bluuebunny/crossref_metadata_2025 huggingface dataset:
The intracellular domain of the Drosophila cholinesterase‐like neural adhesion protein, gliotactin, is natively unfolded
Authors: Zeev‐Ben‐Mordehai Tzviya , Rydberg Edwin H. , Solomon Ariel , Toker Lilly , Auld Vanessa J. , Silman Israel , Botti Simone , Sussman Joel L.
Published: October 2003

Drosophila gliotactin (Gli) is a 109‐kDa transmembrane, cholinesterase‐like adhesion molecule (CLAM), expressed in peripheral glia, that is crucial for formation of the blood‐nerve barrier. The intracellular portion (Gli‐cyt) was cloned and expressed in the cytosolic fraction of Escherichia coli BLR(DE3) at 45 mg/L and purified by Ni‐NTA (nitrilotriacetic acid) chromatography. Although migration on sodium dodecyl sulfate‐polyacrylamide gel electrophoresis (SDS‐PAGE), under denaturing conditions, was unusually slow, molecular weight determination by matrix‐assisted laser desorption/ionization time‐of‐flight (MALDI‐TOF) mass spectrometry (MS) confirmed that the product was consistent with its theoretical size. Gel filtration chromatography yielded an anomalously large Stokes radius, suggesting a fully unfolded conformation. Circular dichroism (CD) spectroscopy demonstrated that Gli‐cyt was >50% unfolded, further suggesting a nonglobular conformation. Finally, 1D‐1H NMR conclusively demonstrated that Gli‐cyt possesses an extended unfolded structure. In addition, Gli‐cyt was shown to possess charge and hydrophobic properties characteristic of natively unfolded proteins (i.e., proteins that, when purified, are intrinsically disordered under physiologic conditions in vitro). Proteins 2003. © 2003 Wiley‐Liss, Inc.
Accessibility of oxygen with respect to the heme pocket in horseradish peroxidase
Authors: Khajehpour Mazdak , Rietveld Ivo , Vinogradov Sergei , Prabhu Ninad V. , Sharp Kim A. , Vanderkooi Jane M.
Published: October 2003

Oxygen and other molecules of similar size take part in a variety of protein reactions. Therefore, it is critical to understand how these small molecules penetrate the protein matrix. The protein system studied in this case is horseradish peroxidase (HRP). We have converted the native HRP into a phosphorescent analog by replacing the heme prosthetic group by Pd‐mesoporphyrin. Oxygen readily quenches the phosphorescence of Pd porphyrins, and this can be used to characterize oxygen diffusion through the protein matrix. Our measurements indicate that solvent viscosity and pH modulate the accessibility of the heme pocket relative to small molecules. The binding of the substrate benzohydroxamic acid (BHA) to the protein drastically impedes oxygen access to the heme pocket. These results indicate that, first, the penetration of small molecules through the protein matrix is a function of protein dynamics, and second, there are specific pathways for the diffusion of these molecules. The effect of substrate and pH on protein dynamics has been investigated with the use of molecular dynamics calculations. We demonstrate that the model of a “fluctuating entry point,” as suggested by Zwanzig (J Chem Phys 1992;97:3587–3589), properly describes the diffusion of oxygen through the protein matrix. Proteins 2003;53:000–000. © 2003 Wiley‐Liss, Inc.
Crystal‐state 3D‐structural characterization of novel 310‐helical peptides
Authors: Crisma Marco , Moretto Alessandro , Rainaldi Mario , Formaggio Fernando , Broxterman Quirinus B. , Kaptein Bernard , Toniolo Claudio
Published: October 2003

The crystal‐state conformations of two octapeptides, pBrBz‐(D‐Iva)8‐OtBu (8I) and Ac‐[L‐(αMe)Val]8‐OH (8II), the heptapeptide Z‐[L‐(αMe)Val]7‐OH (7), the hexapeptide Z‐[L‐(αMe)Leu]6‐OtBu (6) and the tetrapeptide alkylamide Z‐(Aib)2‐L‐Glu(OMe)‐L‐Ala‐L‐Lol (5) were assessed by x‐ray diffraction analyses. Two independent molecules are observed in the asymmetric unit of each L‐(αMe)Val homo‐peptide. All four homo‐peptides are folded in a regular 310‐helical structure (only the C‐terminal H‐bonded conformation of the D‐Iva octapeptide is distorted to a type‐I β‐turn). The hydroxyl groups of the C‐terminal carboxyl moieties of the two L‐(αMe)Val homo‐peptides participate in an oxy‐analogue of the type‐III β‐turn conformation. While the two L‐(αMe)Val 310‐helices are right‐handed, the D‐Iva and L‐(αMe)Leu helices are left‐handed. The tetrapeptide alkylamide is 310‐helical at the N‐terminus, but it is mixed 310/α‐helical at the C‐terminus. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd.
Synthesis, conformation and biological activity of dermorphin and deltorphin I analogues containing N‐alkylglycine in place of residues in position 1, 3, 5 and 6
Authors: Biondi Laura , Giannini Elisa , Filira Fernando , Gobbo Marina , Marastoni Mauro , Negri Lucia , Scolaro Barbara , Tomatis Roberto , Rocchi Raniero
Published: October 2003

Syntheses are described of new dermorphin and [D‐Ala2]deltorphin I analogues in which the phenylalanine, the tyrosine or the valine residues have been substituted by the corresponding N‐alkyl‐glycine residues. Structural investigations by CD measurements in different solvents and preliminary pharmacological experiments were carried out on the resulting peptide–peptoid hybrids. The contribution from aromatic side chain residues is prominent in the CD spectra of dermorphin analogues and the assignment of a prevailing secondary structure could be questionable. In the CD spectra of deltorphin analogues the aromatic contribution is lower and the dichroic curves indicate the predominance of random conformer populations. The disappearance of the aromatic contribution in the [Ntyr1,D‐Ala2]‐deltorphin spectrum could be explained in terms of high conformational freedom of the N‐terminal residue. The kinetics of degradation of the synthetic peptoids digestion by rat and human plasma enzymes were compared with that of [Leu5]‐enkephalin. The binding to opioid receptors was tested on crude membrane preparations from CHO cells stably transfected with the µ‐ and δ‐opioid receptors. The biological potency of peptoids was compared with that of dermorphin in GPI preparations and with that of deltorphin I in MVD preparations. All the substitutions produced a dramatic decrease in the affinity of the peptide–peptoid hybrids for both the µ‐ and δ‐opioid receptors. Nval5 and/or Nval6 containing hybrids behaved as µ‐opioid receptor agonists and elicit a dose‐dependent analgesia (tail‐flick test) when injected i.c.v. in rats. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd.
Potent side‐chain to side‐chain cyclized dermorphin analogues containing a carbonyl bridge
Authors: Filip Katarzyna , Oleszczuk Marta , Pawlak Danuta , Wójcik Jacek , Chung Nga N. , Schiller Peter W. , Izdebski Jan
Published: October 2003

A new family of cyclic opioid peptide analogues related to the 1–4 sequence of dermorphin/deltorphin (Tyr‐D‐Aaa2‐Phe‐Aaa4‐NH2) has been synthesized. The synthesis of the linear precursor peptides was accomplished by the solid‐phase method and ring formation was achieved via a ureido group incorporating the side chain amino functions of D‐Aaa2 (D‐Lys, D‐Orn) and Aaa4 (Lys, Orn, Dab, Dap). The peptides were tested in the guinea‐pig ileum (GPI) and mouse vas deferens (MVD) assays. Most showed very high agonist potency in the GPI assay. The peptide containing D‐Lys in position 2 and Dab in position 4 was 210 times more active than enkephalin, and that containing Orn and Dab, respectively, was 150 times more active than enkephalin. The latter peptide was also very active in the MVD assay, and showed an IC50 MVD/GPI ratio of 0.816. NMR spectra of selected peptides were recorded, and structural parameters were determined. The conformational space of the peptides was examined using the electrostatically driven Monte Carlo method. With the help of the NMR spectra each peptide was described as an ensemble of conformations. The conformations have been interpreted with regard to the opioid activities, and comparisons have been made with a model proposed earlier for enkephalin analogues. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd.
High‐pressure and high‐temperature study of phase transitions in solid germanium
Authors: Di Cicco Andrea , Frasini Anna Chiara , Minicucci Marco , Principi Emiliano , Itiè Jean‐Paul , Munsch Pascal
Published: October 2003

A detailed investigation of the pressure and temperature dependence of the structure of stable and metastable solid Ge phases in the 0–15 GPa and 295–500 K ranges is presented. Structural results including the equation of state, characteristic of coexistence regions of diamond and β‐tin structures, and appearance of metastable phases are discussed and compared with the results presently available in the literature. The isothermal bulk modulus and its derivative are evaluated using temperature‐dependent equations of state for Ge I (cubic) and Ge II (β‐Sn), and for the Ge III (ST12) metastable polymorph at 400 K. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Structure and properties of As25Te35Si40 glass
Authors: Lörinczi A. , Sava F. , Iovu M. , Leonovici M. , Halm Th. , Popescu M. , Hoyer W.
Published: October 2003

The glassy composition As25Te35Si40 was investigated by differential scanning calorimetry (DSC), X‐ray diffraction (XRD), Raman spectroscopy, and infrared absorption (IR) measurements. X‐ray diffraction patterns at room temperature and at temperatures around Tg were recorded and the radial distribution functions have been calculated. A continuous random network model for the ideal homogeneous glass structure has been proposed.
An extended KPS method for calculating multipole polarizabilities – application to crystalline ions
Authors: Yousif Al‐Mulla S. Y.
Published: October 2003

The improvement proposed by Shukla and Easa to the variational calculation of the multipole polarizabilities of atoms and ions has been applied to the Kirkwood–Pople–Schofield approach, to derive a general form of this variational techniqes. This form has been applied to calculate the polarizabilities of free atoms and ions and for atoms and ions in crystalline environments. The accuracy of the results in the KPS method depends on the quality of the initial wavefunction of a given system.
Electrical resistivity of RNi4B compounds (R = Y or rare earth)
Authors: Toliński T. , Kowalczyk A. , Ivanov V.
Published: October 2003

Electrical resistivity studies of RNi4B compounds (R = Y, Ce, Pr, Nd, Sm, Dy, Ho, Er) are presented. The ordering temperatures are well established in the case of the ferromagnetic compounds. YNi4B shows a presence of an impurity carbon‐rich phase with a transition to the superconducting state at temperature of 12 K. This compound was treated as the isostructural non‐magnetic reference compound for the RNi4B series. CeNi4B reveals a shallow Kondo‐like minimum at low temperatures. Spin‐disorder contributions are derived for the compounds and the resistivity in the ferromagnetic region is analysed including the influence of anisotropy effects. In the case of SmNi4B the effect of the crystal field was taken into consideration.
Acoustic studies of the ferroelastic phase transition in the K3Na(CrO4)2 crystal
Authors: Charnaya E. V. , Mroz B. , Radzhabov A. K. , Tien C. , Tylczynski Z. , Wur C. S.
Published: October 2003

Ultrasonic studies of the K3Na(CrO4)2 crystal were carried out within a temperature range of 185 to 295 K. Temperature dependences of the velocity and attenuation coefficient for the xx and zz longitudinal acoustic waves and the yx and zx transverse waves were measured. Noticeable anomalies in velocity and attenuation for transverse as well as for longitudinal waves were found near the ferroelastic phase transition which temperature was 235.5 K. The anomalies in the c44 and c66 elastic moduli were treated on the base of the Landau theory assuming the component ε4 as the primary order parameter and (ε2–ε1)/2 as the secondary one. Six elastic moduli, c11, c33, c44, c66, c12, and c14 were evaluated at room temperature.
Effect of charge carrier–phonon coupling on the energy of shallow donors in CdSe quantum dots
Authors: Feddi E. , El Haouari M. , Assaid E. , Stébé B. , El Khamkhami J. , Dujardin F.
Published: October 2003

The effects of low electric field and finite‐barrier height on the ground state energy of a donor impurity confined in a polar CdSe spherical quantum dot embedded in a non‐polar matrix were studied. Calculations were carried out in the framework of the effective mass approximation using the Hassé variational approach. The effect of the quantum confinement was described by a finite deep potential taking into account the interactions between the charge carriers (electron and ion) and the confined longitudinal optical phonons (LO‐phonons). It was found that the binding energy and the polarizability depend strongly on LO‐phonon effects. So, the phonon corrections should not be ignored or neglected whatever the dot size and the degree of confinement. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Topological excitations near a spinless atom in layered antiferromagnets with an axial magnetic field
Authors: Fonseca M. P. P. , Pereira A. R.
Published: October 2003

We have investigated the effect of a nonmagnetic impurity on the configuration and energy of topological excitations in the isotropic two‐dimensional Heisenberg antiferromagnet in the presence of an external uniform magnetic field applied perpendicular to the XY plane. This model is expected to have the XY‐like low‐temperature phase and show the Kosterlitz–Thouless transition due to a XY‐like degeneracy of a canted spin‐flop ground state. The spins in the spin‐flop state may simultaneously tip into the out‐of‐plane directions while forming a vortex. Thus, we consider as the excitation for our study, the out‐of‐plane vortex. Our calculations show that an effective interaction between the two defects, the out‐of‐plane vortex and the nonmagnetic impurity, can be attractive at short range. These results can also be applied to two‐dimensional easy‐plane ferromagnets with weak anisotropy. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A method for phase diagrams of spin‐1 Ising ferromagnetic systems
Authors: Polat H. , Akįncį Ü. , Sökmen İ.
Published: October 2003

A method in Ising models is introduced by using the effective field theory (EFT) with correlations. In the present method, for the spin‐1 Ising ferromagnetic systems with three coordination numbers q (q = 3, 4 and 6), we have derived a set of linear equations by taking as a basis the thermal averages of a central spin and a perimeter spin at the site i, which is defined within spin identities and differential operator technique. By solving numerically the set of linear equations derived individually for the Ising systems, we have evaluated the phase diagrams of both the spin‐1 Ising ferromagnetic systems with a single‐ion anisotropy and the spin‐1 transverse Ising ferromagnetic systems with a transverse field. The present results of critical transverse field for the spin‐1 transverse Ising systems improve those obtained by the pair approximation. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Interpretation of the optical spectra and EPR parameters for Yb3+ in LiYF4 crystal
Authors: Dong H. N. , Zheng W. C. , Wu S. Y.
Published: October 2003

In this paper, the crystal‐field energy levels, the EPR g‐factors g∥, g⟂ of Yb3+ and hyperfine structure constants A∥, A⟂ of 171Yb3+ and 173Yb3+ isotopes in LiYF4 crystal are calculated from the crystal‐field theory. All the calculated results (seven energy levels and six EPR parameters) are in reasonable agreement with the observed values. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
First‐principles study on elastic properties and phase stability of III–V compounds
Authors: Wang S. Q. , Ye H. Q.
Published: October 2003

The results of first‐principles plane‐wave pseudopotential calculations of the elastic constants for a total of 25 III–V binary phases of both zincblende and wurtzite poly‐types are presented. In addition, the study shows that the relaxation of internal parameters is extremely important to the accuracy of the results. A larger anisotropy factor favors the wurtzite structure while the zincblende structure is preferred for lower anisotropy factors. The boron phases have quite different behavior in both their elastic and structural properties from the other III–V compounds. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Computation of optical properties of Si‐based photonic crystals with varying pore diameters
Authors: Hillebrand R. , Jamois C. , Schilling J. , Wehrspohn R. B. , Hergert W.
Published: October 2003

Two‐dimensional Si‐based photonic crystals of triangular lattice type are routinely fabricated by electrochemical pore etching of prestructured Si‐wafers. The radius of the pores can be modulated during the growth process. Based on Maxwell's equations, we theoretically study the optical properties (band structures, electromagnetic fields) of such photonic crystals by applying models with modulated pore diameters. The models are systematically varied with respect to the pore diameters and the pore profiles in the growth direction. Thus, the dielectric contrast between the central narrow core and the outer wide cladding parts can be controlled in analogy to slab structures. We identify conditions for the confinement of the electromagnetic fields inside the core region. The confinement is quantified by correlating the fields with the pore geometry. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Study on additive effective interaction between vertical Bloch lines
Authors: Tang G. D. , Liu Y. , Hu H. N. , Liu Y. P. , Sun H. Y. , Nie X. F.
Published: October 2003

The properties of hard magnetic domains in garnet bubble films were studied. The formula for the domain wall energy of circular hard magnetic domains was improved by adding an assumptive effective interaction energy term between vertical Bloch lines. This satisfactorily interpreted the behavior of hard domains subjected to a static bias magnetic field, which had remained unclear for many years, and also successfully interpreted the temperature character of the hard domains. Therefore, this assumptive effective interaction energy can act as a clue to derive exactly the interaction between vertical Bloch lines. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Growth of group II–VI semiconductor quantum dots with strong quantum confinement and low size dispersion
Authors: Pandey Praveen K. , Sharma Kriti , Nagpal Swati , Bhatnagar P. K. , Mathur P. C.
Published: October 2003

CdTe quantum dots embedded in glass matrix are grown using two‐step annealing method. The results for the optical transmission characterization are analysed and compared with the results obtained from CdTe quantum dots grown using conventional single‐step annealing method. A theoretical model for the absorption spectra is used to quantitatively estimate the size dispersion in the two cases. In the present work, it is established that the quantum dots grown using two‐step annealing method have stronger quantum confinement, reduced size dispersion and higher volume ratio as compared to the single‐step annealed samples. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Far‐infrared absorption due to shallow acceptors in semi‐insulating GaAs in dependence on EL2 bleaching
Authors: Gomeniuk Y. V. , Alt H. Ch. , Kretzer U.
Published: October 2003

Far‐infrared absorption in semi‐insulating GaAs due to electronic transitions of shallow acceptors was measured in dependence on conditions of bleaching the GaAs intrinsic defect EL2. The far‐infrared spectra were compared with the results of near‐infrared spectroscopy of EL2 fundamental state. It was found that under conditions of low intensity illumination the neutral acceptors can coexist with the neutral EL2 defect. The model is proposed which explains the effects that were not observed previously, such as depopulation of neutral shallow acceptors at low temperature, and the charge redistribution between different shallow acceptor levels at increasing temperature for the samples co‐doped with zinc and carbon. It is shown that far‐infrared spectroscopy is suitable for quantitative evaluation of the shallow acceptor concentration in GaAs material. The corresponding calibration factors are given. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Minority carrier diffusion lengths and optical self‐absorption coefficient in undoped GaN
Authors: Matoussi A. , Boufaden T. , Guermazi S. , Eljani B. , Mlik Y. , Toureille A.
Published: October 2003

In this paper we report electron beam induced current (EBIC) measurements on Schottky diodes on undoped GaN samples grown by the metal organic vapor phase epitaxy method on porous silicon substrates. A 2D simulation model was applied to perform the theoretical EBIC profiles and to compare with the experimental one. A minority carrier diffusion length (L) for holes of 0.72 μm was measured in the space charge region, indicating constant diffusivity of 6.48 cm2/s and a lifetime coefficient of 0.8 ns. An increase of L is observed as the probe source is moved from the Schottky junction to the bulk material. This increase was related to the polarization effects that are preponderant in group III–nitride devices. Far from the depletion layer (greater than 0.91 μm) the measured current is produced by the reabsorbed recombination radiation process. This corresponds to an optical self‐absorption coefficient of ap = 0.112 μm−1. The results show that the transport parameters depend on the growth technology. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Dynamic and thermodynamic properties of solid helium in the reduced all‐neighbours approximation of the self‐consistent phonon theory
Authors: Malinowska‐Adamska C. , Słoma P. , Tomaszewski J.
Published: October 2003

The results of studies of physical properties of solid helium obtained with the help of the reduced all‐neighbours approximation of the self‐consistent phonon theory are presented. The results of calculation of the temperature and pressure variations of the quantities describing the dynamics and thermodynamics of solid He‐3 and He‐4 obtained in terms of the (exp m) Buckingham the (n m) Lennard‐Jones and the (exp exp) Morse renormalized potentials are given and compared with experimental and other theoretical data. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Temperature dependence of the indirect band gap and related optical parameters of (NH4)2ZnCl4:xSr2+ single crystals
Authors: Gaffar M. A. , Abu El‐Fadl A. , Bin Anooz S.
Published: October 2003

Optical transmittance measurements were carried out near the absorption edge of (NH4)2ZnCl4:xSr2+ single crystals, where x = 0.00, 0.020, 0.039, 0.087 or 0.144 wt%. The dependence of the absorption coefficient (α) on photon energy in the range 3.4–6.4 eV and on temperature in the range 276–350 K was examined. With increasing temperature the absorption edge was shifted to the lower energy side; this shift was attributed to the temperature dependence of electron–lattice interactions. Due to the presence of Sr2+ in (NH4)2ZnCl4:xSr2+ a change in the absorption band centred at 5.30 eV was observed. In the case of higher strontium doping, the optical absorption coefficient showed a ‘pre‐transition’ stage just before the onset of the band‐to‐band transition. Exponential dependence of α on hν according to the Urbach rule was observed and the Urbach parameters were determined. The steepness parameter was strongly affected by doping; its behaviour at 319 K evidently showed the antiferroelectric to commensurate phase transition. The temperature dependence of Eg was also estimated using data for the steepness parameter, and hence Eg at different temperatures and Sr2+ concentrations was evaluated. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A new concept for the calculation of the mobile dislocation density in constitutive models of strain hardening
Authors: Roters F.
Published: October 2003

A new concept for the calculation of the mobile dislocation density in constitutive models is presented. In contrast to earlier approaches this concept does not use rate equations to calculate the evolution of the mobile dislocation density but is based on the minimization of the flow stress in each increment. In comparison to a concept using a constant value for the mobile dislocation density the new concept results in a more realistic stress strain relation, especially when applied to strain rate change experiments. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Relaxation phenomena in the Blume–Emery–Griffiths model near the critical and multicritical points
Authors: Erdem R. , Ekiz C. , Keskin M.
Published: October 2003

The relaxation behaviour of the Blume–Emery–Griffiths (BEG) model Hamiltonian with bilinear and biquadratic nearest‐neighbour ferromagnetic exchange interaction and crystal field interactions is studied by using the molecular field approximation (MFA) and Onsager's theory of irreversible thermodynamics. First the equilibrium behaviour and the phase diagrams of the model in MFA are given briefly in order to understand the relaxation behaviour. Then, Onsager theory is applied to the model and the set of linear differential equations, which is also called the kinetic or rate equations, is obtained. By solving these equations a set of relaxation times is calculated and examined for temperatures near the critical and multicritical points. It is found that one of the relaxation times (τ1) is sharply cusped at the triple and critical points, whereas it approaches infinity near the critical‐end point. On the other hand, the other relaxation time (τ2) displays a jump‐discontinuity behaviour at the triple and critical points but it has a cusp at the critical‐end point. A maximum of τ2 has also been observed above the critical‐end point. Moreover, similar calculations are performed for non‐zero magnetic field (H) to investigate the effect of H on relaxation times. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Influence of interface between two ferroelectrics in a film on polarization distribution
Authors: Lü Tianquan , Zheng Zhiren , Sun Punan
Published: October 2003

Using Ginzburg and Devonshire theory the polarization distribution is studied for a ferroelectric film consisting of two different materials with an interface parallel to the spontaneous polarization. The numerical results show that a much thinner transition layer between two materials can influence the polarization in a larger range. The temperature and the Curie‐temperature difference between two bulk materials are two sensitive influencing factors and the change of the thickness of the transition layer has little influence. The rise of temperature or Curie‐temperature difference between two bulk materials will widen the distribution range of inhomogeneous polarization. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Ordering and strain‐induced D–D interaction in Lu–D
Authors: Blanter M. S. , Granovskiy E. B. , Magalas L. B.
Published: October 2003

Specific values of D–D strain‐induced (elastic) interaction energy are used to analyze the unusual structure of the ordered solid solution Lu–D. Formation of the chains of interstitial atoms is due to both electronic and elastic interaction of the interstitials. At the same time, the main reason for the chain‐pair formation is the strain‐induced long‐range elastic interaction. Pairs of chains in antiphase are more advantageous than pairs of chains in phase from energy considerations. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The Heisenberg model on a stacked‐triangular lattice: spin Green function approach
Authors: Du A. , Li J. , Wei G. Z.
Published: October 2003

Using a spin Green function approach, we have studied the magnetic properties of a stacked‐triangular Heisenberg model, in which the triangular lattice is in the xy plane and the triangular nets are stacked in parallel along the z axis. We consider both the quasi‐two‐ and the quasi‐one‐dimensional cases and suppose the interaction between the nearest‐neighbor spins to be antiferromagnetic or ferromagnetic. By computing the magnetization and the transition temperature of the system, we find that the geometrical frustration introduced by the antiferromagnetic exchange in a triangular lattice brings about an additional spin fluctuation, which results in a decrease of the staggered magnetization and a lowering of the transition temperature compared to the system without geometrical frustration. In the quasi‐two‐dimensional case, the exchange strength |J| in the xy plane is much larger than |J′| along the z direction (|J| ≫ |J′|), and in the quasi‐one‐dimensional case (|J| ≪ |J′|) the transition temperatures can be expressed in approximation forms as TN = S(S + 1)|J|/[aln (|J/J′|) + b and TN = cS(S + 1)(|JJ′|)1/2, respectively. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Atomic‐scale simulations of the interaction between dislocations and tilt grain boundaries in α‐iron
Authors: Saraev D. , Schmauder S.
Published: October 2003

The interaction of lattice dislocations with symmetric and asymmetric tilt grain boundaries has been simulated for different grain boundary misorientation angles by means of the molecular dynamics method using embedded atom method (EAM) potentials. An edge dislocation is equidistantly placed between a grain boundary and a free surface. The movement of the dislocation occurs during relaxation in the absence of external stress and is a result of competitive attractions from the grain boundary and the free surface. The evolution of the position of the dislocation is analysed. An attraction force from the grain boundary has been found in all cases. The strongest attraction has been observed for the cases when the glide plane of the dislocation is perpendicular to the grain boundary. A similar effect has been found for low and room temperatures. An analysis of microscopic stresses has also been performed. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Gallium‐rich reconstructions on GaAs(001)
Authors: Pristovsek M. , Tsukamoto S. , Ohtake A. , Koguchi N. , Orr B. G. , Schmidt W. G. , Bernholc J.
Published: October 2003

Ga‐rich reconstructions on GaAs(001) surfaces were prepared by annealing and Ga dosing of Molecular Beam Epitaxy grown samples and analyzed in‐situ by Reflectance Anisotropy Spectroscopy and Reflection High‐Energy Electron Diffraction. Annealing or dosing gallium above about 800 K invariably results in a (4 × 2)/c(8 × 2) reconstruction. Lowering the temperature or annealing below 800 K results in a (2 × 6)/(3 × 6) reconstruction. By dosing the (2 × 6)/(3 × 6) reconstruction with more than 0.2 monolayer of gallium, it transforms into a (4 × 6) reconstruction. The observed translational symmetries and measured RAS spectra are compared with results of first‐principles calculations. None of the (2 × 6) structures proposed in the literature is energetically stable. The RAS spectrum calculated for the ζ(4 × 2) model resembles reasonably the data measured for the (4 × 2) surface. The RAS spectra calculated for (2 × 6) symmetries indicate that mixed Ga‐As dimers likely are a structural element of the corresponding surface reconstructions. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Homogeneous linewidth of quantum well excitons from resonance fluorescence spectra
Authors: Schwedt D. , Nacke Ch. , Stolz H. , Eshlaghi S. , Reuter D. , Wieck A.
Published: October 2003

We report high resolution measurements of resonance fluorescence spectra of high quality GaAs quantum wells after small bandwidth cw excitation. The resulting spectra can be well described with means of light scattering from a statistically distributed ensemble of three‐level‐systems. Using this model we are able to separate the homogeneous linewidth from the inhomogeneous ensemble response. Thus, we present a simple linear tool for sample characterization. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Composition dependent energy band gaps for the ternary alloy Si1−x−yGexCy
Authors: Shim Kyurhee , Bae Jung‐Wook , Lim Jong‐Soo , Lee Kyong‐Won , Kim Yunsoo , Rabitz Herschel
Published: October 2003

The universal tight binding method based on sp3s* basis functions is used to calculate the electronic structure of the ternary alloy Si1−x−yGexCy. The dependences of the fundamental band gaps (E(Γ), E(Δ), E(L), and E(X)) are obtained and investigated for small concentrations of carbon (0 ≤ y ≤ 0.05). It is found that the presence of carbon in the alloy Si1−x−yGexCy results in a very significant change (i.e., reduction) of the alloy bond length with a small change of the energy band gaps. The energy band gap increases upon adding carbon to the strained alloy. However, the energy band gap decreases upon adding carbon while keeping the alloy lattice matched to the substrate Si. The calculated band gaps are in good agreement with the limited available experimental data and ab initio results. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Zero‐phonon lines in the d → f luminescence of LiYF4 : Er3+
Authors: Chen Yonghu , Kirm Marco , Negodin Evgueni , True Marcus , Vielhauer Sebastian , Zimmerer Georg
Published: October 2003

High‐resolution analysis of spin‐allowed and spin‐forbidden VUV d → f luminescence of a heavy rare earth ion in a wide band gap host crystal clearly yields zero‐phonon lines, indicating intermediate coupling. Although the chosen system (LiYF4 : Er3+) has a complicated ground‐state structure, zero‐phonon lines for nearly all of the eight Stark levels of the ground state are observed. Striking similarities between d → f and f → f emission support the assignments. (© 2003 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
SMILIB: Rapid Assembly of Combinatorial Libraries in SMILES Notation
Authors: Schüller Andreas , Schneider Gisbert , Byvatov Evgeny
Published: October 2003

A software tool was developed for fast combinatorial library enumeration (SMILIB). Its particular features are its simplicity to use, high flexibility in constructing combinatorial libraries and high speed of library construction. SMILIB offers the possibility to construct very large combinatorial libraries using the flexible and portable SMILES format. Libraries are generated at rates of approximately 30,000 molecules per minute. Combinatorial building blocks are attached to scaffolds by means of linkers rather than to concatenate them directly. This allows for creation of easily customized libraries using linkers of different size and chemical nature. A web interface for a limited web‐based version of the software is available at URL: www.modlab.de. An unlimited binary version of SMILIB for command line execution on Linux systems is available from this URL.
Development of a Genetic Algorithm to Design and Identify Peptides that can Cross the Blood‐Brain Barrier
Authors: Teixidó Meritxell , Belda Ignasi , Roselló Xavier , González Sonia , Fabre Myriam , Llorá Xavier , Bacardit Jaume , Garrell Josep M. , Vilaró Senen , Albericio Fernando , Giralt Ernest
Published: October 2003

The design of peptide drugs to treat central nervous system (CNS) diseases is hampered by our ignorance of the factors that determine whether a given peptide can cross the blood‐brain‐barrier (BBB). We are developing an approach to this problem that combines computer‐aided ligand design, parallel synthesis of peptide libraries, and biological evaluation using in vitro BBB models. We present a genetic algorithm (GA) to search for peptides that can cross the BBB. In the design and optimization of this GA we used a genetic meta‐algorithm to optimize the GA parameters. The GA is validated in silico by virtual screening of a peptide library of more than 1015 molecules. We used a virtual fitness function dervied from statistical analysis of the few experimental data on peptide‐BBB permeability available.
Automated Sorting of Beads from a “One‐Bead‐Two‐Compounds” Combinatorial Library of Metalloproteinase Inhibitors
Authors: Christensen Caspar , Groth Thomas , Bruun Schiødt Christine , Tækker Foged Niels , Meldal Morten
Published: October 2003

The development and use of an instrument that automatically separates non‐fluorescent beads from fluorescent beads are described. The scope of the instrument was tested by on‐bead screening of a solid phase combinatorial library synthesized on the aqueous compatible PEGA library resin [1]. The one‐bead‐two‐compounds library [12] consisted of approx. 160.000 putative phosphinic peptide inhibitors, encoded by ladder synthesis [22] for facile analysis by MALDI‐TOF mass spectrometry, and each bead also contained a common fluorescence‐quenched substrate. The library was screened for activity against MMP‐9; several beads with inhibitory activity were selected from the library by the novel fully automated sorting method and analyzed by MALDI‐TOF MS for structural elucidation.
Collection of Bioactive Reference Compounds for Focused Library Design
Authors: Schneider Petra , Schneider Gisbert
Published: October 2003

A collection of reference molecules for ligand‐based library design was compiled from the recent scientific literature. Selected properties of this set of 4,236 drugs and drug candidates were analyzed and compared to previous studies. Lipophilicity and molecular weight distributions revealed a trend toward larger, more lipophilic molecules of newer drug candidates. Using the compound collection as a source of reference data, a method for visualization of molecule distributions in a pharmacophore space by self‐organizing maps (SOM) was developed which can be used for virtual library design. Potential applications of this “pharmacophore road map” approach are discussed.
Epothilones: Quantitative Structure Activity Relations Studied by Support Vector Machines and Artificial Neural Networks
Authors: Bleckmann Annalen , Meiler Jens
Published: October 2003

In this paper the relation between the structure of epothilones (a new class of anti‐tumour agents) and their potential to influence the tubulin‐microtubule equilibrium is investigated. Insights into the character of the tubulin‐epothilone interactions are derived as the accuracy and reliability of support vector machines and artificial neural networks to model such relations quantitatively is compared. Both methods are well qualified to model relationships between the structure of epothilone derivatives and their anti‐tumour activities. Artificial neural networks achieve lower residual standard deviations (22%) compared to support vector machines (25%) and better classification results (89% compared to 75%). However, the reproducibility of the results is greater for support vector machines, which suggests a stronger convergence. The mapping of the influence of individual structural descriptors on the three‐dimensional epothilone structure suggests one side of the rather flat molecule to be more important for its activity. The “LIBSVM” software which is used for simulating the support vector machines is freely available from www.csie.ntu.edu.tw/~cjlin/libsvm. The Program “Smart” which is used for simulating artificial neural networks is free for academic use and can be obtained together with the database of epothilones and their activities from www.jens‐meiler.de.
CGLIB—a constraint‐based graphics library
Authors: Zhou Neng‐Fa
Published: October 2003

CGLIB is a high‐level graphics library for B‐Prolog, a constraint logic programming system. The library provides primitives for creating and manipulating graphical objects and a set of constraints including not‐overlap, grid, table and tree constraints that facilitate the specification of the layouts of objects. The library adopts a construct called action rules which is available in B‐Prolog for creating agents and programming interactions among agents or between agents and the user. The library is a fully working system implemented in B‐Prolog, Java and C. It can be used in many areas such as drawing editors, interactive user interfaces, document authoring, animation, information visualization, intelligent agents and games. The high‐level abstraction of the library and the use of constraints and action rules in the specification of layouts and behaviors can significantly enhance the productivity of the development of graphics. We demonstrate through several examples the effectiveness of the library as a tool for developing graphics‐rich and interactive user interfaces. Copyright © 2003 John Wiley & Sons, Ltd.
Managing business lifecycle using ebIOP
Authors: Tambag Y. , Cosar A.
Published: October 2003

In this paper, we describe how ebIOP (an ebXML compliant B2B interoperability platform) manages the business lifecycle by providing an example scenario. ebIOP provides a common storage for ebIOP components (ebXML applications). ebIOP defines an ebIOP component to be a software implementation of one or more ebXML specifications which is a solution of an e‐commerce pattern (description of an e‐commerce problem). ebIOP contains a server that listens to a port over the TCP/IP protocol for client requests and provides one or more ebIOP components to interact with the partners of the company.

We show how ebIOP could be used to handle the business lifecycle with application of the ebIOP to the RosettaNet partner interface processes (PIPs). In the example, a part of the RosettaNet PIPs are registered to an ebXML registry using the ebIOP Registry Client Component, parties that support RosettaNet PIPs register/update their profiles in the ebXML registry. A party prepares an ebXML business process by combining some of the RosettaNet PIPs in a logical order and searches for possible trading partners using the ebIOP Registry Client Component. After locating the trading partners, all partners prepare agreements among themselves and they execute the business process using the ebIOP B2BServer Component. Copyright © 2003 John Wiley & Sons, Ltd.
A fast and compact elimination method of empty elements from a double‐array structure
Authors: Oono Masaki , Atlam El‐Sayed , Fuketa Masao , Morita Kazuhiro , Aoe Jun‐ichi
Published: October 2003

A double‐array is a well‐known data structure to implement the trie. However, the space efficiency of the double‐array degrades with the number of key deletions because the double‐array keeps empty elements produced by the key deletion. This paper presents a fast and compact elimination method of empty elements using properties of the trie nodes that have no siblings. The present elimination method is implemented by C language. From simulation results for large sets of keys, the present elimination method is about 30–330 times faster than the conventional elimination method and maintains high space efficiency. Copyright © 2003 John Wiley & Sons, Ltd.
Untangling the balancing and searching of balanced binary search trees
Authors: Austern Matthew H. , Stroustrup Bjarne , Thorup Mikkel , Wilkinson John
Published: October 2003

A balanced binary search tree can be characterized by two orthogonal issues: its search strategy and its balancing strategy. In this paper, we show how to decouple search and balancing strategies so that they can be expressed independently of each other, communicating only by basic operations such as rotations. Different balancing strategies, such as red–black trees and splay trees, and different search applications, such as key search and rank search, can be combined arbitrarily. As a new result, we show how optimal string search can be expressed as a search application on any balanced binary tree.

We implement our framework in C++, with the heavy use of templates and inlining. It keeps balancing and searching separate, while still delivering a performance that compares favorably to widely used binary tree implementations. Common services, such as correctness checks and timing measurements, do not have to be rewritten for each tree implementation. The common framework simplifies experimentation with trees and search algorithms; as a demonstration, we present some simple comparisons of red–black trees, splay trees and treaps. Copyright © 2003 John Wiley & Sons, Ltd.
Repeated exposure to amphetamine disrupts dopaminergic modulation of excitatory synaptic plasticity and neurotransmission in nucleus accumbens
Authors: Li Yong , Kauer Julie A.
Published: October 2003

The mesolimbic dopamine system is essential for reward‐seeking behavior, and drugs of abuse perturb the normal functioning of this pathway. The nucleus accumbens (NAc) is a major terminal field of the mesolimbic dopamine neurons and modifications in neuronal structure and function in NAc accompany repeated exposure to psychomotor stimulants and other addictive drugs. Glutamatergic afferents to the NAc are thought to be crucial to the development of several aspects of addictive behavior, including behavioral sensitization and relapse to cocaine self‐administration. Here we examine glutamatergic neurotransmission and synaptic plasticity in NAc neurons in vitro before and after repeated amphetamine treatment in vivo. We find that dopamine attenuates the response of NAc neurons to repetitive activation of glutamatergic afferents and thereby blocks long‐term potentiation (LTP) induced by high‐frequency afferent stimulation. Dopamine's effects are mimicked by dopamine receptor agonists and by amphetamine. In a second set of experiments, animals were treated with amphetamine daily for 6 days and brain slices were prepared after 8–10 days of withdrawal. In these slices, LTP in the NAc appears normal. However, acute exposure of such slices to amphetamine no longer modulates synaptic transmission or LTP induction. Thus, repeated exposure to amphetamine produces long‐lasting changes in the modulation of glutamatergic synaptic transmission by amphetamine in the NAc. Our results support the notion that after psychostimulant exposure, excitatory synapses on NAc neurons alter their response to further psychostimulant for long periods of time. Synapse 51:1–10, 2004. © 2003 Wiley‐Liss, Inc.
Functional analysis of MOR‐1 splice variants of the mouse mu opioid receptor gene Oprm
Authors: Bolan Elizabeth A. , Pan Ying‐Xian , Pasternak Gavril W.
Published: October 2003

A series of mu opioid receptor gene Oprm splice variants have been reported that differ only at their C‐terminus. These variants all contain exons 1, 2, and 3 of the gene, the exons responsible for coding all seven transmembrane domains. Whereas MOR‐1 also has exon 4 that encodes for an additional 12 amino acids at the tip of the C‐terminus, the other MOR‐1 variants have unique amino acid sequences distinct from those in MOR‐1 due to alternative splicing. All these variants are mu‐selective in binding assays. The current study explored the ability of these variants to stimulate [35S]GTPγS binding to assess them functionally. Only mu opioids stimulated [35S]GTPγS binding. Among the mu opioids we noted marked differences in their maximal stimulation among the clones. This was most prominent with β‐endorphin, which stimulated [35S]GTPγS binding in the MOR‐1E expressing cells to a greater degree than [D‐Ala2,MePhe4,Gly(ol)5]enkephalin (DAMGO; 130%) and was far less effective than DAMGO in MOR‐1C cells (44%). The rank order of maximal stimulation of the drugs varied among the clones as well. Dynorphin A, β‐endorphin and morphine were most effective in stimulating [35S]GTPγS binding in MOR‐1E, while M6G and fentanyl were most effective in MOR‐1 expressing cells. The potency (EC50) of some of the drugs also varied extensively among the clones, with a poor correlation between the potency of the drugs to stimulate [35S]GTPγS binding and their binding affinity. Together, these findings reveal marked functional differences among the variants that only can be explained by their structural differences at the tip of their C‐terminus. Synapse 51:11–18, 2004. © 2003 Wiley‐Liss, Inc.