bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ideal amino acid exchange forms for approximating substitution matrices
Authors: Pokarowski Piotr , Kloczkowski Andrzej , Nowakowski Szymon , Pokarowska Maria , Jernigan Robert L. , Kolinski Andrzej 
Published: July 2007

AbstractWe have analyzed 29 published substitution matrices (SMs) and five statistical protein contact potentials (CPs) for comparison. We find that popular, ‘classical’ SMs obtained mainly from sequence alignments of globular proteins are mostly correlated by at least a value of 0.9. The BLOSUM62 is the central element of this group. A second group includes SMs derived from alignments of remote homologs or transmembrane proteins. These matrices correlate better with classical SMs (0.8) than among themselves (0.7). A third group consists of intermediate links between SMs and CPs ‐ matrices and potentials that exhibit mutual correlations of at least 0.8. Next, we show that SMs can be approximated with a correlation of 0.9 by expressions c0 + xixj + yiyj + zizj, 1≤ i, j ≤ 20, where c0 is a constant and the vectors (xi), (yi), (zi) correlate highly with hydrophobicity, molecular volume and coil preferences of amino acids, respectively. The present paper is the continuation of our work (Pokarowski et al., Proteins 2005;59:49–57), where similar approximation were used to derive ideal amino acid interaction forms from CPs. Both approximations allow us to understand general trends in amino acid similarity and can help improve multiple sequence alignments using the fast Fourier transform (MAFFT), fast threading or another methods based on alignments of physicochemical profiles of protein sequences. The use of this approximation in sequence alignments instead of a classical SM yields results that differ by less than 5%. Intermediate links between SMs and CPs, new formulas for approximating these matrices, and the highly significant dependence of classical SMs on coil preferences are new findings. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Analysis of zinc‐ligand bond lengths in metalloproteins: Trends and patterns
Authors: Tamames Bruno , Sousa Sérgio Filipe , Tamames Juan , Fernandes Pedro Alexandrino , Ramos Maria João 
Published: July 2007

AbstractZinc is one of the biologically most abundant and important metal elements, present in a plethora of enzymes from a broad array of species of all phyla. In this study we report a thorough analysis of the geometrical properties of Zinc coordination spheres performed on a dataset of 994 high quality protein crystal structures from the Protein Data Bank, and complemented with Quantum mechanical calculations at the DFT level of theory (B3LYP/SDD) on mononuclear model systems. The results allowed us to draw interesting conclusions on the structural characteristics of Zn centres and to evaluate the importance of such effects as the resolution of X‐ray crystallographic structures, the enzyme class in which the Zn centre is included, and the identity of the ligands at the Zn coordination sphere. Altogether, the set of results obtained provides useful data for the enhancement of the atomic models normally applied to the theoretical and computational study of zinc enzymes at the quantum mechanical level (in particular enzymatic mechanisms), and for the development of molecular mechanical parameters for the treatment of zinc coordination spheres with molecular mechanics or molecular dynamics in studies with the full enzyme. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Structure of Xanthomonas axonopodis pv. citri YaeQ reveals a new compact protein fold built around a variation of the PD‐(D/E)XK nuclease motif
Authors: Guzzo Cristiane R. , Nagem Ronaldo A. P. , Barbosa João A. R. G. , Farah Chuck S. 
Published: July 2007

AbstractThe YaeQ family of proteins are found in many Gram‐negative and a few Gram‐positive bacteria. We have determined the first structure of a member of the YaeQ family by X‐ray crystallography. Comparisons with other structures indicate that YaeQ represents a new compact protein fold built around a variation of the PD‐(D/E)XK nuclease motif found in type II endonucleases and enzymes involved in DNA replication, repair, and recombination. We show that catalytically important residues in the PD‐(D/E)XK nuclease superfamily are spatially conserved in YaeQ and other highly conserved YaeQ residues may be poised to interact with nucleic acid structures. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Locating Jews by ethnicity: a reply to D. Voas (2007), ‘Estimating the Jewish Undercount in the 2001 Census: A Comment on Graham and Waterman (2005) “Underenumeration of the Jewish Population in the UK 2001 Census”’
Authors: Graham David J. , Waterman Stanley 
Published: July 2007

AbstractThe inclusion of identity questions in censuses opens up new and complex horizons for quantitative analysis. In this Reply we examine these difficulties, especially those associated with the enumeration and interpretation of such data. We present Census data to illustrate these problems and which support the claim that many Jews in Britain identify not only by religion but also, or instead, by ethnicity. Copyright © 2007 John Wiley & Sons, Ltd.
On the Capture of Gas Dissolved in a Solid by a Moving Gas Bubble
Authors: Mikhlin E. Ya. , Semionov L. P. 
Published: July 2007

AbstractA solution is found of the equation describing the entering of gas atoms dissolved in a solid into a moving gas bubble. Its behaviour enables one to confirm the recent analysis [1] of conditions under which the gas entering a moving bubble will be essentially different from that of an unmoved one.
Investigations into Ripple Wavelength in Evaporated Thin Films by Lorentz Microscopy
Authors: Suzuki T. 
Published: July 2007

AbstractA systematic experimental study of ripple wavelength by Lorentz microscopy in NiFe alloy films was carried out. The following should be noted: 1. The only possible way to determine experimentally a meaningful wavelength is to evaluate visually well‐defined ripple high‐contrast lines on a photomicrograph. 2. The average wavelength determined in this way is of the order of 1 μm. This value is in reasonable agreement with the main wavelength predicted by the theories developed by others. However, the predicted slight dependence of this observed wavelength on substrate deposition temperature and alloy composition was not observed. On the other hand, the strong dependence of the measured wavelength on the external magnetic fields is in good agreement with that predicted theoretically.
Faraday Ellipticity of Hot Electrons in Many‐Valley Semiconductors
Authors: Gupta B. M. 
Published: July 2007

AbstractThe Faraday ellipticity of hot electrons is investigated in the infrared region for the case of many‐valley semiconductors. It is shown that the anisotropy in ellipticity is independent of the magnitude and direction of the external magnetic field in the linear approximation. The increase in the magnitude of anisotropy of the ellipticity with the heating field is presented by graphs for various directions of the heating field. The anisotropy of the Faraday rotation with the magnitude and direction of the heating field is discussed.
Transverse Magnetoresistance in Plastically Deformed n‐Type Germanium
Authors: Balázs J. , Pödör B. 
Published: July 2007

AbstractThe transverse magnetoresistance in plastically bent n‐type Ge has been measured at 77 °K. In the bent samples the magnetoresistance coefficients were strongly increased and at the same time the mobility was reduced. This effect is caused by the scattering of electrons on dislocations. A theoretical model is presented for evaluating the magneto‐resistance coefficients, taking into account anisotropic scattering caused by the dislocations, and the conduction band structure of Ge. The theoretical results agree well with the experimental ones.
Extrinsic Photoconductivity of Fast‐Electron‐Irradiated Undoped CdS Single Crystals
Authors: Wruck D. 
Published: July 2007

AbstractThe extrinsic photoconductivity of undoped platelet‐type CdS crystals irradiated with 280 keV electrons was investigated at liquid nitrogen and room temperatures in the photon energy range 0.1 to 2.5 eV, using polarized light in the range 0.6 to 2.5 eV. A sensitive ac method was used, superimposing a chopped measuring beam on a constant bias illumination level. At least six photoconductivity bands were found. The bands in the range 0.6 to 2.5 eV are weakly polarized, the higher intensity occurring for E ⟂ c. The fine structure of the low‐energy quenching band previously observed by Hemila and Bube [28] was reproduced but was found to be caused by atmospheric absorption bands. Most of the bands in the photoconductivity spectrum correspond to absorption bands found by Boyn [8] in thick crystals. — The present results, assuming the threshold energies for atomic displacement in CdS determined by Kulp and Kelley [2, 3] to be valid, together with the results of trap analysis made also in this work, absorption measurements [8], and our earlier investigations of the trap spectrum, electron lifetime, and dark conductivity of deuteron‐bombarded CdS crystals [27] suggest an assignment of the photoconductivity bands to intrinsic lattice defects and to donor‐acceptor associates involving intrinsic defects and residual impurities.
Magnetic Hyperfine and Quadrupole Interactions of F‐Centres in NaCl as Measured by ENDOR
Authors: Deigen M. F. , Zevin V. Ya. , Ischenko S. S. , Baran N. P. , Ruban M. A. , Teslenko V. V. 
Published: July 2007

AbstractThe hyperfine and quadrupole interactions of F‐centres in NaCl were investigated by the ENDOR method. The constants of hyperfine interactions with nuclei of coordination shells I to X surrounding the vacancy have been determined. The quadrupole interaction with nuclei of shells II, IV, VI, and VIII has been recorded and measured. General expressions for ENDOR frequencies are given in single‐particle approximation, allowance being made for the deviation of the nuclear spin quantization axis from the direction of the constant magnetic field H0 and for corrections due to second order perturbation theory. The angular dependence of ENDOR spectra has been investigated in detail and fully explained on the basis of theoretical formulae. The constants were determined at T = 20, 77, and 300 °K.
Low Temperature Reversal in Anisotropic Ferromagnetic Films
Authors: Bostanjoglo O. 
Published: July 2007

AbstractThe magnetic reversal of anisotropic iron and 83% Ni—17% Fe films was studied by Lorentz microscopy at 4 to 300 °K. Below 15 °K for permalloy and 30 °K for iron the usual Barkhausen jumps vanish. In permalloy now wall motion at constant field consisting of tiny jumps (≪ 0.5 μm) sets in at a critical field. Below the critical field wall deflections are reversible. In iron the low temperature wall motion consists of short circle Bloch line jumps (≪ 0.1 μm), formation of small bordering domains and their reversal by rotation. These processes take place in constant fields.
High Temperature Resistivity Measurements on Chromium
Authors: Anderson J. M. , Stewart A. D. , Ramsay I. 
Published: July 2007

AbstractThe resistivity of single crystals of chromium has been investigated in the temperature range 300 to 2000 °K. Anomalous behaviour above 1300 °K is reported and this is attributed to an electronic rearrangement taking place which affects the relative positions of the Fermi level and the minimum in the density of states curve for the d‐band.
Contribution to the Theory of the Thermopower of Alkali Metals at Low Temperatures
Authors: Rösler M. 
Published: July 2007

AbstractThe diffusion thermopower is calculated by means of the usual variational method in the simplest approximation. A careful calculation of the variational expressions yields a thermopower formula valid for all temperatures, which enables a qualitative understanding of the measurements also for Li in contrast to previous variational calculations. An approximative evaluation of this thermopower formula at low temperatures for Li, Na, and K shows that, firstly, the diffusion thermopower is in no case linearly dependent on the temperature and, secondly, the diffusion thermopower can also be different in sign.
On the Temperature Dependence of Hole Mobility in Silicon
Authors: Asche M. , Von Borzeskowski J. 
Published: July 2007

AbstractThe influence of the non‐parabolicity of the valence band on the hole mobility in Si is investigated. The numerical and experimental results can be fitted if for the holes the non‐parabolicity of the energy spectrum as well as their scattering on acoustic and optical phonons are taken into account.
Influence of the Non‐Hermitean Splitting Terms on Excitonic Spectra
Authors: Zimmermann R. 
Published: July 2007

AbstractA treatment of the Bethe‐Salpeter equation leads to additional short‐range interaction terms in the effective‐mass equation of the exciton theory. These non‐Hermitean splitting terms decrease the excitation energies and cause the triplet energy to be the first to become zero if the energy gap is reduced.
Surface Scattering of Electrons in Magnetic Surface States
Authors: Mertsching J. , Fischbeck H. J. 
Published: July 2007

AbstractThe scattering rate 1/τ of magnetic surface states due to scattering at a rough surface is calculated in the Born approximation. In the regime of small angle scattering, we obtain 1/τ ∼ B in small magnetic fields B, 1/τ ∼ B4/3 (n + 3/4)1/3 for intermediate field strengths, and 1/τ ∼ B2 in larger fields. The B4/3 (n + 3/4)1/3 law agrees with the quasiclassical theory of surface scattering which holds for magnetic surface states with a large quantum number n in a rather large range of magnetic field strengths. When large angle scattering is predominant, a scattering rate 1/τ ∼ B is obtained throughout.
Influence of Crystal Orientation and Oxide Structure on the Interface States of GeGeO2
Authors: Flietner H. , Oertel G. 
Published: July 2007

AbstractHexagonal, tetragonal, and amorphous oxides were prepared on 111‐, 110‐, and 100‐surfaces of germanium. Interface‐states were determined by the ac‐field effect. The hexagonal oxide shows on the 111‐surface, the tetragonal on the 100‐surface the lowest density of surface states. Amorphous oxide does not show significant differences for the three orientations. This shows clearly, that the matching of the lattices at the interface is of importance for the existence of surface states.
Determination of the Effective Masses of the Electron Jack, Hole Octahedron, and Ellipsoids of Molybdenum by Cyclotron Resonance Measurements
Authors: Herrmann R. , Krüger H. 
Published: July 2007

AbstractThe anisotropic behaviour of the effective masses in the {100} plane in molybdenum was determined by cyclotron resonance measurements. The authors succeeded in measuring resonances from all parts of the Fermi surface — electron jack, hole octahedron, and hole ellipsoids — with effective masses between μ = 3.9 and μ = 0.4. From the cut‐off angles of the different resonances and the behaviour of the corresponding effective masses as a function of the angle between the magnetic field and the [011] axis, conclusions could be drawn as to details of the Fermi surface. The mean velocity on the hole octahedron was estimated. The measurements were made at f = 9.25 GHz and T = 1.6 °K, the vector of the high‐frequency current being parallel to the [011] axis.
On the Dynamical Theory of Hydrogen‐Bonded Ferroelectrics. I. Dampings and Shifts
Authors: Stamenković S. , Novaković L. 
Published: July 2007

AbstractThe frequency shifts and damping constants of the protonic collective motion in hydrogen‐bonded ferroelectrics due to both the proton—proton and proton—lattice interactions are calculated using the method of temperature dependent Green's functions. Some parameters describing the tunnelling frequency of the proton and the above mentioned interactions are reconsidered. The final results are interpreted from the standpoint of the dynamical and kinematical interactions in the boson representation of the fictitious spin as well as of a thermodynamical quasi‐equilibrium approximation.
Strain‐Broadened EPR Lines of 3d5 Ions in Td Symmetry Study of Fe3+ in ZnS
Authors: Parrot R. , Tronche G. 
Published: July 2007

AbstractAn investigation is made of the angular variations of EPR linewidths of 3d5 ions in crystals with Td symmetry where the effect of internal shear stresses is preponderant. Broadening depends on the R tensor describing the Stark effect and on a single parameter related to the fluctuations of the internal electric field. The chosen model applies correctly to the Fe3+ centre in cubic ZnS.
Absorption Spectra of Tellurium in the Spectral Range from 18 to 460 cm−1
Authors: Grosse P. , Richter W. 
Published: July 2007

AbstractThe absorption spectra of undoped monocrystalline tellurium were measured in the spectral range from 18 to 460 cm−1 at 300, 77, and 4 °K. The spectra can be analysed by absorption through 1‐, 2‐, and 3‐phonon sum processes in the spectral range from 90 to 460 cm−1. In the remaining range additional measurements with doped samples at 40 cm−1 show the absorption constant to be proportional to the free carrier concentration.
Investigation of the Electronic Structure of β′‐NiAl by Means of the Photoemission Technique
Authors: Nilsson P. O. 
Published: July 2007

AbstractUV photoemission electron distributions from clean β′‐NiAl surfaces are reported. Two features are observed which can be related to peaks in the density of states 0.8 and 2.1 eV below the Fermi level. The result is in agreement with a recent density of states calculation by Connolly and Johnson [10].
Cation Distribution in Aluminum‐Substituted Yttrium Iron Garnets by Mössbauer Effect Spectroscopy
Authors: Czerlinsky E. R. , Macmillan R. A. 
Published: July 2007

AbstractAs a part of continuing search for magnetic materials with improved properties and broader applicability in microwave devices, recoil‐free nuclear resonance absorption was measured on eleven different compositions of Y3AltFe5−tO12 powder specimens with t ranging from 0.39 to 4. To avoid magnetic line splitting, measurements were made above the Curie temperature. The quadrupole splittings of the Fe57 nuclei in the garnet structure caused two absorption doublets for each composition. From the intensities of the lines, the distribution of Fe3+ and Al3+ on the tetrahedral and octahedral sites with regard to the composition was obtained. Some of the powders had been subjected to an identical and controlled heat treatment to establish their cation equilibrium at the same temperature. With both the cation distribution and the equilibrium temperature defined, the stabilization energy was determined for each compound. This quantity is a measure for the “site preference”, in our particular case of Al3+ in AlYIG materials. The results on the distribution are compared with earlier work on AlYIG, GaYIG, and AlYGaG. The electric field gradients resulting from the position of the doublet lines are compared with other investigations on the same compounds.
Nuclear Magnetic Resonance Study of Hyperfine Fields in Dilute Fe Alloys
Authors: Mendis E. F. , Anderson L. W. 
Published: July 2007

AbstractThe hyperfine field spectra of ten Fe alloy systems have been studied. Nuclear magnetic resonance fast‐passage techniques have been used to obtain direct plots of the distributions of hyperfine fields. The systems studied were FeAl, FeSi, FeV, FeCr, FeMn, FeCo, FeNi, FeGe, FePd, and FeSn. In general, four alloys of each system were studied, with the impurity concentration varying from 10−3 to 1.5 × 10−2. All the experimental hyperfine field distributions include satellite resonances. These satellites are interpreted as arising from different sets of Fe near‐neighbours of an impurity. The intensities and line shapes of the satellites are studied. The results of the study are compared with the results of spin‐echo NMR and Mössbauer effect studies to obtain (for most of the alloys) the hyperfine field shifts at the first five near‐neighbor sites.
Nucleation in Solid Solution Stimulated by Non‐Equilibrium Electrons. I. General Theory
Authors: Stoyanov S. , Kashchiev D. , Geoegiev M. 
Published: July 2007

AbstractA nucleation process proceeding at trapped electron sites in a solid solution of metal atoms within an insulating solid is considered. As a result of the more difficult migration of the condensing atoms, nucleation in a solid may follow a way which differs essentially from the condensation in a Wilson cloud chamber. By means of a properly defined effective supersaturation, expressions for the quasi‐steady state nucleation rate as well as for the total number of nuclei formed within a given time are derived. The analysis indicates that the presence of even a small number of trapped non‐equilibrium electrons may lead to a substantial increase of the nucleation rate. Inasmuch as the occurrence of non‐equilibrium electrons in a solid may be due to various reasons an application of the present theory might be attempted in various cases.
On the Role of Collective Oscillations in the Electron Mechanism of Superconductivity
Authors: Geilikman B. T. 
Published: July 2007

AbstractThe spectrum of collective oscillations for a metal with overlapping — broad and narrow — bands is found. The essential influence of acoustical plasmons on the pairing in the high temperature electronic mechanism of superconductivity for such metals is shown. The conditions for high temperature superconductivity in the case of metal—nonmetal compounds, specifically with organic substances are discussed.
Theory of Cyclotron Resonance of Fröhlich Polarons in High Magnetic Fields
Authors: Evrard R. , Kartheuser E. , Devreese J. 
Published: July 2007

AbstractCyclotron resonance of polarons in ionic crystals is studied by means of a Born‐Oppenheimer type method. The Lee, Low, Pines approximation is made for the electron—phonon interaction and so the translational invariance along the magnetic field direction is exploited. Our approach is therefore valid at weak and intermediate couplings and cyclotron frequencies ωc larger than the L.O. phonon frequency ω, which requires rather intense magnetic fields. For relatively large electron—phonon coupling (α ≧ 4) the results also apply qualitatively for weak magnetic fields. The ground state energy and the energy of two excited levels are obtained. The excited states which are treated here are internal excited states of the polaron system and they are different from the normal Landau levels. The stability of some of these states is enhanced under the action of the magnetic field. This leads us to predict absorption at new cyclotron frequencies in ionic crystals especially relevant for intermediate coupling strengths α ≈ 4.
Zur statistischen Begründung der Kontinuumsphysik
Authors: Kröner E. 
Published: July 2007

AbstractEine strenge Begründung der Kontinuumsphysik bedarf der Grundlagen der Statistik. Dies wird am Beispiel der Elektrostatik gezeigt. Die Betrachtung ergibt, daß zur vollständigen phänomenologischen Beschreibung des Zustands der Materie die Angabe der mittleren Felder nicht genügt, daß vielmehr das Wahrscheinlichkeitsdichte‐Funktional oder — gleichwertig — der unendliche Satz von Korrelationsfunktionen der betreffenden Felder angegeben werden muß, weil man andernfalls nur bei hinreichender Kleinheit der Fluktuationen im Material zu befriedigender Näherung kommt. Dies wird durch eine Rechnung über die Elastizität von regellos aufgebauten Kupfervielkristallen quantitativ belegt. Der Ansatz Spannung = Elastizitätsmodul × Dehnung für das Materialgesetz enthält hier eine grundsätzliche Unsicherheit von 0,6%.