bluuebunny/crossref_metadata_2025 huggingface dataset:
Why are both ends of the polypeptide chain on the outside of proteins?
Authors: Hovmöller Sven , Zhou Tuping
Published: March 2004

Protein folding starts before the whole polypeptide has been synthesized by the ribosome. No matter how long the polypeptide is or how intricate the fold, both ends of the chain always end up on the surface. From a topological point of view, this is surprising; one would have expected to find the starting (N‐terminal) end inside the core of the folded protein, just as in a ball of yarn. We suggest here that the reason for this apparent paradox is that the first amino acid of the emerging polypeptide chain is gripped during protein synthesis, perhaps by the ribosome, and is not released until the whole polypeptide has been synthesized. This binding would greatly decrease the degrees of freedom for the protein‐folding process and could also explain why knots are so rare in proteins. Gripping would also guarantee that the N‐terminal is accessible on the protein surface as required for binding of ubiquitin, which regulates the natural degradation of proteins and avoids buildup of protein aggregates, such as those found in Huntington's, Alzheimer's, Parkinson's, and other neurodegenerative diseases. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Characterization of Arabidopsis thaliana stellacyanin: A comparison with umecyanin
Authors: Harrison Mark D. , Dennison Christopher
Published: March 2004

The cupredoxin domain of a putative type 1 blue copper protein (BCB) from Arabidopsis thaliana was overexpressed and purified. A recursive polymerase chain reaction method was used to synthesize an artificial coding region for the cupredoxin domain of horseradish stellacyanin (commonly known as umecyanin), prior to overexpression and purification. The recombinant proteins were refolded from inclusion bodies and reconstituted with copper, and their in vitro characteristics were studied. Recombinant umecyanin, which is nonglycosylated, has identical spectroscopic and redox properties to the native protein. The UV/Vis and EPR spectra of recombinant BCB and umecyanin demonstrate that they have comparable axial type 1 copper binding sites. Paramagnetic 1H NMR spectroscopy highlights the similarity between the active site architectures of BCB and umecyanin. The reduction potential of recombinant BCB is 252 mV, compared to 293 mV for recombinant umecyanin. Identical pKa values of 9.7 are obtained for the alkaline transitions in both proteins. This study demonstrates that BCB is the A. thaliana stellacyanin and the results form the biochemical basis for a discussion of BCB function in the model vascular plant. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Exploring protein native states and large‐scale conformational changes with a modified generalized born model
Authors: Onufriev Alexey , Bashford Donald , Case David A.
Published: March 2004

Implicit solvation models provide, for many applications, a reasonably accurate and computationally effective way to describe the electrostatics of aqueous solvation. Here, a popular analytical Generalized Born (GB) solvation model is modified to improve its accuracy in calculating the solvent polarization part of free energy changes in large‐scale conformational transitions, such as protein folding. In contrast to an earlier GB model (implemented in the AMBER‐6 program), the improved version does not overstabilize the native structures relative to the finite‐difference Poisson–Boltzmann continuum treatment. In addition to improving the energy balance between folded and unfolded conformers, the algorithm (available in the AMBER‐7 and NAB molecular modeling packages) is shown to perform well in more than 50 ns of native‐state molecular dynamics (MD) simulations of thioredoxin, protein‐A, and ubiquitin, as well as in a simulation of Barnase/Barstar complex formation. For thioredoxin, various combinations of input parameters have been explored, such as the underlying gas‐phase force fields and the atomic radii. The best performance is achieved with a previously proposed modification to the torsional potential in the Amber ff99 force field, which yields stable native trajectories for all of the tested proteins, with backbone root‐mean‐square deviations from the native structures being ∼1.5 Å after 6 ns of simulation time. The structure of Barnase/Barstar complex is regenerated, starting from an unbound state, to within 1.9 Å relative to the crystal structure of the complex. Proteins 2004;55:000–000. © 2004 Wiley‐Liss, Inc.
GEMDOCK: A generic evolutionary method for molecular docking
Authors: Yang Jinn‐Moon , Chen Chun‐Chen
Published: March 2004

We have developed an evolutionary approach for flexible ligand docking. This approval, GEMDOCK, uses a Generic Evolutionary Method for molecular DOCKing and an empirical scoring function. The former combines both discrete and continuous global search strategies with local search strategies to speed up convergence, whereas the latter results in rapid recognition of potential ligands. GEMDOCK was tested on a diverse data set of 100 protein–ligand complexes from the Protein Data Bank. In 79% of these complexes, the docked lowest energy ligand structures had root‐mean‐square derivations (RMSDs) below 2.0 Å with respect to the corresponding crystal structures. The success rate increased to 85% if the structure water molecules were retained. We evaluated GEMDOCK on two cross‐docking experiments in which each ligand of a protein ensemble was docked into each protein of the ensemble. Seventy‐six percent of the docked structures had RMSDs below 2.0 Å when the ligands were docked into foreign structures. We analyzed and validated GEMDOCK with respect to various search spaces and scoring functions, and found that if the scoring function was perfect, then the predicted accuracy was also essentially perfect. This study suggests that GEMDOCK is a useful tool for molecular recognition and may be used to systematically evaluate and thus improve scoring functions. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Melittin as model system for probing interactions between proteins and cyclodextrins
Authors: Khajehpour Mazdak , Troxler Thomas , Nanda Vikas , Vanderkooi Jane M.
Published: March 2004

Cylcodextrin sugars are cyclic sugars that have a hydrophilic exterior and a hydrophobic center. This enables cyclodextrins to solubilize hydrophobic molecules in aqueous media. Cyclodextrins may inhibit aggregation by intercalating surface aromatic residues and competing with interprotein aromatic clusters (π–π interactions). In order to investigate this concept, the interaction of hydroxypropyl‐β‐cyclodextrin (HPBCD) with melittin is studied with steady‐state and time‐resolved fluorescence, fluorescence polarization, circular dichroism, and IR spectroscopy. HPBCD inhibits the aggregation of melittin. This inhibition and the spectroscopic results are consistent with the lone aromatic tryptophan of the peptide being intercalated within HPBCD. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Microbial genomes have over 72% structure assignment by the threading algorithm PROSPECTOR_Q
Authors: Kihara Daisuke , Skolnick Jeffrey
Published: March 2004

The genome scale threading of five complete microbial genomes is revisited using our state‐of‐the‐art threading algorithm, PROSPECTOR_Q. Considering that structure assignment to an ORF could be useful for predicting biochemical function as well as for analyzing pathways, it is important to assess the current status of genome scale threading. The fraction of ORFs to which we could assign protein structures with a reasonably good confidence level to each genome sequences is over 72%, which is significantly higher than earlier studies. Using the assigned structures, we have predicted the function of several ORFs through “single‐function” template structures, obtained from an analysis of the relationship between protein fold and function. The fold distribution of the genomes and the effect of the number of homologous sequences on structure assignment are also discussed. Proteins 2004;55:000–000. © 2004 Wiley‐Liss, Inc.
Locating the stabilizing residues in (α/β)8 barrel proteins based on hydrophobicity, long‐range interactions, and sequence conservation
Authors: Gromiha M. Michael , Pujadas Gerard , Magyar Csaba , Selvaraj Samuel , Simon Istvan
Published: March 2004

In nature, 1 out of every 10 proteins has an (α/β)8 (TIM)‐barrel fold, and in most cases, pairwise comparisons show no sequence similarity between them. Hence, delineating the key residues that induce very different sequences to share a common fold is important for understanding the folding and stability of TIM‐barrel domains. In this work, we propose a new consensus approach for locating these stabilizing residues based on long‐range interactions, hydrophobicity, and conservation of amino acid residues. We have identified 957 stabilizing residues in 63 proteins from a nonredundant set of 71 TIM‐barrel domains. Most of these residues are located in the 8‐stranded β‐sheet, with nearly one half of them oriented toward the interior of the barrel and the other half oriented toward the surrounding α‐helices. Several stabilizing residues are found in the N‐ and C‐terminal loops, whereas very few appear in the α‐helices that surround the internal β‐sheet. Further, these 957 residues are placed in 434 stabilizing segments of various sizes, and each domain contains 1–10 of these segments. We found that 8 segments per domain is the most abundant one, and two thirds of the proteins have 7–9 stabilizing segments. Finally, we verified the identified residues with experimental temperature factors and found that these residues are among the ones with less mobility in the considered proteins. We suggest that our new protocol serves as a powerful tool to identify the stabilizing residues in TIM‐barrel domains, which can be used as potential candidates for studying protein folding and stability by means of protein engineering experiments. Proteins 2004;55:000–000. © 2004 Wiley‐Liss, Inc.
Temperature dependence of the free energy landscape of the src‐SH3 protein domain
Authors: Guo Weihua , Lampoudi Sotiria , Shea Joan‐Emma
Published: March 2004

The temperature dependence of the free energy landscape of the src‐SH3 protein domain is investigated through fully atomic simulations in explicit solvent. Simulations are performed above and below the folding transition temperature, enabling an analysis of both protein folding and unfolding. The transition state for folding and unfolding, identified from the free energy surfaces, is found to be very similar, with structure in the central hydrophobic sheet and little structure throughout the rest of the protein. This is a result of a polarized folding (unfolding) mechanism involving early formation (late loss) of the central hydrophobic sheet at the transition state. Unfolding simulations map qualitatively well onto low‐temperature free energy surfaces but appear, however, to miss important features observed in folding simulations. In particular, details of the folding mechanism involving the opening and closing of the hydrophobic core are not captured by unfolding simulations performed under strongly denaturing conditions. In addition, free energy surfaces at high temperatures do not display a desolvation barrier found at lower temperatures, involving the expulsion of water molecules from the hydrophobic core. Proteins 2004;55:000–000. © 2004 Wiley‐Liss, Inc.
Data‐based model and parameter evaluation in dynamic transcriptional regulatory networks
Authors: Cavelier German , Anastassiou Dimitris
Published: March 2004

Finding the causality and strength of connectivity in transcriptional regulatory networks from time‐series data will provide a powerful tool for the analysis of cellular states. Presented here is the design of tools for the evaluation of the network's model structure and parameters. The most effective tools are found to be based on evolution strategies. We evaluate models of increasing complexity, from lumped, algebraic phenomenological models to Hill functions and thermodynamically derived functions. These last functions provide the free energies of binding of transcription factors to their operators, as well as cooperativity energies. Optimization results based on published experimental data from a synthetic network in Escherichia coli are presented. The free energies of binding and cooperativity found by our tools are in the same physiological ranges as those experimentally derived in the bacteriophage lambda system. We also use time‐series data from high‐density oligonucleotide microarrays of yeast meiotic expression patterns. The algorithm appropriately finds the parameters of pairs of regulated regulatory yeast genes, showing that for related genes an overall reasonable computation effort is sufficient to find the strength and causality of the connectivity of large numbers of them. Proteins 2004;55:000–000. © 2004 Wiley‐Liss, Inc.
Identification of protons position in acid–base enzyme catalyzed reactions: The hepatitis C viral NS3 protease
Authors: Shokhen Michael , Albeck Amnon
Published: March 2004

General acid–base catalysis is a key element of the catalytic activity of most enzymes. Therefore, any explicit molecular modeling of enzyme‐catalyzed chemical reactions requires correct identification of protons location on the catalytic groups. In this work, we apply our quantum mechanical/self‐consistent reaction field in virtual solvent [QM/SCRF(VS)] method for identification of the position of protons shared by the enzyme catalytic groups and the polar groups of the inhibitor in a covalent tetrahedral complex (TC) of the hepatitis C virus NS3 protease with a peptidyl α‐ketoacid inhibitor. To identify the relevant protonation states, we have analyzed relative stabilities of R and S configurations of the TC that depend on the specific proton distribution over the polar groups and correlated it with experimental NMR and X‐ray crystallography data, both at low and neutral pH ranges. The tentative assignment of the single resonance in the 13C NMR spectrum of the hemiketal carbon at physiological pH to the S configuration of TC is confirmed. Both R and S configurations are equally stable at acidic pH in our modeling, in good agreement with the 13C NMR observation. Proteins 2004;9999:000–000. © 2004 Wiley‐Liss, Inc.
Expanded turn conformations: Characterization and sequence‐structure correspondence in α‐turns with implications in helix folding
Authors: Dasgupta Bhaskar , Pal Lipika , Basu Gautam , Chakrabarti Pinak
Published: March 2004

Like the β‐turns, which are characterized by a limiting distance between residues two positions apart (i, i+3), a distance criterion (involving residues at positions i and i+4) is used here to identify α‐turns from a database of known protein structures. At least 15 classes of α‐turns have been enumerated based on the location in the ϕ,ψ space of the three central residues (i+1 to i+3)—one of the major being the class AAA, where the residues occupy the conventional helical backbone torsion angles. However, moving towards the C‐terminal end of the turn, there is a shift in the ϕ,ψ angles towards more negative ϕ, such that the electrostatic repulsion between two consecutive carbonyl oxygen atoms is reduced. Except for the last position (i+4), there is not much similarity in residue composition at different positions of hydrogen and non‐hydrogen bonded AAA turns. The presence or absence of Pro at i+1 position of α‐ and β‐turns has a bearing on whether the turn is hydrogen‐bonded or without a hydrogen bond. In the tertiary structure, α‐turns are more likely to be found in β‐hairpin loops. The residue composition at the beginning of the hydrogen bonded AAA α‐turn has similarity with type I β‐turn and N‐terminal positions of helices, but the last position matches with the C‐terminal capping position of helices, suggesting that the existence of a “helix cap signal” at i+4 position prevents α‐turns from growing into helices. Our results also provide new insights into α‐helix nucleation and folding. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Theoretical studies of the spin‐Hamiltonian parameters for Er3+ in CaWO4 and SrWO4
Authors: Wu Shao‐Yi , Dong Hui‐Ning , Yan Wei‐Zi , Gao Xiu‐Ying
Published: March 2004

The spin‐Hamiltonian parameters g factors g‖, g⟂ and hyperfine structure parameters A‖ and A⟂ for Er3+ (167Er) in CaWO4 and SrWO4 are theoretically studied by using the perturbation formulas of the spin‐Hamiltonian parameters for a 4f11 ion in tetragonal symmetry. In these formulas, the contributions to the spin‐Hamiltonian parameters arising from the second‐order perturbation terms and the admixture of various states are considered. The crystal‐field parameters for the tetragonally distorted tetrahedra are calculated from the superposition model and the local structural data of the impurity Er3+ ions at the host Ca2+ and Sr2+ sites. The theoretical parameters are in agreement with the experimental values. The validity of the results is discussed. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
PbS nanoparticles in Langmuir–Blodgett films: kinetics of formation and growth
Authors: Savin Yu. N. , Vitushkina S. V.
Published: March 2004

The formation and growth of lead sulfide nanocrystals in lead stearate Langmuir–Blodgett (LB) films are investigated by optical absorption spectroscopy. Kinetics of the concentration changes of lead ions in the different states formed during the growth process, as well as the evolution of the nanocrystal average size versus growth time, are studied. A nonlinear dependence of the nanoparticle growth rate versus time is found. The idea of diffusive decomposition of solid solutions is used to analyze the experimental results. It is shown that high concentrations of metal ions at the interfaces of monolayers of LB films, as well as diffusion restrictions of mass‐transfer processes, play a decisive role in the formation and growth of nanocrystals in ordered organic matrices. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Exchange and correlation effects in strained‐layer semiconductor quantum wells
Authors: Tong C. , Kim M. R. , Kim S. K. , Han B. H. , Rhee J. K.
Published: March 2004

We examine the exchange and the correlation effects for a quasi‐two‐dimensional InxGa1−xAs/InGaAsP QW systems with strain, considering the complexities related to the effect of valence‐band mixing. The many‐body effects due to exchange interaction and screening of Coulomb interaction are calculated within the random‐phase approximation. The valence‐band structure is obtained by solving the Luttinger–Kohn Hamiltonian to evaluate the valence‐band mixing and the strain effects properly. The dependence of the many‐body effects on strain and sheet carrier density is shown to become more important as the screening of the Coulomb interaction is included. Also, it is shown that the exchange and correlation energy becomes important as indium mole fraction and sheet carrier density increase. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The diluted transverse Ising model with competing bulk and surface ordering
Authors: Khaya L. , Benayad N. , Dakhama A.
Published: March 2004

The phase diagram of the three‐dimensional transverse Ising system with competing surface and bulk exchange interactions is studied by the use of an effective‐field method within the framework of a single‐site cluster theory. In addition to this pure case, which shows qualitatively interesting features, we investigated the effects of the bond dilution on the obtained phase diagram. In particular, we studied the influence of the surface dilution parameter on the surface transitions. We find a number of characteristic behaviours of the surface both in the absence and in the presence of the surface transverse field. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Lowest energy structures of anionic Sin (n = 11–25) clusters
Authors: Li Bao‐xing , Xu Qing
Published: March 2004

Using full‐potential linear‐muffin‐tin‐orbital molecular‐dynamics (FP‐LMTO‐MD) method based on single‐parent evolution algorithm, we have studied the geometric and electronic structures of anionic Si11–25 clusters. For the anionic Sin (n = 11–20) clusters (except for n = 15 and n = 19), the ground state structures are in good agreement with the results obtained by using density functional theory with the gradient‐corrected functionals Perdew‐Wang‐Becke 88 (PWB). For n = 15 and 19, our results are in excellent agreement with those optimized using generalized gradient approximation (GGA) functionals based on single‐parent evolution method. In special, we have found the ground state structures for the anionic Si21–25 clusters using FP‐LMTO‐MD based on single‐parent evolution method. It is found that all the lowest energy structures include a sub‐unit of tricapped trigonal prism (TTP). Some lowest‐energy structures for the anions are different from those of neutrals. In addition, some energy orderings are also different by comparison with those of their corresponding neutral clusters. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Time resolved photoluminescence study of Si modulation doped GaN/Al0.07Ga0.93N multiple quantum wells
Authors: Haratizadeh H. , Monemar B. , Paskov P. P. , Holtz P. O. , Pozina G. , Kamiyama S. , Iwaya M. , Amano H. , Akasaki I.
Published: March 2004

The effects of the Si doping level on the recombination dynamics and carrier (exciton) localization in modulation doped GaN/Al0.07Ga0.93N multiple‐quantum‐well (MQW) structures were studied by means of photoluminescence (PL) and time‐resolved PL measurements. All samples with different doping levels show a QW emission which is blue shifted with respect to the 3.48 eV PL peak from the GaN buffer layer. The decay time at the peak position remains nearly constant in the range of 320–420 ps at 2 K for all doping levels. For the undoped and low‐doped samples (3 × 1018 cm−3), which have less free electrons in the QWs, a non‐exponential PL decay behaviour at 2 K is attributed to localized exciton recombination. The more highly doped samples (5 × 1018 cm−3 to 1020 cm−3) show almost exponential decay curves at 2 K, suggesting the recombination of free electrons and localized holes. This localization effect appears even at high electron concentrations to cancel the expected lowering of the radiative lifetime with doping at 2 K; such a lowering is clearly observed at elevated temperatures for the highly doped samples, however. The internal polarization‐induced fields of the medium and highly‐doped samples are partly screened by the electrons originating from the doping in the barriers. Only the PL peak of the undoped and low‐doped samples shows a redshift with time delay, related to the photogenerated carriers. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electrical field induced order–order transitions in rare earth manganites
Authors: Bärner K. , Annaorazov M. , Yang C. P. , Morchshakov V.
Published: March 2004

Varistor‐like electrical transport is found in Nd2/3Sr1/3MnOz and Pr0.7Sr0.3MnO3 compounds, with evidence of magnetic order–order transitions superimposed. The transition temperatures move under a magnetic field which establishes the spin‐dependent character of these phenomena. We also discuss the possibilty that the electrical field induces such transitions, as the transition appears and/or shifts at certain applied currents (or potentials). (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Horizontal line nodes in superconducting Sr2RuO4
Authors: Litak G. , Annett J. F. , Györffy B. L. , Wysokiński K. I.
Published: March 2004

We analyze the possibilities of triplet pairing in Sr2RuO4 based upon an idea of interlayer coupling. We have considered two models differing by the effective interactions. In one model the quasi‐particle spectra have horizontal line nodes on all three Fermi surface sheets, while in the other the spectra have line or point nodes on the α and β sheets and no nodes on the γ sheet. Both models reproduce the experimental heat capacity and penetration depth results, but the calculated specific heat is sightly closer to experiment in the second solution with nodes only on the α and β sheets. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Correlation between ferroelectricity and electronic density of states near the Fermi level in BaTiO3
Authors: Hidaka M. , Tokiwa N. , Takahashi S. , Choi J.‐Y. , Lee J. M.
Published: March 2004

The electronic density of states in BaTiO3 is studied by means of X‐ray absorption near‐edge structure in a vicinity of a Ti K edge and Ba L edges. A 4pπ band of the Ti ion and a 5dπ band of the Ba ion having a high‐density unoccupied state occupy a level just above the Fermi level (EF). The pre‐edge peaks give that, in addition to an O2− 2p valence band, the electronic density of states below EF are composed of negative‐charge‐transfer bands 3d1, 3d1$ \underline {\rm L} $ and 3d2$ \underline {\rm L} $2 of Ti ions and 4f1, 4f1$ \underline {\rm L} $ and 4f2$ \underline {\rm L} $2 of Ba ions. The 3d1, 3d1$ \underline {\rm L} $ and 3d2$ \underline {\rm L} $2 bands of Ti ions gives that a mixture of the different oxidation states Ti2+ and Ti3+ is present in addition to Ti4+. The 4f1, 4f1$ \underline {\rm L} $ and 4f2$ \underline {\rm L} $2 bands are induced by a hybridization between Ba2+ 4d and O2– 2p orbitals via an electronic configuration interaction between the 4f and 4d orbitals of the Ba ion. The disappearance of the 4f1, 4f1$ \underline {\rm L} $ and 4f2$ \underline {\rm L} $2 bands in the ferroelectric phase suggests that the collective displacement of Ba ions from ideal ionic sites of the cubic perovskite‐type structure reduces the hybridization between the Ba and O ions. This gives that the effective charge on the O ions is increased and induces a large dipole moment between the O ions and the Ti ions, which are at an off‐center position of TiO6 octahedra in the ferroelectric phase. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Influence of an inclined anisotropy on formation of spatially inhomogeneous phase in two‐dimensional ferromagnet
Authors: Fridman Yu. A. , Klevets Ph. N. , Spirin D. V.
Published: March 2004

Phase states of ultrathin magnetic film with an inclined anisotropy are investigated. It is shown, that in a 2D film with easy‐axis, easy‐plane anisotropies, and inclined out‐of‐plane anisotropy the realization of spatially inhomogeneous phase is possible only at specific orientation of an external magnetic field. If orthorhombic anisotropy is implemented in the film plane, then the spatially inhomogeneous phase realizes at arbitrary orientation of in‐plane external field. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Shallow donor impurities in different shaped double quantum wells under the electric field
Authors: Kasapoglu E. , Sokmen I.
Published: March 2004

The binding energy of the donor impurity in double triangle quantum well (DTQW), double graded (DGQW) and double square (DSQW) GaAs–(Ga,Al)As quantum wells under the electric field is calculated by using a variational approach. The results have been obtained in the presence electric field applied along the growth direction as a function of the impurity position, barrier width and the geometric shape of the double quantum wells. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Density‐functional‐based tight‐binding approach to phonon spectra of conjugated polymers
Authors: Lynge T. B. , Pedersen T. G.
Published: March 2004

We apply a computationally efficient method for calculating phonon spectra to the two conjugated polymers trans‐polyacetylene and poly(para‐phenylene). The starting point of the calculation is a relaxation of the atomic coordinates based on the Density‐Functional‐Based Tight‐Binding (DFTB) approach of Porezag et al. From the relaxed geometry we calculate the force constant matrix of a suitably sized super cell and calculate the dynamical matrix by Fourier transformation.

The only input required for the computation is the parametrized DFTB Hamilton and overlap matrix elements, and as a non‐self consistent TB‐method the present approach is highly efficient and therefore able to treat molecules of considerable size. The method has previously been successfully applied to vibrations in hydrocarbon molecules and single‐wall nanotubes. We demonstrate here that the approach is equally applicable to polymers, as the equilibrium configurations as well as the phonon spectra are found to be in reasonable agreement with other results from the literature. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Adaptive backstepping control for a class of nonlinear systems using neural network approximations
Authors: Tan K. K. , Huang S. N. , Lee T. H.
Published: March 2004

In this paper, an adaptive neural network (NN) backstepping technique is developed for tracking control of a class of nonlinear systems. NNs are used to compensate for the unknown nonlinear functions in the system. A systematic backstepping approach is established to synthesize the adaptive NN control scheme that ensures the boundedness of all the signals in the closed‐loop system, and yields a small tracking error. The issue of transient performance is also addressed under an analytical framework. The effectiveness of the proposed scheme is demonstrated by computer simulations. Copyright © 2004 John Wiley & Sons, Ltd.
Delay‐dependent anti‐windup strategy for linear systems with saturating inputs and delayed outputs
Authors: Tarbouriech S. , Gomes Da Silva J.M. , Garcia G.
Published: March 2004

This paper addresses the problem of the determination of stability regions for linear systems with delayed outputs and subject to input saturation, through anti‐windup strategies. A method for synthesizing anti‐windup gains aiming at maximizing a region of admissible states, for which the closed‐loop asymptotic stability and the given controlled output constraints are respected, is proposed. Based on the modelling of the closed‐loop system resulting from the controller plus the anti‐windup loop as a linear time‐delay system with a dead‐zone nonlinearity, constructive delay‐dependent stability conditions are formulated by using both quadratic and Lure Lyapunov–Krasovskii functionals. Numerical procedures based on the solution of some convex optimization problems with LMI constraints are proposed for computing the anti‐windup gain that leads to the maximization of an associated stability region. The effectiveness of the proposed technique is illustrated by some numerical examples. Copyright © 2004 John Wiley & Sons, Ltd.
Nonlinear path following control of non‐holonomic vehicles with the human as actuator in a parking application
Authors: Kochem M. , Isermann R.
Published: March 2004

This paper describes and compares several controllers for precision tracking control of non‐holonomic vehicles at low speeds with the driver as actuator in the control loop. A possible application for the developed controllers is a driver assistance system for supporting the driver in a backward parking procedure. The system, designed as a comfort feature, provides the driver with optical and acoustical information through an appropriate human–machine interface (HMI) on how to steer the vehicle into the previously scanned parking spot. Without having an active steering in the vehicle, the driver remains in full control over the vehicle's motion. This paper outlines the main ideas and concepts of the system and focusses on the developed control structures. Finally, experimental results underline the validity of the chosen approach. Copyright © 2004 John Wiley & Sons, Ltd.
Adaptive sliding mode control of air–fuel ratio in internal combustion engines
Authors: Souder Jason S. , Hedrick J. Karl
Published: March 2004

A simplified model of an internal combustion engine is used to derive a sliding mode control law. Adaptive update laws are derived for two fueling parameters that describe fuel flow into the cylinders, and a third parameter that describes air flow into the cylinders. The update laws allow the sliding mode control gain, which is usually increased to overcome model uncertainty, to be reduced. This improves the tracking performance of the sliding mode controller in the presence of the feedback time delays. The parameter update laws are modified to bound the parameter values and allow all three parameter update laws to run simultaneously. The effect of the sampling rate on the adaptive sliding mode controller performance and air–fuel ratio biasing via gain selection are also addressed. Copyright © 2004 John Wiley & Sons, Ltd.
Pressure and temperature‐based adaptive observer of air charge for turbocharged diesel engines
Authors: Stefanopoulou A. G. , Storset O. F. , Smith R.
Published: March 2004

In this paper we design an adaptive air charge estimator for turbocharged diesel engines using intake manifold pressure, temperature and engine speed measurements. This adaptive observer scheme does not depend on mass air flow sensors and can be applied to diesel engines with no exhaust gas recirculation (EGR). The performance of the adaptive scheme is shown in simulations to be comparable to conventional air charge estimation schemes if perfect temperature measurements are available. The designed scheme cannot estimate fast transients and its performance deteriorates with temperature sensor lags. Despite all these difficulties, this paper demonstrates that (i) the proposed scheme has better robustness to modelling errors because it provides a closed‐loop observer design, and (ii) robust air charge estimation is achievable even without air flow sensors if good (fast) temperature sensors become available. Finally, we provide a rigorous proof and present the implementation challenges as well as the limiting factors of this adaptation scheme and point to hardware and temperature sensor requirements. Copyright © 2004 John Wiley & Sons, Ltd.
Control of an electro‐mechanical valve actuator for a camless engine
Authors: Haskara İ. , Kokotovic V. V. , Mianzo L. A.
Published: March 2004

In an electro‐mechanical valve actuated engine, the valves are driven by solenoid‐type actuators and cam‐shaft is eliminated. Individual control of each valve provides flexibility in valve timings over all engine conditions and fully exploits the benefits of variable valve timing. This paper pertains to the closed‐loop control of an electro‐mechanical valve actuator. The primary emphasis is on the soft‐seating problem, in which the valve and the moving actuator parts need to be brought to a soft‐stop at the end of their travels. The actuator control features which provide reliable valve motion are discussed in detail. Several illustrative experimental results are also presented. Copyright © 2004 John Wiley & Sons, Ltd.
Modular adaptive robust control of SISO nonlinear systems in a semi‐strict feedback form
Authors: Chantranuwathana Supavut , Peng Huei
Published: March 2004

In this paper, a modular modification of the adaptive robust control (ARC) technique is presented. The modular design has all of the original ARC properties with an estimation‐based update law instead of a Lyapunov‐based update law. In this design, the controller is divided into two modules: a control module and an identification module. A key new idea is to seta prioribounds on the time derivatives of the estimates to be maintained by the update law. As a result, their effects on the system tracking accuracy can be dominated by the control law. A modification is proposed for the standard gradient and least‐square update laws to guarantee the bounds. This modification also makes the controller robust against the generalized (unparameterized) uncertainties considered in the ARC formulation while allowing asymptotic output tracking without the generalized uncertainties. Both the ARC and the modular ARC techniques are applied to a force control problem for an active suspension system. Simulations and experimental results are provided to show that the update law of the modular design is less sensitive to measurement noise which results in smaller force tracking error and smaller control gain. Copyright © 2004 John Wiley & Sons, Ltd.
Exploring the structural effects of internetworking
Authors: Brews Peter J. , Tucci Christopher L.
Published: March 2004

Extant theory presents conflicting perspectives on how internetworking might affect the organizational structures of established firms. One prediction is that internetworking could narrow organizational scope and deepen specialization, reduce hierarchy, and increase external partnering. A second contends that internetworking might increase scope, expand hierarchy, and decrease external partnering. Analysis of a multinational sample of 469 firms reveals that deeply internetworked firms are more focused and specialized, less hierarchical, and more engaged in external partnering than less intensively internetworked organizations are. No scope broadening or hierarchy expansion effects are observed. Copyright © 2004 John Wiley & Sons, Ltd.
Three‐dimensional ultrasound‐validated large‐core needle biopsy: is it a reliable method for the histological assessment of breast lesions?
Authors: Delle Chiaie L. , Terinde R.
Published: March 2004

Objective

The use of three‐dimensional (3D) ultrasound may help to determine the exact position of the needle during breast biopsy, thereby reducing the number of core samples that are needed to achieve a reliable histological diagnosis. The aim of this study was to demonstrate the efficacy of 3D ultrasound‐validated large‐core needle biopsy (LCNB) of the breast.

Methods

A total of 360 core needle biopsies was obtained from 169 breast lesions in 146 patients. Additional open breast biopsy was performed in 111 women (127/169 breast lesions); the remaining 42 lesions were followed up for at least 24 months. 3D ultrasound visualization of the needle in the postfiring position was used to classify the biopsy as central, marginal or outside the lesion. Based on this classification it was decided whether another sample had to be obtained.

Results

A median of two core samples per lesion provided for all the lesions a sensitivity for malignancy of 96.9%, specificity of 100%, false‐positive rate of 0% and false‐negative rate of 3.1%, and for the excised lesions a sensitivity of 96.5%, specificity of 100%, false‐positive rate of 0%, false‐negative rate of 3.5% and an underestimation rate of 3.4%.

Conclusions

3D ultrasound validation of the postfiring needle position is an efficient adjunct to ultrasound‐guided LCNB. The advantages of 3D ultrasound validation are likely to include a reduction in the number of core samples needed to achieve a reliable histological diagnosis (and a possible reduction in the risk of tumor cell displacement), reduced procedure time and lower costs. Copyright © 2004 ISUOG. Published by John Wiley & Sons, Ltd.
Validation of fractional moving blood volume measurement with power Doppler ultrasound in an experimental sheep model
Authors: Hernandez‐Andrade E. , Jansson T. , Ley D. , Bellander M. , Persson M. , Lingman G. , Maršál K.
Published: March 2004

Objective

To compare fractional moving blood volume (FMBV) estimation using power Doppler ultrasound (PDU) with blood flow estimation using radioactive microspheres (RMS) for evaluation of fetal organ blood perfusion.

Methods

Blood flow was measured in the adrenal gland of nine exteriorized fetal lambs. Five fetal lambs underwent total umbilical cord occlusion in order to induce changes in the adrenal blood flow (asphyxia group). Four lambs were used as sham controls (control group). Three RMS injections, with coincident PDU recordings of the adrenal gland, were performed in each lamb. In the asphyxia group, measurements were taken before the cord occlusion, 5 min later and when the mean blood pressure decreased below 25 mmHg. In the control group, the measurements were done with an interval of 5 min. FMBV normalized for attenuation of PDU signals, and mean pixel intensity (MPI) were estimated offline. After completion of the study, adrenal blood perfusion was calculated according to the reference sample microsphere technique, using the isotope activity and expressed in mL/min/100 g. The correlation between RMS and FMBV and MPI, respectively, was analyzed individually for each lamb.

Results

In the asphyxia group, all lambs showed a marked reduction in the adrenal blood perfusion towards the third RMS injection. In the control group, the adrenal perfusion showed small variations throughout the experiment. In the total material, there was a higher correlation between FMBV and RMS (median, r = 0.90; range, 0.43–0.99) than between MPI and RMS (median, r = 0.55; range, −0.53 to 0.99).

Conclusion

The FMBV method of quantifying PDU signals correlates highly with blood flow perfusion estimation using RMS in the fetal lamb adrenal gland. Copyright © 2004 ISUOG. Published by John Wiley & Sons, Ltd.
Fractional moving blood volume estimation in the fetal lung using power Doppler ultrasound: a reproducibility study
Authors: Hernandez‐Andrade E. , Thuring‐Jönsson A. , Jansson T. , Lingman G. , Maršál K.
Published: March 2004

Objective

To evaluate the reproducibility of fractional moving blood volume (FMBV) estimation in the fetal lung using power Doppler ultrasound (PDU).

Methods

The lung blood perfusion of 20 normally grown singleton fetuses at 32–35 weeks of gestation was evaluated by two experienced observers using PDU. Each observer recorded two consecutive sequences of images from the posterior part of the fetal lung and calculated FMBV offline. FMBV expresses the percentage of blood movement within a defined region of interest (ROI). Repeatability and agreement were evaluated by means of the intraclass (intraCC) and interclass (interCC) correlation coefficients.

Results

FMBV was successfully evaluated in 17/20 fetuses by both observers (kappa index 0.82; 95% CI 0.51–0.93). The intraCC for repeatability for Observer A was 0.92 (95% CI 0.78–0.96), and for Observer B 0.90 (95% CI 0.74–0.96). The mean difference between the first and the second measurement was 0.7% (SD 4.5%). The interCC for repeatability over time and between the operators was 0.70 (95% CI 0.56–0.76) and the mean difference between the observers was 0.6% (SD 4.65%). The interCC for agreement was 0.92 (95% CI 0.84–0.95) and the mean difference in FMBV results when both observers analyzed the same sequences offline was 0.6% (SD 3.85%).

Conclusion

In the hands of experienced operators, using a well‐defined ROI and standard settings, FMBV estimation is a reproducible method of quantifying power Doppler signals recorded from fetal lung blood perfusion. Copyright © 2004 ISUOG. Published by John Wiley & Sons, Ltd.
Fetal middle cerebral artery peak systolic velocity in the investigation of non‐immune hydrops
Authors: Hernandez‐Andrade E. , Scheier M. , Dezerega V. , Carmo A. , Nicolaides K. H.
Published: March 2004

Objective

In some cases of non‐immune hydrops there is congenital or acquired fetal anemia. The aim of this study was to investigate the potential value of fetal middle cerebral artery peak systolic velocity (MCA‐PSV) in the assessment and management of non‐immune hydrops due to anemia.

Methods

Fetal MCA‐PSV and fetal hemoglobin concentration, in blood obtained by cordocentesis, were measured in 16 singleton pregnancies referred to our unit for further investigations because of a diagnosis of non‐immune hydrops fetalis. In all cases a detailed ultrasound examination demonstrated moderate or severe ascites, with or without skin edema, and pericardial or pleural effusions. Furthermore, there were no obvious malformations to account for the hydrops. In each fetus the measured MCA‐PSV and hemoglobin concentration were expressed as delta values (the difference in SD from the normal mean for gestation). Regression analysis was used to determine the significance of the association between delta MCA‐PSV and delta fetal hemoglobin concentration. In addition, we searched our database to identify the sonographic features and hemoglobin concentration of fetuses with congenital infection.

Results

In the 16 cases of non‐immune hydrops there were seven with parvovirus B19 infection, one each of α‐thalassemia and primary cardiomyopathy and seven with no obvious explanation for the hydrops. There was a significant association between delta MCA‐PSV and delta hemoglobin concentration (delta hemoglobin = (delta MCA‐PSV + 0.1437)/−0.4154; R2 = 0.7202; P < 0.0001). In 10 of the cases the fetal hemoglobin concentration was more than 4 SD below the normal mean for gestation and in all these cases the MCA‐PSV was more than 2 SD above the normal mean for gestation. Our computer search identified an additional nine fetuses with parvovirus B19 infection and in all cases the predominant sonographic finding was ascites and the hemoglobin concentration was more than 4 SD below the normal mean. In contrast, only 3/14 fetuses with cytomegalovirus, toxoplasmosis, coxsackie B or Treponema infection had ascites and only 2/14 had a hemoglobin deficit of 4–6 SD.

Conclusion

In the management of non‐immune hydrops, measurement of fetal MCA‐PSV can help identify the subgroup with fetal anemia. Copyright © 2004 ISUOG. Published by John Wiley & Sons, Ltd.
Pre‐eclampsia and peripartum cardiomyopathy in molar pregnancy: clinical implication for maternally imprinted genes
Authors: Billieux M.‐H. , Petignat P. , Fior A. , Mhawech P. , Blouin J.‐L. , Dahoun S. , Vassilakos P.
Published: March 2004

Molar pregnancies are associated with increased maternal complications, notably pre‐eclampsia, but peripartum cardiomyopathy has been rarely observed. Here we report on a 34‐year‐old woman, gravida 2 para 1, who presented to our obstetric clinic for routine screening at 16 weeks of gestation. Elevated maternal serum alpha‐fetoprotein and free beta‐human chorionic gonadotropin were observed. Amniocentesis revealed a triploid constitution (69,XXX) and ultrasound examination showed growth restriction, fetal anomalies, placentomegaly and a total placenta previa. On admission at 18 weeks' gestation, the patient developed vaginal bleeding and pre‐eclampsia. She underwent a Cesarean delivery and 6 h later developed congestive heart failure requiring intensive care support. Molecular analysis of the conceptus and parental DNA demonstrated an excess of paternal genomic contribution. The over‐representation of the paternal chromosome complement may support the role of genomic imprinting in the clinical course of this case. Copyright © 2004 ISUOG. Published by John Wiley & Sons, Ltd.
Rotation‐rate continuity in bi‐axial plastic deformation
Authors: Bish R.L.
Published: March 2004

The hypothesis of rotation‐rate continuity, which is associated with the deformation of homogeneous, isotropic bodies by slip, is applied to the plastic flow of a cold‐worked metal (or strain‐aged mild‐steel) under the assumption of bi‐axial strain. In a special case, two classes of rotationally continuous slip‐line fields are shown to exist on curved principal surfaces. The first of these reduces to Hill's equiangular net under plane strain, further special cases of this field being the circular‐centred‐fan and the rectangual‐net. A second class of special solutions consists, again under plane‐strain, of two orthogonally intersecting families of logarithmic spirals. A slip‐line field that occurs in the drawing of a circular cup obeys this condition, as it applies to a curved principal surface. The general condition for continuity of rotation‐rate within a slip‐line net, located on a curved principal surface, is then derived and it is shown that Prandtl's solution to the plane‐strain compression problem obeys this general condition; except in a pair of thin layers adjacent to the platens.