bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative sequence and structure analysis reveal features of cold adaptation of an enzyme in the thermolysin family
Authors: Adekoya Olayiwola A. , Helland Ronny , Willassen Nils‐Peder , Sylte Ingebrigt 
Published: November 2005

AbstractKnowledge about the structural features underlying cold adaptation is important for designing enzymes of different industrial relevance. Vibriolysin from Antarctic bacterium strain 643 (VAB) is at present the only enzyme of the thermolysin family from an organism that thrive in extremely cold climate. In this study comparative sequence‐structure analysis and molecular dynamics (MD) simulations were used to reveal the molecular features of cold adaptation of VAB. Amino acid sequence analysis of 44 thermolysin enzymes showed that VAB compared to the other enzymes has: (1) fewer arginines, (2) a lower Arg/(Lys + Arg) ratio, (3) a lower fraction of large aliphatic side chains, expressed by the (Ile + Leu)/(Ile + Leu + Val) ratio, (4) more methionines, (5) more serines, and (6) more of the thermolabile amino acid asparagine. A model of the catalytic domain of VAB was constructed based on homology with pseudolysin. MD simulations for 3 ns of VAB, pseudolysin, and thermolysin supported the assumption that cold‐adapted enzymes have a more flexible three‐dimensional (3D) structure than their thermophilic and mesophilic counterparts, especially in some loop regions. The structural analysis indicated that VAB has fewer intramolecular cation–π electron interactions and fewer hydrogen bonds than its mesophilic (pseudolysin) and thermophilic (thermolysin) counterparts. Lysine is the dominating cationic amino acids involved in salt bridges in VAB, while arginine is dominating in thermolysin and pseudolysin. VAB has a greater volume of inaccessible cavities than pseudolysin and thermolysin. The electrostatic potentials on the surface of the catalytic domain were also more negative for VAB than for thermolysin and pseudolysin. Thus, the MD simulations, the structural patterns, and the amino acid composition of VAB relative to other enzymes of the thermolysin family suggest that VAB possesses the biophysical properties generally following adaptation to cold climate. Proteins 2006. © 2005 Wiley‐Liss, Inc.
The CDR1 of the human λVI light chains adopts a new canonical structure
Authors: del Pozo Yauner L. , Ortiz E. , Becerril B. 
Published: November 2005

AbstractWe performed a comparative analysis of the conformation of the CDR1 of the human λVI variable domains JTO and WIL and the equivalent loop of the λI light chains RHE and KOL, which are representative of the type I canonical structure for λ light chains. On the basis of the differences found in the main chain conformation, as well as the identity of the residues at key positions, we showed that the L1 of some λVI light chains adopts a conformation that represents a new type of canonical structure. The conformation of the L1 of those λVI light chains, is primarily determined by the presence of an Arg residue at position 25. The analysis of the λVI light chain sequences so far reported, showed that near 25% of those proteins have Gly at position 25 instead of Arg, which represents an allotypic variant of the λVI variable locus. The presence of Gly at position 25 in the L1 of λVI light chains would imply a different conformation for this loop. Additionally, the position 68 in λVI light chains, which is at the top of the FR3 loop, showed such spatial orientation and variability that suggested its participation in the conformation of the antigen recognition surface in this subgroup of λ chains. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Explosion of a hot‐oil circuit as a consequence of process, plant engineering, and management shortcomings
Authors: Piccinini N. , Demichela M. 
Published: November 2005

AbstractOn June 3, 1993, an explosion occurred at the Mediterranea refinery, in Milazzo, Sicily. Seven people died and eighteen people were injured with burns. An explosion in the accumulation tank 27V‐16 involved hot‐oil circuits subserving the refining units Topping 3, Topping 4, and HDT‐RC. The explosion was caused by a sudden overpressure in the 27V‐16 tank, probably as a result of the sudden vaporization of a small quantity of water. Shortcomings in the process design and in the management were at the origin of the accident, in particular:

Some process choices undertaken a couple of years before the accident, such as the use of gas oil from a Topping column in place of diathermic oil and the use of a combustible gas in place of nitrogen.
Some operational mistakes in the 13F‐2 oven conduction and the failure (or inadequacy or exclusion) of control systems or automatic and manual safety devices.
A detailed Fault Tree connects the process, design and management shortcomings identified. © 2005 American Institute of Chemical Engineers Process Saf Prog, 2006
Electric properties of single‐crystal PMN‐31% PT/epoxy 1–3 piezoelectric composites
Authors: Wang Haixia , Xu Haiqing , He Tianhou , Zhao Xiangyong , Luo Haosu , Yin Zhiwen 
Published: November 2005

AbstractPMN‐31% PT/expoxy 1–3 piezoelectric composites with a different volume fraction of PMN‐31% PT single crystals from 0.4 to 0.7 have been studied as regards fabrication and electric properties. The 〈001〉 oriented piezoelectric composites exhibit functional properties of low dielectric constant, high electromechanical coupling coefficient (0.80), and low acoustic impendence compared to the 〈110〉 oriented ones. The vibration characteristics of the piezoelectric composites strongly depend on the rod geometry and the volume fraction. The results obtained indicate that these piezoelectric composites with better global properties are promising candidates for biomedical imaging and underwater transducer applications. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Study of prelocalized graphite/styrene acrylonitrile conducting composites for device applications
Authors: Sachdev V. K. , Panwar Varij , Singh H. , Mehra N. C. , Mehra R. M. 
Published: November 2005

AbstractConductive polymer composites were prepared by compression molding of prelocalized graphite on to styrene acrylonitrile (SAN) particles. The electrical conductivity is found to be strongly dependent on the graphite content. Three different series were prepared for different processing and material parameters. A low percolation threshold has been noticed when only 1 wt% of graphite is incorporated. Resistivity as low as ∼14 Ω cm has been achieved in a composite with SAN resin particles of 180–212 µm size and graphite 10–20 µm at 90 °C, 105 MPa and 15 min. An electrically conducting network of graphite channels has been observed using scanning electron microscopy. V–I characteristic reveals that at a lower percentage of graphite the increase in current with increase in electric field is due to the hopping/tunneling of electrons, while for higher percentages of graphite ohmic behavior similar to metals has been observed. The data has been analyzed using percolation model. The value of the exponent t that determines the increase in electrical conductivity above the percolation threshold is found to be close to the values given in the literature. The theoretically calculated values of conductivity are found to be in satisfactory agreement with the experimental ones. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Modeling of spatially inhomogeneous solar cells by a multi‐diode approach
Authors: Grabitz P. O. , Rau U. , Werner J. H. 
Published: November 2005

AbstractAn equivalent circuit model consisting of parallel connected diodes with different electronic quality simulates the electronic properties of solar cells with spatially inhomogeneous material quality. Variations of the local saturation current density result in a degradation of the open circuit voltage, the fill factor and, in consequence, of the overall power conversion efficiency. However, a local series resistance introduced into this network limits this degradation by preventing areas with high saturation current density to dominate the electronic losses of the entire device. Analyzing the integral current/voltage‐curves of the networks shows the diode ideality larger than unity to result from resistive limitations to the spatially inhomogeneous current flow. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Twinning and extended defects in hcp metals with large c/a ratio: modelling and microscopic observations
Authors: Béré A. , Braisaz T. , Ruterana P. , Nouet G. 
Published: November 2005

AbstractIn hexagonal metals of largest c/a ratio, experimental observations hardly agree with the theoretical models of extended defects. For Zn and Cd, we have developed a semi‐empirical tight‐binding method to calculate the energy of extended defects. It was then possible to obtain a good correlation for polytypes or basal stacking faults. For the (10$ \bar 1 $2) twin, two possible interfaces have been shown to be stable in agreement with the available experimental results for Zn. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Deformation mechanisms of silicon during nanoscratching
Authors: Gassilloud R. , Ballif C. , Gasser P. , Buerki G. , Michler J. 
Published: November 2005

AbstractThe deformation mechanisms of silicon {001} surfaces during nanoscratching were found to depend strongly on the loading conditions. Nanoscratches with increasing load were performed at 2 µm/s (low velocity) and 100 µm/s (high velocity). The load‐penetration‐distance curves acquired during the scratching process at low velocity suggests that two deformation regimes can be defined, an elasto‐plastic regime at low loads and a fully plastic regime at high loads. High resolution scanning electron microscopy of the damaged location shows that the residual scratch morphologies are strongly influenced by the scratch velocity and the applied load. Micro‐Raman spectroscopy shows that after pressure release, the deformed volume inside the nanoscratch is mainly composed of amorphous silicon and Si‐XII at low scratch speeds and of amorphous silicon at high speeds. Transmission electron microscopy shows that Si nanocrystals are embedded in an amorphous matrix at low speeds, whereas at high speeds the transformed zone is completely amorphous. Furthermore, the extend of the transformed zone is almost independent of the scratching speed and is delimited by a dislocation rich area that extends about as deep as the contact radius into the surface. To explain the observed phase and defect distribution a contact mechanics based decompression model that takes into account the load, the velocity, the materials properties and the contact radius in scratching is proposed. It shows that the decompression rate is higher at low penetration depth, which is consistent with the observation of amorphous silicon in this case. The stress field under the tip is computed using an elastic contact mechanics model based on Hertz’s theory. The model explains the observed shape of the transformed zone and suggests that during load increase, phase transformation takes place prior to dislocation nucleation. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Structural and luminescence properties of In‐rich InGaN layers grown on InN templates by RF‐MBE
Authors: Naoi H. , Kurouchi M. , Takado S. , Muto D. , Araki T. , Nanishi Y. 
Published: November 2005

AbstractStructural and luminescence properties of In‐rich Inx Ga1−x N (0.71 ≤ x ≤ 1) layers are comprehensively studied. The layers were grown on (0001) sapphire substrates by radio‐frequency plasma‐assisted molecular‐beam epitaxy, employing two types of underlying structures: low‐temperature‐grown InN (LT‐InN) buffer layers and high‐temperature‐grown InN templates grown on LT‐InN buffer layers. The insertion of the InN templates has improved not only surface morphology but also both a ‐axis and c ‐axis orientations of In‐rich Inx Ga1−x N layers. In addition, by using InN templates of dramatically improved crystalline quality with the full width at half maximum of (0002) X‐ray rocking curves as narrow as 1 arcmin, which have been recently achieved by optimizing nitridation conditions of sapphire substrates, the crystalline quality of In0.8Ga0.2N layers was even further improved. On the other hand, however, photoluminescence (PL) line width showed no noticeable variation between the Inx Ga1−x N layers grown on InN templates and those on LT‐InN buffer layers. Possible factors that determine PL line width and compositional fluctuation of these In‐rich Inx Ga1−x N are discussed. Interference fringes of X‐ray diffraction (ω –2θ scan) have been observed from the high crystalline‐quality InN templates of the excellent c ‐axis orientation for the first time. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Continuous wave and time resolved spectroscopy of InAsN/GaAsN based quantum dots
Authors: Taliercio T. , Valvin P. , Intartaglia R. , Sallet V. , Harmand J. C. , Guillet T. , Lefebvre P. , Bretagnon T. , Gil B. 
Published: November 2005

AbstractWe present a study of the optical properties of quantum dots based on a new family of semiconductors: III–V dilute nitrides such as (In,Ga)(N,As). Continuous wave and time resolved photoluminescence (PL) experiments allowed us to evaluate the impact of N incorporation during the growth of InAs/GaAs quantum dots. Previous work [V. Sallet et al., to be submitted to J. Cryst. Growth (2005); O. Schumann et al., J. Appl. Phys. 96, 2832 (2004)] showed that increasing the flux of N atoms into the growth chamber modifies drastically the size of the dots which leads to a bimodal growth. Two populations of dots with different sizes appear. The quantum dot PL line broadens and a second PL line appears at higher energy. Time resolved PL allows us to identify the nature of this second PL line: second population of quantum dots. A second decay time is observed which we interpret as being the consequence of the perturbation of the electronic states of the quantum dots. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Exciton dark states in the recombination kinetics of InAs quantum dots
Authors: Vinattieri Anna , Zamfirescu Marian , Gurioli Massimo , Colocci Marcello , Sanguinetti Stefano , Noetzel Richard 
Published: November 2005

AbstractTime‐resolved photoluminescence experiments in high quality InAs/GaAs quantum dots clearly show the interplay between radiative recombination and thermalization processes. In particular from temperature dependent PL spectra, we prove that the carrier recombination dynamics is ruled by the thermal population in optically inactive exciton states, related to the population of the first excited hole levels. Moreover time‐resolved spectra do not show any relaxation bottleneck, indicating an efficient carrier capture and a fast energy relaxation of the photogenerated carriers. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Optical properties of Ge nanowires grown on Si(100) and (111) substrates: Nanowire–substrate heterointerfaces
Authors: Kamenev B. V. , Sharma V. , Tsybeskov L. , Kamins T. I. 
Published: November 2005

AbstractThe cover picture of the present issue of physica status solidi (a) contains two scanning electron micrographs showing approximately 40 nm diameter Ge nanowires grown by the vapor–liquid–solid (VLS) technique on Si(100) (upper right figure) and Si(111) (lower left figure) substrates, respectively. The figures are provided by the authors T. I. Kamins (Hewlett‐Packard Laboratories) and L. Tsybeskov (New Jersey Institute of Technology).
Dipolar contribution to the birefringence and second‐order susceptibility of organic materials
Authors: Trivedi Rashmi , Sen Pratima , Sen Pranay K. 
Published: November 2005

AbstractIncorporating the dipolar contribution and using density matrix analysis, the linear and nonlinear opti‐ cal susceptibilities are calculated in polar organic crystal. The dipolar contribution successfully explains the origin of ordinary and the extraordinary refractive indices of polar materials in the infrared regime. The results are applied to a sample of Urea. The calculated values of the refractive indices, hyperpolarizability and second‐order optical susceptibility are well in agreement with the experimentally reported values. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Local and general aspects of current profiles in quantum magnetotransport
Authors: Cresti Alessandro , Grosso Giuseppe , Pastori Parravicini Giuseppe 
Published: November 2005

AbstractWe present a formal and numerical analysis of current distribution through two‐dimensional electron gas systems threaded by a magnetic field. The nonequilibrium Keldysh formalism is elaborated into a procedure well suited to describe both local features of carrier flow and universal features connected to the spatial chirality produced by strong magnetic fields. The interplay between disorder and chirality is illustrated by numerical simulations of significant models. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Molecular Modeling of Meta II Rhodopsin
Authors: Ślusarz Rafał , Ślusarz Magdalena J. , Lammek Bernard , Ciarkowski Jerzy 
Published: November 2005

AbstractA model believed to be representative for activated class A G protein‐coupled receptors is proposed. It consists of rhodopsin and the transducin α C‐terminal peptide [Gtα(338–350)] docked to it. The model utilizes the resolved interactions/distances, found to be essential in the activated rhodopsin (RD*) and the structure of Gtα(338–350) that is known to stabilize RD*. Long‐term molecular dynamics (14.8 ns) in fully hydrated lipid bilayer model is applied to the system to refine and verify conformational changes in rhodopsin itself and the structure of the complex. A concomitant role of Gtα and Gtγ C‐termini in stabilizing RD* could possibly be resolved assuming a receptor dimer as a requisite for G protein activation.
A new approach for the two‐electron cumulant in natural orbital functional theory
Authors: Piris Mario 
Published: November 2005

AbstractThe cumulant expansion gives rise to a useful decomposition of the two‐matrix D in which the pair correlated matrix (cumulant) is disconnected from the antisymmetric product of the one‐matrix Γ. A new explicit antisymmetric approach for the two‐particle cumulant matrix in terms of two symmetric matrices, Δ and Λ, as functionals of the occupation numbers is proposed for singlet ground states of closed‐shell systems. It produces a natural orbital functional that reduces to the exact expression for the total energy in two‐electron systems. The functional form of matrix Λ is readily generalized to any system with an even number of electrons. The diagonal elements of Δ equal the square of the occupation numbers, and the N‐representability positivity necessary conditions of the two‐matrix impose several bounds on the off‐diagonal elements of matrix Δ. The well‐known mean value theorem and the partial sum rule obtained for the off‐diagonal elements of Δ provide a prescription for deriving a practical functional. In particular, when the mean values {J} of the Coulomb interactions {Jij} for a given orbital i taking over all orbitals j ≠ i are assumed to be equal {Kii/2}, a functional close to self‐interaction‐corrected GU functional is obtained, but the two‐matrix fermionic antisymmetric holds. An additional term for the matrix elements of Λ between HF occupied orbitals is proposed to ensure a correct description of the occupation numbers for the lowest occupied levels. The functional is tested in fully variational finite basis set calculations of 57 molecules. It gives reasonable molecular energies at the equilibrium geometries. The calculated values of dipole moments are in good agreement with the available experimental data. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Density functional study of structural and electronic properties of AlnN (1 ≤ n ≤ 12) clusters
Authors: Guo Ling , Wu Hai‐Shun 
Published: November 2005

AbstractLow‐lying equilibrium geometric structures of AlnN (n = 1–12) clusters obtained by an all‐electron linear combination of atomic orbital approach, within spin‐polarized density functional theory, are reported. The binding energy, dissociation energy, and stability of these clusters are studied within the local spin density approximation (LSDA) and the three‐parameter hybrid generalized gradient approximation (GGA) due to Becke–Lee–Yang–Parr (B3LYP). Ionization potentials, electron affinities, hardness, and static dipole polarizabilities are calculated for the ground‐state structures within the GGA. It is observed that symmetric structures with the nitrogen atom occupying the internal position are lowest‐energy geometries. Generalized gradient approximation extends bond lengths as compared with the LSDA lengths. The odd–even oscillations in the dissociation energy, the second differences in energy, the highest occupied molecular orbital–lowest unoccupied molecular orbital (HOMO–LUMO) gaps, the ionization potential, the electron affinity, and the hardness are more pronounced within the GGA. The stability analysis based on the energies clearly shows the Al7N cluster to be endowed with special stability. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Ab initio study of Rg2I− (Rg = Ar, Kr, Xe)
Authors: Li X. , Zhao Y. , Jing X. , Liu F. , Hao F. 
Published: November 2005

AbstractThe equilibrium geometries, vibrational frequencies, and dissociation energies of rare gas iodine clusters Rg2I−(Rg = Ar, Kr, Xe) were calculated at the Hartree–Fock (HF), second‐order Møller–Plesset (MP2), the coupled cluster method with single and double excitation and a noniterative correction for triple excitations method [CCSD(T)] levels. The title species have bent C2v structure of about 60° angle. The electron correlation effects and relativistic effects on the geometry and stability were investigated at CCSD(T) level. Both effects stabilize title species. The calculated electron affinities are in good agreement with the experimental results available. The effect of high angular momentum functions (g and h) was studied. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Blue‐shifted and red‐shifted hydrogen bonds: Theoretical study of the CH3CHO· · ·HNO complexes
Authors: Yang Yong , Zhang Weijun , Gao Xiaoming 
Published: November 2005

AbstractThe blue‐shifted and red‐shifted H‐bonds have been studied in complexes CH3CHO…HNO. At the MP2/6‐31G(d), MP2/6‐31+G(d,p) MP2/6‐311++G(d,p), B3LYP/6‐31G(d), B3LYP/6‐31+G(d,p) and B3LYP/6‐311++G(d,p) levels, the geometric structures and vibrational frequencies of complexes CH3CHO…HNO are calculated by both standard and CP‐corrected methods, respectively. Complex A exhibits simultaneously red‐shifted CH…O and blue‐shifted NH…O H‐bonds. Complex B possesses simultaneously two blue‐shifted H‐bonds: CH…O and NH…O. From NBO analysis, it becomes evident that the red‐shifted CH…O H‐bond can be explained on the basis of the two opposite effects: hyperconjugation and rehybridization. The blue‐shifted CH…O H‐bond is a result of conjunct CH bond strengthening effects of the hyperconjugation and the rehybridization due to existence of the significant electron density redistribution effect. For the blue‐shifted NH…O H‐bonds, the hyperconjugation is inhibited due to existence of the electron density redistribution effect. The large blue shift of the NH stretching frequency is observed because the rehybridization dominates the hyperconjugation. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006