bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hidden order in the GroEL‐GroES‐(ADP)7 chaperonin: Forms, folding, and ADP‐binding sites
Authors: Janner A. 
Published: February 2003

AbstractA molecular crystallography approach reveals the existence of a hidden order in GroEL‐GroES‐(ADP)7. The new crystallographic symmetry concepts required are first illustrated for a hypothetical planar molecule. Their application to the chaperonin complex leads to molecular forms with vertices having integral coordinates (the indices) with respect to a symmetry‐adapted basis and to folding points approximated by ideal Cα positions with rational indices connected by integral scale‐rotations, just as for the vertices of the molecular forms. The Mg+2‐ions at nucleotide binding sites are symmetry‐related in a similar way to Cα's folding points. Proteins 2003;51:126–136. © 2003 Wiley‐Liss, Inc.
Efficient identification of side‐chain patterns using a multidimensional index tree
Authors: Hamelryck Thomas 
Published: February 2003

AbstractConvergent evolution often produces similar functional sites in nonhomologous proteins. The identification of these sites can make it possible to infer function from structure, to pinpoint the location of a functional site, to identify enzymes with similar enzymatic mechanisms, or to discover putative functional sites. In this article, a novel method is presented that (a) queries a database of protein structures for the occurrence of a given side chain pattern and (b) identifies interesting side‐chain patterns in a given structure. For efficiency and to make a robust statistical evaluation of the significance of a similarity possible, patterns of three residues (or triads) are considered. Each triad is encoded as a high‐dimensional vector and stored in an SR (Sphere/Rectangle) tree, an efficient multidimensional index tree. Identifying similar triads can then be reformulated as identifying neighboring vectors. The method deals with many features that otherwise complicate the identification of meaningful patterns: shifted backbone positions, conservative substitutions, various atom label ambiguities and mirror imaged geometries. The combined treatment of these features leads to the identification of previously unidentified patterns. In particular, the identification of mirror imaged side‐chain patterns is unique to the here‐described method. Interesting triads in a given structure can be identified by extracting all triads and comparing them with a database of triads involved in ligand binding. The approach was tested by an all‐against‐all comparison of unique representatives of all SCOP superfamilies. New findings include mirror imaged metal binding and active sites, and a putative active site in bacterial luciferase. Proteins 2003;51:96–108. © 2003 Wiley‐Liss, Inc.
Prediction of folding rates and transition‐state placement from native‐state geometry
Authors: Micheletti Cristian 
Published: February 2003

AbstractA variety of experimental and theoretical studies have established that the folding process of monomeric proteins is strongly influenced by the topology of the native state. In particular, folding times have been shown to correlate well with the contact order, a measure of contact locality. Our investigation focuses on identifying additional topologic properties that correlate with experimentally measurable quantities, such as folding rates and transition‐state placement, for both two‐ and three‐state folders. The validation against data from 40 experiments shows that a particular topological property that measures the interdependence of contacts, termed cliquishness or clustering coefficient, can account with statistically significant accuracy both for the transition state placement and especially for folding rates. The observed correlations can be further improved by optimally combining the distinct topological information captured by cliquishness and contact order. Proteins 2003;51:74–84. © 2003 Wiley‐Liss, Inc.
Characterization of the electrophile binding site and substrate binding mode of the 26‐kDa glutathione S‐transferase from Schistosoma japonicum
Authors: Cardoso Rosa M.F. , Daniels Douglas S. , Bruns Christopher M. , Tainer John A. 
Published: February 2003

AbstractThe 26‐kDa glutathione S‐transferase from Schistosoma japonicum (Sj26GST), a helminth worm that causes schistosomiasis, catalyzes the conjugation of glutathione with toxic secondary products of membrane lipid peroxidation. Crystal structures of Sj26GST in complex with glutathione sulfonate (Sj26GSTSLF), S‐hexyl glutathione (Sj26GSTHEX), and S‐2‐iodobenzyl glutathione (Sj26GSTIBZ) allow characterization of the electrophile binding site (H site) of Sj26GST. The S‐hexyl and S‐2‐iodobenzyl moieties of these product analogs bind in a pocket defined by side‐chains from the β1‐α1 loop (Tyr7, Trp8, Ile10, Gly12, Leu13), helix α4 (Arg103, Tyr104, Ser107, Tyr111), and the C‐terminal coil (Gln204, Gly205, Trp206, Gln207). Changes in the Ser107 and Gln204 dihedral angles make the H site more hydrophobic in the Sj26GSTHEX complex relative to the ligand‐free structure. These structures, together with docking studies, indicate a possible binding mode of Sj26GST to its physiologic substrates 4‐hydroxynon‐2‐enal (4HNE), trans‐non‐2‐enal (NE), and ethacrynic acid (EA). In this binding mode, hydrogen bonds of Tyr111 and Gln207 to the carbonyl oxygen atoms of 4HNE, NE, and EA could orient the substrates and enhance their electrophilicity to promote conjugation with glutathione. Proteins 2003;51:137–146. © 2003 Wiley‐Liss, Inc.
Influence of Nd3+ concentration on its optical absorption and luminescence properties in potassium borate glass
Authors: Ratnakaram Y. C. , Abdul Altaf Md. , Chakradhar R. P. S. , Rao J. L. , Ramakrishna J. 
Published: February 2003

AbstractSpectroscopic and laser properties of Nd3+ doped potassium borate glass have been studied for different Nd3+ concentrations ranging from 0.5 to 2.0 mol%. From the absorption spectra, optical band gaps (Eopt) and various spectroscopic parameters (E1, E2, E3, ξ4f and α) are determined. Using Judd‐Ofelt intensity parameters Ω2, Ω4 and Ω6, radiative lifetimes (τR), branching ratios (β) and integrated absorption cross sections (Σ) have been calculated for certain excited states of Nd3+ for all the Nd3+ concentrations. From the spectral profiles of the hypersensitive transition, it is observed that there is slight change in the environment of Nd3+ ion in different concentrations of Nd3+ doped potassium borate glass. The radiative lifetimes (τR) for certain excited levels are minimum when the concentration is high. From the emission spectra, peak wavelengths (λp), effective line widths (Δλeff) and stimulated emission cross‐sections (σp) have been obtained for the three transitions 4F3/2 → 4I9/2, 4F3/2 → 4I11/2 and 4F3/2 → 4I13/2 of Nd3+ and are compared for different concentrations.
Structural properties and ionic conductivities of CuCr1–xVxS2 solid solutions
Authors: Almukhametov R. F. , Yakshibayev R. A. , Gabitov E. V. , Abdullin A. R. , Kutusheva R. M. 
Published: February 2003

AbstractIn the Cu(1 – x)CrxVS system CuCr1–xVxS2 solid solutions isostructural with CuCrS2 and Cu3VS4 were found by replacement of Cr by V up to x = 0.20. The oxidation states of Cr and V were determined from structural data and paramagnetic susceptibility measurements. The CuCr1–xVxS2 solid solutions were found to have mixed electronic and Cu+‐cationic conductivity. Copper cationic conductivity increases with increasing unit cell size.
Quantum and thermodynamic properties of proton transfer in hydrogen‐bonded systems
Authors: Xiao‐Feng Pang 
Published: February 2003

AbstractThe quantum and thermodynamic properties of proton transfer along hydrogen‐bonded molecular systems have been studied by our model at zero temperature and finite temperature, respectively. The dynamic equations of the proton transfer along the molecular chains have been obtained using the quantum‐mechanical method. Some quantum features of the proton–soliton are given. We also give the specific heats, resulting from the motion of the solitons in the systems with finite temperature, and find the critical temperature of the soliton in the protein molecules by quantum mechanics. The critical temperatures are in the region of 310.73–328.51 K for different helix‐type protein molecules with three channels. This shows that the solitons in these biopolymers are stable at biological temperatures.
F centers in LiF: A nuclear magnetic resonance study
Authors: Klempt T. , Kanert O. , Suter D. 
Published: February 2003

AbstractIonizing radiation like γ‐rays, electrons, or swift heavy ions create a variety of point defects in dielectric materials. The largest fraction of the defects consists of the paramagnetic F centers. Here, we study those F centers in LiF by nuclear magnetic resonance. Nuclear spin relaxation (T1) measurements serve as a probe for the F centers offering the possibility to investigate their dynamics as a function of temperature and irradiation dose. Moreover, one is able to estimate the content of the paramagnetic defects from the T1‐data over a wide range of concentration. We further observed and analyzed radiation annealing occurring at temperatures above 360 K.
Alloy‐disorder‐scattering‐limited mobility of electrons in cylindrical quantum well wires
Authors: Ibragimov G. B. 
Published: February 2003

AbstractWe study the effect of the alloy‐disorder‐scattering on the electron transport in a quasi‐one‐dimensional semiconductor. Analytical calculations of the alloy‐disorder‐limited momentum relaxation time for carrier scattering in a cylindrical quantum wire using an infinite well model. The transverse part of the carrier wave function is taken to be a Bessel function. It is found that the one‐dimensional mobility is significantly greater than two‐dimensional mobility. It is shown that the alloy‐disorder‐scattering‐limited mobility increases with increasing wire radius and increases with increasing temperature. We compare our results with different scattering mechanisms for one‐dimensional systems. Results are also included for the alloy composition dependence of the mobility.
Diffusion, surface alloy formation, and spin alignment in Fe/Cr(001) systems and superlattices
Authors: Kellou A. , Aourag H. 
Published: February 2003

AbstractWe present first principle calculations, based on the generalized gradient approximation (GGA), of Fe/Cr(001) layered structures and superlattices. The energetics of ferromagnetic overlayer (Fe) deposition on antiferromagnetic substrate (Cr(001)) is investigated. We have found that Cr layers prefer antiferromagnetic (af) coupling in Cr(001) thin films. The same coupling is found between Fe and Cr layers in Fe/Cr (001) systems. The last Fe and Cr layers are more or less af coupled in Fen/Crn(001) superlattices. The deposition of Fe overlayer on Cr(001) favors bilayer rather than monolayer formation, which leads to an ordered surface alloy formation. More detailed investigations have confirmed that surface alloy formation is possible for Fe50Cr50/3Cr(001), in agreement with ultra‐high vacuum scanning tunneling microscope observations, which confirm that Fe atoms incorporate into the Cr surface, forming a well‐ordered surface alloy of Fe50Cr50.
Correlation between the structural and antiferromagnetic phase transitions in ZnCr2Se4
Authors: Hidaka M. , Tokiwa N. , Fujii M. , Watanabe S. , Akimitsu J. 
Published: February 2003

AbstractStructural properties of normal‐type spinel ZnCr2Se4 have been studied as a function of temperature by means of neutron diffraction. It is found that the structural phase transition (TC) from a cubic to orthorhombic symmetry simultaneously occurs at the antiferromagnetic phase transition temperature (TN ∼ 21 K), where the cubic and orthorhombic symmetry is 7Oh‐Fd3m and 24D2h‐Fddd, respectively. The structural phase transition is mainly characterized by the cooperative displacements of Se2– ions, which are induced by a magnetostriction resulting from the magnetic interaction of Cr3+ ions in CrSe4 chains along [110]. The antiferromagnetic magnetic structure below TN is made by a spiral magnetic coupling between the ferromagnetic CrSe4 chains around crystallographic screw axes, which are parallel to an orthorhombic C axis. The spiral long‐range order of the spins of Cr3+ is incommensurate and its periodicity of q along a reciprocal lattice axis C* shows temperature dependence from about 0.47 (2.5 K) to 0.43 (18 K). The spiral periodicity of the spin order along the C axis shows a first order transition at about 21 K.
14N NMR study of the domain structure of tetramethylammonium cadmium chloride (TMCC)
Authors: Mulla‐Osman S. , Michel D. , Czapla Z. 
Published: February 2003

AbstractQuadrupolar perturbed 14N NMR investigations are performed on single crystals of tetramethylammonium cadmium chloride, (CH3)4NCdCl3 (TMCC), in the temperature range of 297 to 80 K. At the phase transitions at 118 and 104 K the quadrupole coupling tensor (QCT) shows abrupt changes in accordance with their first order type. The largest QCT component is parallel to the hexagonal c‐axis in the high temperature phase and rotates by 90° at the transition into the monoclinic phase II at 118 K. In complete agreement with a recent 35Cl NMR study, the 14N spectra in phase II show clearly a ferro‐elastic twin domain structure. The saturated rotational angle between the epitaxially grown domains of Exp ≈ 4 is in a good agreement with the theoretical value of S = 3.55 calculated from the ferro‐elastic strain tensor. The ordering behaviour below the phase transition at 118 K is related with the rotation of the largest component VZZ of the QCT in a plane perpendicular to the c‐axis and with changes of its principal axes values. The component VZZ is parallel to the N bond direction. A shift of the N atoms within the plane in relation with the phase transition was also found in recent low temperature X‐ray diffraction measurements. In the whole temperature range investigated, the 14N NMR spectra are exclusively determined by the lattice symmetry but not by distortions of the local tetrahedral symmetry at the N sites of the tetramethylammonium groups.
Band offset of quantum wells computed from charge measurements
Authors: Biswas Dipankar , Chakrabarti Satyajit , Dasgupta Sudipto , Kundu Sudakshina , Datta Resmi 
Published: February 2003

AbstractBand discontinuity is an important parameter for the design of heterojunction based electronic and opto electronic devices. An alternative method for band offset measurement in quantum wells has been outlined in this paper. The band offset is determined from a comparison of experimental results and theoretical computations of the temperature dependent total charge content of a quantum well. In spite of the simplicity of the measurement procedures the result at its best has an error around ±2%.
Charge carrier diffusion in energy landscape created by static charges: Poole–Frenkel model revised
Authors: Novikov S. V. 
Published: February 2003

AbstractEffect of static charges on charge carrier transport in disordered organic materials is considered. We show that the mobility dependence on temperature and concentration of charged traps differs drastically from the prediction of the model of isolated charged trap (Poole–Frenkel model), yet, by accident, the mobility field dependence remains the same with the logarithm of the mobility being proportional to the square root of the electric field. The ultimate reason for the difference is a long range nature of the Coulomb interaction of a carrier with charged traps. This interaction produces huge fluctuations of carrier energy in the medium overcoming carrier interaction with the isolated static charge. A possibility to observe this quasi‐Poole–Frenkel transport regime in experiments is discussed. We argue that the model of isolated charged trap may be applied only to the case of charge transport in extremely thin transport layers.
Theoretical analysis of d electron effects on the electronic properties of wurtzite and zincblende GaN
Authors: Bouhafs B. , Litimein F. , Dridi Z. , Ruterana P. 
Published: February 2003

AbstractWe investigate the electronic properties of the technologically important wide‐band‐gap semiconductor GaN employing ‘state‐of‐the‐art’ DFT‐LDA calculations using a FP‐LAPW code. The Ga 3d electrons are treated both as core or as valence electrons and the wurtzite as well as the zincblende modifications of GaN are investigated. In particular, we address the influence of the lattice configuration and of the d electrons to the electronic structure of w‐GaN and c‐GaN. Band structures, densities of states, orbital‐resolved densities of states, total and partial valence charge densities, and ionicity factors are analysed in great detail. The calculated values of the energy gaps, bandwidths, spin–orbit, crystal‐field splittings, and the correct band degeneracies are compared to experimental and/or ab initio results. Several features of w‐GaN resemble those of c‐GaN. Most of the calculated band parameters, of band gaps, total and upper‐valence bandwidths, and antisymmetric gap for w‐GaN are close to those of c‐GaN within 1%. The charge distributions have similar features meaning that this material has the same ionicity factor with or without Ga 3d hybridization in both structures. By examining the pressure dependence of the energy band gaps, the value of the hydrostatic deformation potential of the band gap has also been calculated.
Superfluid fraction of a charged boson fluid at non‐integer dimensions and superconducting films
Authors: Kim Sang‐Hoon , Koo Kim Chul , Nahm Kyun 
Published: February 2003

AbstractThe superfluid fraction of a charged boson fluid at non‐integer dimensions between 2 and 3 is studied. Interaction between particles is assumed to be Coulombic, and Bogoliubov approximation is applied for a weak coupling regime. The theoretical results are compared with the superfluid densities of superconducting films, showing an universal splitting behavior. The qualitative similarity between the charged boson fluid and the superconducting films gives a strong clue for the origin of the universality observed in the superconducting films.
Effective nonlinear response in random mixture of coated granular cylinders
Authors: Gao Lei 
Published: February 2003

AbstractEffective dielectric response of granular composites consisting of coated cylindrical inclusions embedded in a host medium is investigated in both the dilute and nondilute cases. We assume that the shell and the host are linear with the dielectric function ϵs0 and ϵh0, while the core has the field‐dependent dielectric function ϵc = ϵc0 + χc|Ec|β, where ϵc0 and χc are the linear dielectric function and nonlinear susceptibility, respectively. General expressions for the effective linear dielectric function and third‐order nonlinear susceptibility of the three‐phase system are analytically obtained with perturbative expansion method. The partially resonant circumstances, in which the dielectric response of the components satisfies ϵs0 + ϵh0 or ϵs0 + ϵc0 = 0, and the conductance case in which the coated inclusions possess superconducting shells (ϵs0 → ∞) of zero thickness (t → 0), are examined in detail. We show that under the partially resonant conditions the coated cylindrical inclusions are equivalent to solid cylinders with larger nonlinear susceptibility and volume fractions than these of original cylindrical cores, and thus the effective nonlinear susceptibility χe of the composite system may be greatly enhanced. For the conductance case, we find that the coated cylinders behave as solid cylinders with a larger linear dielectric function than ϵc0.
Specific heat capacity of AuTe2I below 100 K
Authors: Gmelin Eberhard 
Published: February 2003

AbstractThe heat capacity of AuTe2I was measured in the temperature range of 0.7 K < T < 100 K. The resulting low temperature limiting Debye temperature and electronic contribution were determined to be θ0 = (140 ± 1.5) K and γ = (1.54 ± 0.04) mJ/mol K2, respectively, the latter in reasonable agreement with earlier results from Hall effect and Shubnikov de Haas experiments.
Polaronic exciton in a parabolic quantum dot
Authors: Senger R. T. , Bajaj K. K. 
Published: February 2003

AbstractA calculation of the variations of the energy and oscillator strength of the ground state of an exciton in an ionic quantum dot as a function of the dot size, using a parabolic confining potential and a variational approach, is presented. The strong exciton–phonon interaction is taken into account by using an effective potential between the electron and the hole as derived by Pollmann and Büttner. The values of the exciton binding energies calculated using this potential are compared with those obtained using statically screened Coulomb potential and are found to be considerably larger for all values of the quantum dot size. In small quantum dots, the electron–hole correlation is reduced as the single particle energies scale at a much faster rate than the interaction energy. This is manifested in the behavior of oscillator strength, which becomes less dependent on the form of the effective interaction as the quantum dot size is reduced.
Epitaxial formation of a multilayer Pd–Ta surface alloy on a Ta substrate
Authors: Szczepkowicz A. , Ciszewski A. 
Published: February 2003

AbstractA thick palladium layer (∼5 nm) is deposited onto a curved tantalum surface. The system is submitted to several annealing cycles. Structural changes within 0–5 nm below the surface are observed using Field Ion Microscopy. At 800 K, an atomic intermixing of adsorbate and substrate is observed. Pd atoms are detected within the first five atomic layers of the Ta substrate. At 1100 K, a multilayer alloy is formed at the surface, oriented epitaxially with respect to the Ta{100} planes.
Simultaneous measurements of crystal optical characteristics of deuterated triglycine sulphate
Authors: Kushnir O. S. 
Published: February 2003

AbstractThe birefringence, rotation angle of the optical indicatrix and the gyration along the polar direction are studied in the paraelectric and ferroelectric phases of deuterated triglycine sulphate crystals using the HAUP‐type universal null‐polarimetric technique. The gyration effect in the multidomain ferroelectric phase is found to be negligibly small, in accordance with the symmetry considerations, while the changes in the birefringence and the indicatrix rotation occurring in the course of the phase transition may be described by electrooptical coupling due to the quadratic spontaneous effect.
Structural modulation of spinel ZnCr2Se4 in the vicinity of antiferromagnetic phase transition induced by an applied magnetic field
Authors: Hidaka M. , Yoshimura M. , Takahasi S. , Watanabe S. , Akimitsu J. 
Published: February 2003

AbstractMagnetic and structural phase transitions of normal‐type spinel ZnCr2Se4 have been studied as functions of applied magnetic field and temperature by means of neutron diffraction. It is found that the spiral spin order of Cr3+ ions is largely affected by the magnetic field, and the satellite‐like magnetic reflections are largely decreased in the magnetic field of 0.6 T < H < 1.2 T and disappear at H ≥ 1.2 T, when the magnetic field was applied vertically to an orthorhombic axis [001]. This means that the spiral configuration of the ferromagnetic CrSe4 chains is perfectly disordered around two‐fold screw axes in an orthorhombic symmetry phase (Fddd structure) by the magnetic field H ≥ 1.2 T, though the structural phase transition (TC) between cubic and orthorhombic symmetry phases simultaneously occurs at the antiferromagnetic phase transition temperature (TN ≈︂ 21 K) in no magnetic field. It is also found that the main reflections show a magnetic field dependence similar to that of the magnetic reflections. Pseudo‐tetragonal displacements of Se ions below TN are modulated by the applied magnetic field. The 3 T magnetic field induces a metastable structural transition at about 15 K, after initially cooling down to about 2 K in no applied magnetic field. The transition is related to the modulation from pseudo‐tetragonal to pseudo‐cubic displacements of Se ions.