , Tabet J. C. 
Published: August 2002

AbstractPost‐source decay (PSD) of three different nylon oligomers desorbed under matrix‐assisted laser desorption/ionization (MALDI) conditions was studied and their fragmentation pathways were investigated. The fragmentation of the protonated oligomers is very similar to that of peptides. The bn+, yn+ and zn+ series of ions were observed in abundance in the PSD spectrum. The end groups and the length of the spacer in the repeating unit influence the fragmentation of the different polyamides and the relative abundances of the product ions. Competitive dehydration and deamination reactions were observed, and depend on the nature of the end groups and the repeating units. The PSD spectra are very similar to collision‐induced dissociation (CID) spectra obtained under low‐energy conditions, implying that the selected precursor ions possess similar average internal energies. All the peaks observed in the PSD spectrum can be rationalized by reasonable fragmentation mechanisms. Copyright © 2002 John Wiley & Sons, Ltd.
Highly robust stainless steel tips as microelectrospray emitters
Authors: Ishihama Yasushi , Katayama Hiroyuki , Asakawa Naoki , Oda Yoshiya 
Published: August 2002

AbstractTapered stainless steel spray tips for sheathless microelectrospray ionization (µESI) have been developed. The fabrication procedure for the tapered stainless steel tips was optimized using an electropolishing technique followed by removal of the burr. Using the tip as the µESI emitter, a stable ESI spray was obtained at a flow rate of 20 nL/min. The sensitivity of the µESI system was almost two orders greater than that of the conventional ion spray system. The tip was highly stable, and was successfully used for over 1000 h. Moreover, these stainless steel tips were suitable for use with sheathless capillary electrophoresis/mass spectrometry (CE/MS) and capillary liquid chromatography/mass spectrometry (LC/MS) for routine analysis in proteomic and pharmaceutical applications. Copyright © 2002 John Wiley & Sons, Ltd.
Electrospray ionization mass spectrometric studies of phosphorus oxychloride directed synthesis of homo‐oligopeptide ester libraries
Authors: Zhou Ning , Lu Kui , Liu Yan , Chen Yi , Tang Guo , Cao Shu‐Xia , Qu Ling‐Bo , Zhao Yu‐Fen 
Published: August 2002

AbstractWith the assistance of phosphorus oxychloride, α‐amino acids were assembled into homo‐peptides, which were analyzed by electrospray ionization mass spectrometry (ESI‐MS) and multistage electrospray ionization mass spectrometry (ESI‐MS/MS). On quenching with water or various alcohols, the reaction mixtures yielded the corresponding peptides or peptide esters, respectively. This paper reports a simple method to synthesize the homo‐oligo‐peptide‐ester conjugated library by phosphorus oxychloride activation. Copyright © 2002 John Wiley & Sons, Ltd.
Does thermal degradation occur in laser spray ionization?
Authors: Hiraoka K. , Asakawa Y. , Ueda K. , Hori A. , Sakai T. , Okazaki S. , Nakamura M. 
Published: August 2002

AbstractA laser spray interface for use in liquid chromatography/mass spectrometry (LC/MS) has been investigated with respect to the degradation of the thermally labile compounds, ribostamycin, acetylcholine chloride, and cholesterol 3‐sulfate sodium salt. It was confirmed that few fragment ions were formed when the laser beam was focused at the center of the stainless steel capillary, i.e., no wall heating. When the laser beam was slightly off‐center, the sample ions suffered from thermal degradation by the heated wall of the stainless steel capillary to give fragment ions, which would be useful for the structural elucidation of the sample molecules. Copyright © 2002 John Wiley & Sons, Ltd.
Experimentation and modelling of HTTP over satellite channels
Authors: Kruse Hans , Allman Mark , Griner Jim , Tran Diepchi 
Published: August 2002

AbstractThis paper investigates the performance of various versions of the hyper text transfer protocol (HTTP) over a geosynchronous satellite link. Both HTTP/1.0, the currently popular form of the protocol, and HTTP/1.1, the recently standardized form of HTTP, are studied. Next, we quantify the impact of a moderate bit‐error rate on the performance of HTTP. Finally, we expand the mathematical model of HTTP presented in Heidemann, Obraczka and Touch (IEEE/ACM Transactions on Networking 1997; 5:616–630) to encompasses a wider range of HTTP behaviour. We show this model accurately predicts HTTP throughput by comparing it with HTTP transfers made over a satellite channel. Published in 2001 by John Wiley & Sons, Ltd.
An architecture for Internet service via broadband satellite networks
Authors: Bharadwaj Vijay G. , Baras John S. , Butts Norman P. 
Published: August 2002

AbstractHigh bandwidth satellites offer the promise of a rapidly deployable communications infrastructure with a natural support for mobility. However, many widely used versions of the Transmission Control Protocol perform poorly over satellite links, and this presents an obstacle to the deployment of such systems. We present an architecture that overcomes these problems and allows easy integration of heterogeneous networks into the larger Internet. We also present some results from our initial implementation, which uses TCP connection splitting to improve TCP performance over satellite links. Copyright © 2001 John Wiley & Sons, Ltd.
Understanding nature of science as progressive transitions in heuristic principles
Authors: Niaz Mansoor 
Published: August 2002

AbstractThis study has the following objectives: (a) understand nature of science as progressive transitions in heuristic principles as conceptualized by Schwab (1962); (b) reformulate Smith and Scharmann's characterization of nature of science (Smith & Scharmann, 1999) in the light of evidence from history and philosophy of science; and (c) provide a rationale for the inclusion of three more characteristics of nature of science, to the original five suggested by Smith and Scharmann. It is concluded that nature of science manifests in the different topics of the science curriculum as heuristic principles. Science education, by emphasizing not only the empirical nature of science but also the underlying heuristic principles, can facilitate conceptual understanding. © 2001 John Wiley & Sons, Inc. Sci Ed 85:684–690, 2001.
Beyond Interpretation: Initial Evaluation and Technique in Short‐Term Dynamic Psychotherapy. Part I
Authors: Malan David 
Published: August 2002

AbstractThe present article begins by describing the two basic questions in Short‐Term Dynamic Psychotherpy, namely what are the techniques that maximize success, and how may suitable patients be recognized? A consideration of work at the Tavistock Clinic leads to the conclusion that purely interpretative techniques, whether of short‐ or long‐term therapy, are inadequate. In the author's view, Davanloo has developed a technique that largely overcomes these limitations. This is illustrated by an initial interview of great length and complexity, which therefore needs to be divided into two parts. The second part follows. At the end of the second part the practical and theoretical consequences of Davanloo's work will be considered.
Interfacial phenomena and microstructural evolution during superplastic deformation
Authors: Kashyap B. P. 
Published: August 2002

AbstractCertain polycrystalline materials of fine equiaxed grains of size <10µm exhibit tensile ductility of several hundred to a few thousand per cent, called superplasticity, at intermediate strain rates and high temperatures. Experimental and theoretical results on mechanisms for superplastic deformation and concurrent microstructural evolution are reviewed to understand the role of grain boundary phenomena towards enhancement of grain growth and cavitation, etc. Grain boundary sliding (GBS) dominates superplastic flow, the extent of which varies between the grain and interphase boundaries in two‐phase alloys. Accommodation to GBS is provided by diffusional and dislocation mechanisms, which are manifested in the form of grain boundary migration (GBM), grain rotation and grain switching events. Although GBS helps in retaining the initial equiaxed grain shape of superplastic materials, the accommodation processes accelerate grain growth. In the lack of other accommodation processes the cavities are formed, being more pronounced at the boundaries of maximum sliding. The ppm‐level impurities present in superplastic materials do not influence the sliding and flow characteristics under typical superplastic conditions but they do promote cavitation and limit the ductility. The presence of precipitate or hard particles in quasi‐single‐phase superplastic materials inhibits GBM but provides sites for cavitation. Such materials exhibit more dislocation activities than anticipated for accommodation of GBS. The nature of microstructural changes noted during superplastic deformation supports the operation of cooperative GBS, in addition to a large variety of combinations between sliding and accommodation processes. Copyright © 2001 John Wiley & Sons, Ltd.
Deformation microstructures and selected examples of their recrystallization
Authors: Hughes D. A. 
Published: August 2002

AbstractThe elements that are needed to describe a deformation structure—grains, grain boundaries, macroscale banding within crystals, cell blocks, geometrically necessary boundaries and incidental dislocation boundaries (cell boundaries)—are presented and described for fcc metals and alloys of medium to high stacking fault energy. Pertinent to this quantitative description are the local orientations, structural morphology, different boundary misorientations and spacings as a function of strain and deformation conditions. Three specific examples are given in which particular aspects of the deformation structure are shown to direct the recrystallization behavior. Copyright © 2001 John Wiley & Sons, Ltd; first published by Risø National Laboratory.
Two‐band photoluminescence spectra from nanometre Si particle‐embedded Si oxide films
Authors: Ma S. Y. 
Published: August 2002

AbstractNanometre Si particle (NSP)‐embedded Si oxide films were deposited on p‐type Si substrates by the r.f. magnetron sputtering technique using Si and SiO2 composite sputtering targets. All samples were annealed in a nitrogen ambient at 600° for 30 min. X‐ray photoelectron spectroscopy and optical absorption measurements were performed on the samples. The sizes of the NSPs were increased by increasing the relative area of the Si wafer in the co‐sputtering target. The photoluminescence spectra of all the samples exhibited two bands with their peaks located at 370 nm (3.4 eV) in the ultraviolet spectral range and 650–665 nm (1.9 eV) in the orange–red spectral range. The experimental results indicate that there are two types of photoexcitation processes in the NSP‐embedded Si oxide films: one for the orange–red band occurring in the NSPs and the other for the ultraviolet band occurring in the SiO2 layers. Copyright © 2001 John Wiley & Sons, Ltd.