bluuebunny/crossref_metadata_2025_split huggingface dataset:
The discrete null space method for the energy consistent integration of constrained mechanical systems. Part II: multibody dynamics
Authors: Betsch Peter , Leyendecker Sigrid 
Published: January 2006

AbstractIn the present work, rigid bodies and multibody systems are regarded as constrained mechanical systems at the outset. The constraints may be divided into two classes: (i) internal constraints which are intimately connected with the assumption of rigidity of the bodies, and (ii) external constraints related to the presence of joints in a multibody framework. Concerning external constraints lower kinematic pairs such as revolute and prismatic pairs are treated in detail. Both internal and external constraints are dealt with on an equal footing. The present approach thus circumvents the use of rotational variables throughout the whole time discretization. After the discretization has been completed a size‐reduction of the discrete system is performed by eliminating the constraint forces. In the wake of the size‐reduction potential conditioning problems are eliminated. The newly proposed methodology facilitates the design of energy–momentum methods for multibody dynamics. The numerical examples deal with a gyro top, cylindrical and planar pairs and a six‐body linkage. Copyright © 2006 John Wiley & Sons, Ltd.
Parallel asynchronous particle swarm optimization
Authors: Koh Byung‐Il , George Alan D. , Haftka Raphael T. , Fregly Benjamin J. 
Published: January 2006

AbstractThe high computational cost of complex engineering optimization problems has motivated the development of parallel optimization algorithms. A recent example is the parallel particle swarm optimization (PSO) algorithm, which is valuable due to its global search capabilities. Unfortunately, because existing parallel implementations are synchronous (PSPSO), they do not make efficient use of computational resources when a load imbalance exists. In this study, we introduce a parallel asynchronous PSO (PAPSO) algorithm to enhance computational efficiency. The performance of the PAPSO algorithm was compared to that of a PSPSO algorithm in homogeneous and heterogeneous computing environments for small‐ to medium‐scale analytical test problems and a medium‐scale biomechanical test problem. For all problems, the robustness and convergence rate of PAPSO were comparable to those of PSPSO. However, the parallel performance of PAPSO was significantly better than that of PSPSO for heterogeneous computing environments or heterogeneous computational tasks. For example, PAPSO was 3.5 times faster than was PSPSO for the biomechanical test problem executed on a heterogeneous cluster with 20 processors. Overall, PAPSO exhibits excellent parallel performance when a large number of processors (more than about 15) is utilized and either (1) heterogeneity exists in the computational task or environment, or (2) the computation‐to‐communication time ratio is relatively small. Copyright © 2006 John Wiley & Sons, Ltd.
Imperfection sensitivity due to coupled local instability: a non‐convex QP solution algorithm
Authors: Casciaro Raffaele , Mancusi Giovanna 
Published: January 2006

AbstractThe paper deals with the collapse safety of slender elastic structures subjected to local buckling interaction. Using Koiter's asymptotic approach, the mechanical problem is reduced to the search for all the local minima of an indefinite quadratic form over the unit simplex. An efficient recursive branch‐and‐cut algorithm is proposed for solving this non‐convex QP problem, allowing a numerical procedure providing statistical information about the collapse load for a given distribution of random imperfections to be set up. Copyright © 2006 John Wiley & Sons, Ltd.
Time‐parallel implicit integrators for the near‐real‐time prediction of linear structural dynamic responses
Authors: Farhat Charbel , Cortial Julien , Dastillung Climène , Bavestrello Henri 
Published: January 2006

AbstractThe time‐parallel framework for constructing parallel implicit time‐integration algorithms (PITA) is revisited in the specific context of linear structural dynamics and near‐real‐time computing. The concepts of decomposing the time‐domain in time‐slices whose boundaries define a coarse time‐grid, generating iteratively seed values of the solution on this coarse time‐grid, and using them to time‐advance the solution in each time‐slice with embarrassingly parallel time‐integrations are maintained. However, the Newton‐based corrections of the seed values, which so far have been computed in PITA and related approaches on the coarse time‐grid, are eliminated to avoid artificial resonance and numerical instability. Instead, the jumps of the solution on the coarse time‐grid are addressed by a projector which makes their propagation on the fine time‐grid computationally feasible while avoiding artificial resonance and numerical instability. The new PITA framework is demonstrated for a complex structural dynamics problem from the aircraft industry. Its potential for near‐real‐time computing is also highlighted with the solution of a relatively small‐scale problem on a Linux cluster system. Copyright © 2006 John Wiley & Sons, Ltd.
Advanced materials for 193 nm immersion lithography
Authors: Kusumoto Shiro , Shima Motoyuki , Wang Yong , Shimokawa Tsutomu , Sato Hozumi , Hieda Katsuhiko 
Published: January 2006

AbstractRecently 193 nm immersion lithography is considered the most promising next generation technology which will enable a 45 nm and below node device to be manufactured. This will lead to not only depth of focus (DOF) enlargement, but immersion lithography enables the use of a hyper numerical aperture (NA) larger than 1.0 and achieve higher resolution capability. For 193 nm lithography, water is an ideal immersion fluid, providing suitable refractive index and transmission properties. Furthermore the higher refractive index fluid is expected to provide a potential extension of optical lithography to the 32 nm node. This paper describes the critical issues of the water immersion lithography process, such as photoresist component leaching into water, defectivity etc. Leaching materials were analyzed by liquid chromatography‐mass spectrometry (LC‐MS) and were found to be composed of the photoacid generator (PAG) and its decomposed chemicals. The leaching amount is in the order of 10−12 mol/cm2 with a normal 193 nm photoresist. An other issue to be studied is the water‐mark defect caused by small waters droplets left on the exposed wafer. These undesirable phenomenons could be prevented by applying a topcoat material onto the photoresist film. Material design for the topcoat material and its physical and lithographic properties are discussed in detail. Development of a high refractive index fluid is also discussed in this paper. A promising high refractive index fluid HIL‐001 was developed which has a higher refractive index (n = 1.64) than water and high transparency (98%/mm) at 193 nm wavelength. Immersion exposure experiments using high refractive index fluid with and without topcoat material was carried out and 32 nm L/S imaging capability was demonstrated by using a two‐beam interferometric exposure tool. Copyright © 2006 John Wiley & Sons, Ltd.
Molecular characterisation of a prenatally diagnosed 5q15q21.3 deletion and review of the literature
Authors: Malan Valérie , Martinovic Jelena , Sanlaville Damien , Caillat Stéphanie , Perrier Waill Marie‐Christine , Maurin Ganne Marie‐Laure , Tantau Julia , Attie‐Bitach Tania , Vekemans Michel , Morichon‐Delvallez Nicole 
Published: January 2006

AbstractBackgroundUltrasound examination performed on a 32‐year old woman at 30 weeks' gestation showed the presence of fetal malformations. Amniocentesis was performed.Methods and ResultsCytogenetic analysis of cultured amniocytes revealed an interstitial deletion of the long arm of chromosome 5. Molecular studies confirmed that the deletion included the 5q15‐21.3 region and was 14 Mb in size. Therefore, the karyotype was: 46,XY,del(5)(q15q21.3). In addition, analysis of polymorphic DNA markers showed that the deletion was of paternal origin.ConclusionsThe pregnancy was terminated at 34 weeks' gestation. At autopsy, the fetus displayed dysmorphic features, thin limbs and renal abnormalities. The clinical findings observed in the fetus as well as in 20 cases reported previously allowed us to further delineate the phenotype of such interstitial 5q15q21.3 deletions. Copyright © 2006 John Wiley & Sons, Ltd.
Sensitivity analysis and external adjustment for unmeasured confounders in epidemiologic database studies of therapeutics
Authors: Schneeweiss Sebastian 
Published: January 2006

AbstractBackgroundLarge health care utilization databases are frequently used to analyze unintended effects of prescription drugs and biologics. Confounders that require detailed information on clinical parameters, lifestyle, or over‐the‐counter medications are often not measured in such datasets, causing residual confounding bias.ObjectiveThis paper provides a systematic approach to sensitivity analyses to investigate the impact of residual confounding in pharmacoepidemiologic studies that use health care utilization databases.MethodsFour basic approaches to sensitivity analysis were identified: (1) sensitivity analyses based on an array of informed assumptions; (2) analyses to identify the strength of residual confounding that would be necessary to explain an observed drug‐outcome association; (3) external adjustment of a drug‐outcome association given additional information on single binary confounders from survey data using algebraic solutions; (4) external adjustment considering the joint distribution of multiple confounders of any distribution from external sources of information using propensity score calibration.ConclusionSensitivity analyses and external adjustments can improve our understanding of the effects of drugs and biologics in epidemiologic database studies. With the availability of easy‐to‐apply techniques, sensitivity analyses should be used more frequently, substituting qualitative discussions of residual confounding. Copyright © 2006 John Wiley & Sons, Ltd.
An enhanced elastic network model to represent the motions of domain‐swapped proteins
Authors: Song Guang , Jernigan Robert L. 
Published: January 2006

AbstractDomain swapping is a process where two (or more) protein molecules form a dimer (or higher oligomer) by exchanging an identical domain. In this article, based on the observation that domains are rigid and hinge loops are highly flexible, we propose a new Elastic Network Model, domain‐ENM, for domain‐swapped proteins. In this model, the rigidity of domains is taken into account by using a larger spring constant for intradomain contacts. The large‐scale transition of domain swapping is then novelly decomposed into the relative motion between the rigid domains (only 6 degrees of freedom) plus the internal fluctuations of each domain. Consequently, this approach has the potential to produce much more meaningful transition pathways than other simulation approaches that try to find pathways in a search space of large numbers of dimensions. In this article, we also propose a new way to define the overlap measure. Past approaches used an inappropriate comparison of the large‐scale conformation displacement against the computed infinitesimal motions of modes. Here, we propose an infinitesimal version of the large‐scale conformation change and then compare it with the modes of motions. As a result, we obtain much better overlap values. Using this new overlap definition, we are also able for the first time to give a clear, intuitive explanation why “open” forms tend to produce better overlap values than “closed” forms with traditional ENMs. Finally, as an application, we present a simple approach to show how domain‐ENM can be used to generated transition pathways for domain‐swapped proteins. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Evaluation of different biological data and computational classification methods for use in protein interaction prediction
Authors: Qi Yanjun , Bar‐Joseph Ziv , Klein‐Seetharaman Judith 
Published: January 2006

AbstractProtein–protein interactions play a key role in many biological systems. High‐throughput methods can directly detect the set of interacting proteins in yeast, but the results are often incomplete and exhibit high false‐positive and false‐negative rates. Recently, many different research groups independently suggested using supervised learning methods to integrate direct and indirect biological data sources for the protein interaction prediction task. However, the data sources, approaches, and implementations varied. Furthermore, the protein interaction prediction task itself can be subdivided into prediction of (1) physical interaction, (2) co‐complex relationship, and (3) pathway co‐membership. To investigate systematically the utility of different data sources and the way the data is encoded as features for predicting each of these types of protein interactions, we assembled a large set of biological features and varied their encoding for use in each of the three prediction tasks. Six different classifiers were used to assess the accuracy in predicting interactions, Random Forest (RF), RF similarity‐based k‐Nearest‐Neighbor, Naïve Bayes, Decision Tree, Logistic Regression, and Support Vector Machine. For all classifiers, the three prediction tasks had different success rates, and co‐complex prediction appears to be an easier task than the other two. Independently of prediction task, however, the RF classifier consistently ranked as one of the top two classifiers for all combinations of feature sets. Therefore, we used this classifier to study the importance of different biological datasets. First, we used the splitting function of the RF tree structure, the Gini index, to estimate feature importance. Second, we determined classification accuracy when only the top‐ranking features were used as an input in the classifier. We find that the importance of different features depends on the specific prediction task and the way they are encoded. Strikingly, gene expression is consistently the most important feature for all three prediction tasks, while the protein interactions identified using the yeast‐2‐hybrid system were not among the top‐ranking features under any condition. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Correlation between the electric and conical‐uniaxial ferromagnetic phase transitions in the metallic spinel CuCr2Se4
Authors: Tokiwa N. , Hidaka M. 
Published: January 2006

AbstractThe electric resistivity in CuCr2Se4 has been measured below room temperature under applied magnetic fields (H ) up to 1.0 T in the metallic ferromagnetic phase, in addition to magnetization measurements. The temperature dependence of the electric resistivity (ρ ) shows an electric phase transition at about 65 K (T e) and a different linearity of ρ –T curves in the regions of T < 60 K and T > 100 K. Both regions are metallic, while in the intermediate region 60 K < T < 100 K a semiconductor‐like state occurs. The T e transition temperature slightly decreases from about 65 K to 59 K on increasing the magnetic field. The magnetoresistance (MR) shows a crossover to a positive value or a negative one below and above T e, though the MR–T curves depend on the magnetic fields. The magnetization curves deviate from a tentative Brillouin function at about 65 K (H = 50 G), 200 K (H = 400 G), 230 K (H = 800 G) and 170 K (H = 0.2 T), and a weak modulation at about 65 K to 70 K (T 1) under the magnetic fields. It is suspected that the magnetic transition occurring at T 1 is from a conical to a uniaxial ferromagnetic state on heating. The T e electric transition results from a slight change of a Zener band situation, which is induced by a spin‐dependent double‐exchange interaction at T 1. The intermediate semiconductor‐like state is between two different Zener band situations in the conical and uniaxial ferromagnetic states, which are both metallic. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Competition between the intratube curvature and intertube coupling effects in carbon nanotube bundles
Authors: Shao L. B. , Ding J. W. , Xing D. Y. 
Published: January 2006

AbstractTaking into account the intratube curvature and intertube coupling effects, we develop a tight‐binding approach to study the electronic structure in carbon nanotube bundles. It is found that the curvature develops a small energy gap in the electronic density of states of a zigzag nanotube, while the intertube coupling decreases the gap width. The competition between the two factors may lead to creation or destruction of the energy gap in the carbon nanotube bundles. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Lagrange‐mesh method for quantum‐mechanical problems
Authors: Baye Daniel 
Published: January 2006

AbstractThe Lagrange‐mesh method is an approximate variational calculation with the simplicity of a mesh calculation because of the use of a consistent Gauss quadrature. The method can be used for quantum‐mechanical bound‐state and scattering problems with local and non‐local interactions or with a semi‐relativistic kinetic energy, and for solving the time‐dependent Schrödinger equation. No analytical evaluation of matrix elements is needed. The accuracy is exponential in the number of mesh points and is not significantly reduced with respect to the corresponding variational calculations. Lagrange functions can be based on classical or non‐classical orthogonal polynomials as well as on trigonometric and sinc functions, as described in examples. Some singularities can be handled with a regularization technique. Applications to three‐body systems are discussed for various choices of coordinate systems. The helium atom and hydrogen molecular ion are presented as examples. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Implementation of linear‐scaling plane wave density functional theory on parallel computers
Authors: Skylaris Chris‐Kriton , Haynes Peter D. , Mostofi Arash A. , Payne Mike C. 
Published: January 2006

AbstractWe describe the algorithms we have developed for linear‐scaling plane wave density functional calculations on parallel computers as implemented in the onetep program. We outline how onetep achieves plane wave accuracy with a computational cost which increases only linearly with the number of atoms by optimising directly the single‐particle density matrix expressed in a psinc basis set. We describe in detail the novel algorithms we have developed for computing with the psinc basis set the quantities needed in the evaluation and optimisation of the total energy within our approach. For our parallel computations we use the general Message Passing Interface (MPI) library of subroutines to exchange data between processors. Accordingly, we have developed efficient schemes for distributing data and computational load to processors in a balanced manner. We describe these schemes in detail and in relation to our algorithms for computations with a psinc basis. Results of tests on different materials show that onetep is an efficient parallel code that should be able to take advantage of a wide range of parallel computer architectures. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Car–Parrinello molecular dynamics using real space wavefunctions
Authors: Schmid R. , Tafipolsky M. , König P. H. , Köstler H. 
Published: January 2006

AbstractA Car–Parrinello molecular dynamics implementation using real space discretized wavefunctions on equidistant Cartesian grids is presented. By using numerically discretized Laplace operators of higher order for the evaluation of the electronic kinetic energy as well as for the Poisson equation the total energy expression can be evaluated purely with local operations. Details of our implementation of microcanonical and canonical Car–Parrinello joint dynamics of nuclei and wavefunctions are described. For energy conserving molecular dynamics the exact partial derivatives of the energy expression with respect to the numerical wavefunctions must be available. This aspect is discussed for all contributions to the electronic energy. The crucial point is the efficient iterative solution of the Poisson equation. It is shown that energy conserving dynamics with real space wavefunctions is possible. Our object oriented code is fully parallelized and efficient also for the investigation of systems of realistic size. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Excitonic states of ZnSe detected by microwave‐modulated reflectivity
Authors: Wolverson D. , Smith L. C. , Bingham S. J. , Davies J. J. 
Published: January 2006

AbstractSignals ascribed to the 1s, 2s and 3s exciton states of epitaxial ZnSe are observed in experiments aimed at detecting the coherent spin‐flip of conduction band electrons under simultaneous microwave and laser excitation of a ZnSe sample in a magnetic field. The origin of these unexpected signals is investigated, since they must arise from non‐idealities in the experiment which could represent a limiting factor in its application to semiconductor heterostructures. It is shown that both magnetic circular dichroism and magnetic linear dichroism effects could lead to the observation of such signals. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Cyclotron resonance in II–VI semiconductors at THz region
Authors: Imanaka Y. , Takamasu T. , Takehana K. , Oshikiri M. , Kido G. , Nojiri H. , Matsuda Y. H. , Arimoto H. , Takeyama S. , Miura N. , Karczewski G. , Wojtowicz T. , Kossut J. 
Published: January 2006

AbstractCyclotron resonance experiments for various II–VI semiconductors (n‐ZnO, n‐ZnS, n‐ZnSe, n‐CdS, n‐CdSe, n‐CdTe) have been performed at ultra‐high magnetic fields beyond 100 T. Cyclotron resonance and impurity related resonance are observed definitely with the use of THz radiation sources, and the magnetic field dependence of effective mass is obtained at a wide range of a THz region in n‐type CdTe. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
EPR of Nd3+ in congruent and nearly stoichiometric lithium niobate
Authors: Malovichko G. , Grachev V. , Okulov S. , Kokanyan E. , Henecker F. , Hofstaetter A. , Schirmer O. 
Published: January 2006

AbstractThe cover picture refers to the article by Galina Malovichko et al. which has been selected as Editor's Choice for this issue [1]. The lower part of the figure shows a section of the angular dependence of the EPR spectra in the xy‐plane for nearly stoichiometric LiNbO3:Nd3+. The solid lines correspond to non‐magnetic neodymium isotopes of axial C3 symmetry (green) and low C1 symmetry (purple and blue), respectively; the symbols represent experimental data. The upper part of the figure shows possible structures of the nearest surrounding for the C3 and C1 centers and their correspondence to the observed line positions.The first author Galina Malovichko is Associate Professor in the Physics Department at the Montana State University, USA. Her scientific activity is devoted to experimental condensed matter physics, particularly to the study of structures of extrinsic, intrinsic and radiation defects and their influence on crystal prop‐erties. Her group is involved in the characterization of various materials and optimization of their parameters for advanced ap‐plications.
Charge‐carrier mobilities in disordered semiconducting polymers: effects of carrier density and electric field
Authors: Meisel K.D. , Pasveer W.F. , Cottaar J. , Tanase C. , Coehoorn R. , Bobbert P.A. , Blom P.W.M. , de Leeuw D.M. , Michels M.A.J. 
Published: January 2006

AbstractThe cover picture of this issue of physica status solidi (c) has been taken from the article [1].