bluuebunny/crossref_metadata_2025 huggingface dataset:
High‐resolution FMRI at 1.5T using balanced SSFP
Authors: Miller Karla L. , Smith Stephen M. , Jezzard Peter , Pauly John M.
Published: December 2005

The resolution in conventional BOLD FMRI is considerably lower than can be achieved with other MRI methods, and is insufficient for many important applications. One major difficulty in robustly improving spatial resolution is the poor image quality in BOLD FMRI, which suffers from distortions, blurring, and signal dropout. This work considers the potential for increased resolution with a new FMRI method based on balanced SSFP. This method establishes a blood oxygenation sensitive steady‐state (BOSS) signal, in which the frequency sensitivity of balanced SSFP is used to detect the frequency shift of deoxyhemoglobin. BOSS FMRI is highly SNR efficient and does not suffer from image distortions or signal dropout, making this method an excellent candidate for high‐resolution FMRI. This study presents the first demonstration of high‐resolution BOSS FMRI, using an efficient 3D stack‐of‐segmented EPI readout and combined acquisition at multiple center frequencies. BOSS FMRI is shown to enable high‐resolution FMRI data (1 × 1 × 2 mm3) in both visual and motor systems using standard hardware at 1.5 T. Currently, the major limitation of BOSS FMRI is its sensitivity to temporal and spatial field drift. Magn Reson Med, 2006. © 2005 Wiley‐Liss, Inc.
Investigating brain metabolism at high fields using localized 13C NMR spectroscopy without 1H decoupling
Authors: Deelchand Dinesh Kumar , Uğurbil Kâmil , Henry Pierre‐Gilles
Published: December 2005

Most in vivo 13C NMR spectroscopy studies in the brain have been performed using 1H decoupling during acquisition. Decoupling imposes significant constraints on the experimental setup (particularly for human studies at high magnetic field) in order to stay within safety limits for power deposition. We show here that incorporation of the 13C label from 13C‐labeled glucose into brain amino acids can be monitored accurately using localized 13C NMR spectroscopy without the application of 1H decoupling. Using LCModel quantification with prior knowledge of one‐bond and multiple‐bond JCH coupling constants, the uncertainty on metabolites concentrations was only 35% to 91% higher (depending on the carbon resonance of interest) in undecoupled spectra compared to decoupled spectra in the rat brain at 9.4 Tesla. Although less sensitive, 13C NMR without decoupling dramatically reduces experimental constraints on coil setup and pulse sequence design required to keep power deposition within safety guidelines. This opens the prospect of safely measuring 13C NMR spectra in humans at varied brain locations (not only the occipital lobe) and at very high magnetic fields above 4 Tesla. Magn Reson Med, 2006. © 2005 Wiley‐Liss, Inc.
Influence of vascular filling and perfusion on BOLD contrast during reactive hyperemia in human skeletal muscle
Authors: Duteil S. , Wary C. , Raynaud J. S. , Lebon V. , Lesage D. , Leroy‐Willig A. , Carlier P. G.
Published: December 2005

Mechanisms generating BOLD contrast are complex and depend on parameters that are prone to large variations, in particular in skeletal muscle. Here, we simultaneously measured perfusion by ASL, and BOLD response in the calf muscle of 6 healthy volunteers during post‐ischemic reactive hyperemia. We tested whether the relation between the two was altered for varying degrees of leg vascular replenishment induced by prior positioning of the leg at different heights relative to the heart. We found that the BOLD response depended on perfusion, but also on the degree of repletion of leg blood vessels. We conclude that simultaneous determination of perfusion by ASL is important to identify the mechanisms underlying BOLD contrast in the skeletal muscle. Magn Reson Med, 2006. © 2005 Wiley‐Liss, Inc.
Generalized pointwise bias error bounds for response surface approximations
Authors: Goel Tushar , Haftka Raphael T. , Papila Melih , Shyy Wei
Published: December 2005

This paper proposes a generalized pointwise bias error bounds estimation method for polynomial‐based response surface approximations when bias errors are substantial. A relaxation parameter is introduced to account for inconsistencies between the data and the assumed true model. The method is demonstrated with a polynomial example where the model is a quadratic polynomial while the true function is assumed to be cubic polynomial. The effect of relaxation parameter is studied. It is demonstrated that when bias errors dominate, the bias error bounds characterize the actual error field better than the standard error. The bias error bound estimates also help to identify regions in the design space where the accuracy of the response surface approximations is inadequate. It is demonstrated that this information can be utilized for adaptive sampling in order to improve accuracy in such regions. Copyright © 2005 John Wiley & Sons, Ltd.
Local maximum‐entropy approximation schemes: a seamless bridge between finite elements and meshfree methods
Authors: Arroyo M. , Ortiz M.
Published: December 2005

We present a one‐parameter family of approximation schemes, which we refer to as local maximum‐entropy approximation schemes, that bridges continuously two important limits: Delaunay triangulation and maximum‐entropy (max‐ent) statistical inference. Local max‐ent approximation schemes represent a compromise—in the sense of Pareto optimality—between the competing objectives of unbiased statistical inference from the nodal data and the definition of local shape functions of least width. Local max‐ent approximation schemes are entirely defined by the node set and the domain of analysis, and the shape functions are positive, interpolate affine functions exactly, and have a weak Kronecker‐delta property at the boundary. Local max‐ent approximation may be regarded as a regularization, or thermalization, of Delaunay triangulation which effectively resolves the degenerate cases resulting from the lack or uniqueness of the triangulation. Local max‐ent approximation schemes can be taken as a convenient basis for the numerical solution of PDEs in the style of meshfree Galerkin methods. In test cases characterized by smooth solutions we find that the accuracy of local max‐ent approximation schemes is vastly superior to that of finite elements. Copyright © 2005 John Wiley & Sons, Ltd.
Theory and numerics for finite deformation fracture modelling using strong discontinuities
Authors: Fagerström Martin , Larsson Ragnar
Published: December 2005

A general finite element approach for the modelling of fracture is presented for the geometrically non‐linear case. The kinematical representation is based on a strong discontinuity formulation in line with the concept of partition of unity for finite elements. Thus, the deformation map is defined in terms of one continuous and one discontinuous portion, considered as mutually independent, giving rise to a weak formulation of the equilibrium consisting of two coupled equations. In addition, two different fracture criteria are considered. Firstly, a principle stress criterion in terms of the material Mandel stress in conjunction with a material cohesive zone law, relating the cohesive Mandel traction to a material displacement ‘jump’ associated with the direct discontinuity. Secondly, a criterion of Griffith type is formulated in terms of the material‐crack‐driving force (MCDF) with the crack propagation direction determined by the direction of the force, corresponding to the direction of maximum energy release. Apart from the material modelling, the numerical treatment and aspects of computational implementation of the proposed approach is also thoroughly discussed and the paper is concluded with a few numerical examples illustrating the capabilities of the proposed approach and the connection between the two fracture criteria. Copyright © 2005 John Wiley & Sons, Ltd.
Continued fraction absorbing boundary conditions for convex polygonal domains
Authors: Guddati Murthy N. , Lim Keng‐Wit
Published: December 2005

Continued fraction absorbing boundary conditions (CFABCs) are highly effective boundary conditions for modelling wave absorption into unbounded domains. They are based on rational approximation of the exact dispersion relationship and were originally developed for straight computational boundaries. In this paper, CFABCs are extended to the more general case of polygonal computational domains. The key to the current development is the surprising link found between the CFABCs and the complex co‐ordinate stretching of perfectly matched layers (PMLs). This link facilitates the extension of CFABCs to oblique corners and, thus, to polygonal domains. It is shown that the proposed CFABCs are easy to implement, expected to perform better than PMLs, and are effective for general polygonal computational domains. In addition to the derivation of CFABCs, a novel explicit time‐stepping scheme is developed for efficient numerical implementation. Numerical examples presented in the paper illustrate that effective absorption is attained with a negligible increase in the computational cost for the interior domain. Although this paper focuses on wave propagation, its theoretical development can be easily extended to the more general class of problems where the governing differential equation is second order in space with constant coefficients. Copyright © 2005 John Wiley & Sons, Ltd.
Maximum likelihood estimation of stochastic chaos representations from experimental data
Authors: Desceliers Christophe , Ghanem Roger , Soize Christian
Published: December 2005

This paper deals with the identification of probabilistic models of the random coefficients in stochastic boundary value problems (SBVP). The data used in the identification correspond to measurements of the displacement field along the boundary of domains subjected to specified external forcing. Starting with a particular mathematical model for the mechanical behaviour of the specimen, the unknown field to be identified is projected on an adapted functional basis such as that provided by a finite element discretization. For each set of measurements of the displacement field along the boundary, an inverse problem is formulated to calculate the corresponding optimal realization of the coefficients of the unknown random field on the adapted basis. Realizations of these coefficients are then used, in conjunction with the maximum likelihood principle, to set‐up and solve an optimization problem for the estimation of the coefficients in a polynomial chaos representation of the parameters of the SBVP. Copyright © 2005 John Wiley & Sons, Ltd.
An explicit material point finite element method for hyper‐velocity impact
Authors: Zhang X. , Sze K. Y. , Ma S.
Published: December 2005

In this paper, an explicit material point finite element (FE) method is proposed and a computer code EMPFE‐3D is developed for simulating hyper‐velocity impact. The material domain is discretized by a mesh of finite elements. The momentum equations are solved on a predefined computational grid (like the material point method) in the large deformation zone, and on the FE mesh (like the traditional FE method) elsewhere. The grid may be fixed in space or moved in a predefined way. The nodes covered by the grid are treated as material particles, and the remaining nodes are treated as FE nodes. The proposed method yields the same results as the traditional FE method if the grid vanishes. On the other hand, it yields the same results as the material point method if the grid covers the entire material domain at all time steps. The method combines the advantages of Eulerian and Lagrangian descriptions of motion while eliminates their drawbacks due to element entanglement and numerical dissipation. The method is computationally efficient and can be easily implemented in an existing explicit FE code like DYNA3D. Copyright © 2005 John Wiley & Sons, Ltd.
Coupled mechanics and finite element for non‐linear laminated piezoelectric shallow shells undergoing large displacements and rotations
Authors: Varelis Dimitris , Saravanos Dimitris A.
Published: December 2005

A theoretical framework is presented for analysing the coupled non‐linear response of shallow doubly curved adaptive laminated piezoelectric shells undergoing large displacements and rotations. The formulated mechanics incorporate coupling between in‐plane and flexural stiffness terms due to geometric curvature, coupling between mechanical and electric fields, and encompass geometric non‐linearity effects due to large displacements and rotations. The governing equations are formulated explicitly in orthogonal curvilinear co‐ordinates and are combined with the kinematic assumptions of a mixed‐field shear‐layerwise shell laminate theory. Based on the above formulation, a finite element methodology together with an incremental‐iterative technique, based on Newton–Raphson method is formulated. An eight‐node coupled non‐linear shell element is also developed. Various evaluation cases on laminated curved beams and cylindrical panels illustrate the capability of the shell finite element to predict the complex non‐linear behaviour of active shell structures including buckling, which is not captured by linear shell models. The numerical results also show the inherent capability of piezoelectric shell structures to actively induce large displacements through piezoelectric actuators, by jumping between multiple equilibrium states. Copyright © 2005 John Wiley & Sons, Ltd.
Design sensitivity analysis in large deformation elasto‐plastic and elasto‐viscoplastic problems
Authors: Kowalczyk Piotr
Published: December 2005

Implicit time integration algorithm derived by Simo for his large‐deformation elasto‐plastic constitutive model is generalized, for the case of isotropy and associative flow rule, towards viscoplastic material behaviour and consistently differentiated with respect to its input parameters. Combining it with the general formulation of design sensitivity analysis (DSA) for non‐linear finite element transient equilibrium problem, we come at a numerically efficient, closed‐form finite element formulation of DSA for large deformation elasto‐plastic and elasto‐viscoplastic problems, with various types of design variables (material constants, shape parameters). The paper handles several specific issues, like the use of a non‐algorithmic coefficient matrix or sensitivity discontinuities at points of instantaneous structural stiffness change. Computational examples demonstrate abilities of the formulation and quality of results. Copyright © 2005 John Wiley & Sons, Ltd.
Modelling inter‐yarn friction in woven fabric armour
Authors: Zeng X. S. , Tan V. B. C. , Shim V. P. W.
Published: December 2005

The effects of inter‐yarn friction on the ballistic performance of woven fabric armour are investigated in this paper. Frictional sliding between yarns is implemented in a computational model of the fabric that takes the form of a network. Yarn crimp and its viscoelastic properties are taken into account. Ballistic experiments are performed to verify the predictions of the model. Parametric studies show that the ballistic response of woven fabric is very sensitive to yarn friction when the friction coefficient is low but insensitive beyond a certain level. The results also show that very high inter‐yarn friction can lead to premature yarn rupture, thus reducing the ability of the fabric to absorb impact energy. Copyright © 2005 John Wiley & Sons, Ltd.
Efficient algorithm for edge cracked geometries
Authors: Englund J.
Published: December 2005

The stress field in a finite, edge cracked specimen under load is computed using algorithms based on two slightly different integral equations of the second kind. These integral equations are obtained through left regularizations of a first kind integral equation. In numerical experiments it is demonstrated that the stress field can be accurately computed. Highly accurate stress intensity factors and T‐stresses are presented for several setups and extensive comparisons with results from the literature are made. For simple geometries the algorithms presented here achieve relative errors of less than 10−10. It is also shown that the present algorithms can accurately handle both geometries with arbitrarily shaped edge cracks and geometries containing several hundred edge cracks. All computations were performed on an ordinary workstation. Copyright © 2005 John Wiley & Sons, Ltd.
Unreliability of the dot probe task
Authors: Schmukle Stefan C.
Published: December 2005

The dot probe task is a widely used measure of attention allocation to threatening stimuli. The present two studies examine the reliability of different versions of this task using words as well as pictures as stimulus material. Estimates of both internal consistency and retest reliability over one week lead to the conclusion that the dot probe task is a completely unreliable measure of attentional allocation in non‐clinical samples. This unreliability may explain the inconsistent findings for the dot probe task as reported in the literature. Copyright © 2005 John Wiley & Sons, Ltd.
Personality‐relevant attribute‐nouns: a taxonomic study in the Italian language
Authors: Di Blas Lisa
Published: December 2005

The present study was based on psycholexical approach premises and explored the structure of a large set of personality attribute‐nouns in the Italian language. Content inspection (based on Big Five categories) and quantitative indices were used to interpret the attribute‐noun dimensions. Results showed (a) a stable three‐component solution which replicated the Big Three; (b) an unstable five‐factor solution which did not reproduce the Big Five; (c) an unstable six‐factor solution which represented deviations from the Big Five system, which have been found in most psycholexical studies conducted in the Italian language. The six lexical dimensions were interpreted as follows: Conscientiousness (replicating the III of the Big Five); Self‐Assurance (combining the Big Five I assertiveness and IV fearfulness subcategories); Sociability (defined by the Big Five I sociableness and I impulse expression subcategories); Placidity (combining the Big Five II peacefulness, II unassertiveness, and IV irritableness subcategories); Honesty and Humility (comprising the Big Five II modesty and II helpfulness subcategories plus integrity values); Cleverness and Sophistication (defined by the Big Five V subcategories). The conclusion was that personality word organisation in the Italian language reflects the psycholexical Big Three and Big Six, but not the Big Five. Copyright © 2005 John Wiley & Sons, Ltd.
Improvement in mechanical properties of three‐dimensional printing parts made from natural polymers reinforced by acrylate resin for biomedical applications: a double infiltration approach
Authors: Suwanprateeb Jintamai
Published: December 2005

This study demonstrates that a double infiltration technique, when compared to traditional single infiltration, can increase the mechanical properties of natural polymers fabricated by three‐dimensional printing using a water‐based binder. Double infiltration decreases the water absorption and amount of water‐soluble matter, and significantly increases flexural modulus and strength in wet conditions compared to single infiltration. These improvements can be related to the greater remaining load‐bearing area and lower degree of plasticization of the structure. However, no improvements over single infiltration were observed for testing in dry conditions. Copyright © 2006 Society of Chemical Industry
Permafrost creep within a recently deglaciated glacier forefield: Muragl, Swiss Alps
Authors: Kääb A. , Kneisel C.
Published: December 2005

Photogrammetric measurements of surface movement, 1981–94, on the Muragl glacier forefield (Swiss Alps) are compared to direct current resistivity surveys for the same area. At three locations isolated patches of frozen sediments were inferred, each about 10,000–20,000 m2 in area. These were deforming at surface velocities of up to 50 cm per year. The locations where creep was observed coincide well with areas where two‐dimensional (2D) resistivity surveys suggest ice is present within the ground. Copyright © 2005 John Wiley & Sons, Ltd.
Crystal structure of glyceraldehyde‐3‐phosphate dehydrogenase from Plasmodium falciparum at 2.25 Å resolution reveals intriguing extra electron density in the active site
Authors: Robien Mark A. , Bosch Jürgen , Buckner Frederick S. , Van Voorhis Wesley C. E. , Worthey Elizabeth A. , Myler Peter , Mehlin Christopher , Boni Erica E. , Kalyuzhniy Oleksandr , Anderson Lori , Lauricella Angela , Gulde Stacy , Luft Joseph R. , DeTitta George , Caruthers Jonathan M. , Hodgson Keith O. , Soltis Michael , Zucker Frank , Verlinde Christophe L. M. J. , Merritt Ethan A. , Schoenfeld Lori W. , Hol Wim G. J.
Published: December 2005

The crystal structure of D‐glyceraldehyde‐3‐phosphate dehydrogenase (PfGAPDH) from the major malaria parasite Plasmodium falciparum is solved at 2.25 Å resolution. The structure of PfGAPDH is of interest due to the dependence of the malaria parasite in infected human erythrocytes on the glycolytic pathway for its energy generation. Recent evidence suggests that PfGAPDH may also be required for other critical activities such as apical complex formation. The cofactor NAD+ is bound to all four subunits of the tetrameric enzyme displaying excellent electron densities. In addition, in all four subunits a completely unexpected large island of extra electron density in the active site is observed, approaching closely the nicotinamide ribose of the NAD+. This density is most likely the protease inhibitor AEBSF, found in maps from two different crystals. This putative AEBSF molecule is positioned in a crucial location and hence our structure, with expected and unexpected ligands bound, can be of assistance in lead development and design of novel antimalarials. Proteins 2006. © 2005 Wiley‐Liss, Inc.
The histone database: A comprehensive resource for histones and histone fold‐containing proteins
Authors: Mariño‐Ramírez Leonardo , Hsu Benjamin , Baxevanis Andreas D. , Landsman David
Published: December 2005

TheThe Histone Database is a curated and searchable collection of full‐length sequences and structures of histones and nonhistone proteins containing histone‐like folds, compiled from major public databases. Several new histone fold‐containing proteins have been identified, including the huntingtin‐interacting protein HYPM. Additionally, based on the recent crystal structure of the Son of Sevenless protein, an interpretation of the sequence analysis of the histone fold domain is presented. The database contains an updated collection of multiple sequence alignments for the four core histones (H2A, H2B, H3, and H4) and the linker histones (H1/H5) from a total of 975 organisms. The database also contains information on the human histone gene complement and provides links to three‐dimensional structures of histone and histone fold‐containing proteins. The Histone Database is a comprehensive bioinformatics resource for the study of structure and function of histones and histone fold‐containing proteins. The database is available at http://research.nhgri.nih.gov/histones/. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Prediction of protein secondary structure content using amino acid composition and evolutionary information
Authors: Lee Soyoung , Lee Byung‐chul , Kim Dongsup
Published: December 2005

Knowing protein structure and inferring its function from the structure are one of the main issues of computational structural biology, and often the first step is studying protein secondary structure. There have been many attempts to predict protein secondary structure contents. Previous attempts assumed that the content of protein secondary structure can be predicted successfully using the information on the amino acid composition of a protein. Recent methods achieved remarkable prediction accuracy by using the expanded composition information. The overall average error of the most successful method is 3.4%. Here, we demonstrate that even if we only use the simple amino acid composition information alone, it is possible to improve the prediction accuracy significantly if the evolutionary information is included. The idea is motivated by the observation that evolutionarily related proteins share the similar structure. After calculating the homolog‐averaged amino acid composition of a protein, which can be easily obtained from the multiple sequence alignment by running PSI‐BLAST, those 20 numbers are learned by a multiple linear regression, an artificial neural network and a support vector regression. The overall average error of method by a support vector regression is 3.3%. It is remarkable that we obtain the comparable accuracy without utilizing the expanded composition information such as pair‐coupled amino acid composition. This work again demonstrates that the amino acid composition is a fundamental characteristic of a protein. It is anticipated that our novel idea can be applied to many areas of protein bioinformatics where the amino acid composition information is utilized, such as subcellular localization prediction, enzyme subclass prediction, domain boundary prediction, signal sequence prediction, and prediction of unfolded segment in a protein sequence, to name a few. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Solution, solid phase and computational structures of apicidin and its backbone‐reduced analogs
Authors: Kranz Michael , Murray Peter John , Taylor Stephen , Upton Richard J. , Clegg William , Elsegood Mark R. J.
Published: December 2005

The recently isolated broad‐spectrum antiparasitic apicidin (1) is one of the few naturally occurring cyclic tetrapeptides (CTP). Depending on the solvent, the backbone of 1 exhibits two γ‐turns (in CH2Cl2) or a β‐turn (in DMSO), differing solely in the rotation of the plane of one of the amide bonds. In the X‐ray crystal structure, the peptidic COs and NHs are on opposite sides of the backbone plane, giving rise to infinite stacks of cyclotetrapeptides connected by three intermolecular hydrogen bonds between the backbones. Conformational searches (Amber force field) on a truncated model system of 1 confirm all three backbone conformations to be low‐energy states. The previously synthesized analogs of 1 containing a reduced amide bond exhibit the same backbone conformation as 1 in DMSO, which is confirmed further by the X‐ray crystal structure of a model system of the desoxy analogs of 1. This similarity helps in explaining why the desoxy analogs retain some of the antiprotozoal activities of apicidin. The backbone‐reduction approach designed to facilitate the cyclization step of the acyclic precursors of the CTPs seems to retain the conformational preferences of the parent peptide backbone. Copyright © 2005 European Peptide Society and John Wiley & Sons, Ltd.
Site‐specific synthesis of Amadori‐modified peptides on solid phase
Authors: Frolov Andrej , Singer David , Hoffmann Ralf
Published: December 2005

Glycation of peptides and proteins is a slow chemical reaction of reducing sugars modifying the amino groups. The first intermediates of this nonenzymatic glycosylation are the Amadori products that can undergo further chemical reactions, finally leading to advanced glycation end products (AGEs). The formation of AGEs was not only linked to aging of tissues and organs in general but also to several diseases such as diabetes mellitus and Alzheimer's disease. Because of the importance of these modifications and their potential use as diagnostic markers, a global postsynthetic approach on solid phase was developed. The peptides were synthesized by Fmoc/tBu‐chemistry, with the lysine residue to be modified being protected with the very acid‐labile methyltrityl group. Incubation of the peptides with D‐glucose in DMF at elevated temperatures resulted in product yields of 35%. Neighboring residues with bulky protecting groups reduced the yields only slightly. The major by‐products were the unmodified peptide and an oxidation product. Whereas the unmodified peptide eluted before the glycated peptide, all other by‐products eluted later in RP‐HPLC, allowing simple purification. Copyright © 2005 European Peptide Society and John Wiley & Sons, Ltd.
Computational study of energies and structures of 2,4,6‐pyrimidinetrione and its anions
Authors: Daskalova Lalka I. , Binev Ivan
Published: December 2005

Energies and structures of 2,4,6‐pyrimidinetrione, its anion, dianion, and trianion have been studied by means of ab initio and density functional computations. According to these studies, the most stable among the molecular tautomers is the triketo form, followed by the 6‐hydroxy tautomer, in full agreement with earlier theoretical results and with experimental data on the tautomeric equilibrium. The deprotonation energy of 1345.24 kJ mol−1 calculated for 2,4,6‐pyrimidinetrione, corresponds to a moderately strong CH acid, in accordance with its experimental pK = 8.4 (solvent dimethylsulfoxide). The calculated structural changes, caused by the molecule → monoanion conversion, are in good agreement with those found experimentally. Energy and structural changes, worked by both anion → dianion and dianion → trianion conversions, have also been computed and discussed. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Density functional study of the interaction of 3‐(ω‐bromoacetyl)coumarin with phosphites
Authors: Nathaniel Rachel , Mineva Tzonka , Nikolova Rositca , Bojilova Anka
Published: December 2005

Structural parameters and vibrational frequencies of 3‐(ω‐bromoacetyl)coumarin, trialkyl and triphenyl phosphites, β‐oxophosphonates, and vinyl phosphates computed at the density functional level of theory (BP86 and B3LYP) are presented. In addition, atomic reactivity indices (fukui functions and total hardness) were obtained to gain a better understanding of the regioselectivity observed in the reaction of 3‐(ω‐bromoacetyl)coumarin with trisubstituted phosphites. An algorithm based on the atomically resolved hardness tensor was employed. Because the atomic fukui function values of the concurrent reactive centers were found to be alike, no conclusion on that basis can be drawn. Relations between total hardnesses of the six products (β‐oxophosphonates and vinyl phosphates) were found to follow the relative energy stability trend in agreement with the maximum hardness principle. The lower‐energy stability of the vinyl phosphates was attributed mostly to the softening/delocalization of the phosphorus atoms. Phosphorous atom in diphenyl‐1‐(2‐oxo‐2H‐chromen‐3‐yl)‐2‐vinylphosphate was found to be the softest one among the other vinyl phosphates. Unlikely, strong localization/hardening of phosphorus atom in diphenyl‐2‐(2‐oxo‐2H‐chromen‐3‐yl)‐2‐oxoethylphosphonate was obtained. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Anharmonic vibrational spectra of acetylacetone
Authors: Matanović I. , Došlić N.
Published: December 2005

The spectroscopic proprieties of two energetically close conformers of acetylacetone have been investigated using density functional methods. The calculated anharmonic frequencies are in very satisfactory agreement with experimental data. The low height of the conversion barrier explains why the signature of both conformers can be found in the vibrational spectrum. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Effect of solvation and intermolecular interactions on the structure and optical properties of PANI oligomers
Authors: Ivanova A. , Madjarova G. , Tadjer A. , Gospodinova N.
Published: December 2005

Polyaniline (PANI) has attracted lasting interest due to its unconventional electronic, optical, and electro‐optical properties. A rigid backbone polymer, PANI exhibits very strong intra‐ and intermolecular interactions governing its overall behavior. The purpose of this study is to investigate theoretically the contribution of the various inter‐ and intramolecular interactions to the process of organization of PANI macromolecules in aqueous environment. The structure and spectral conduct of oligoanilines (tetramers) in different oxidation states have been calculated at the Monte Carlo/Molecular Mechanics (MC/MM) and quantum chemical (QC) semiempirical level. The effect of protonation on the optical properties of partially and fully oxidized oligomers is discussed. The role of intermolecular interactions and the influence of water as a solvent are estimated for a number of hydrated clusters. Computed results and experimental spectra are compared. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Orbital hardness tensors from hydrogen through xenon from Kohn–Sham perturbed orbitals
Authors: Mineva Tzonka , Heine Thomas
Published: December 2005

A systematic study of the orbital hardness tensor and total hardness for atoms ranging from H to Xe is presented. Results are obtained by the use of an efficient algorithm for the computation of density functional‐based orbital reactivity indices exploring the concept of fractional occupations. So, the orbital reactivity indices are defined within the space spanned by the orbital occupation numbers and the Kohn–Sham one‐electron energies. The explicit treatment of degenerate orbitals within the algorithm makes it particularly suitable for resolving orbital hardness elements for atoms. Very good numerical stability toward basis sets and exchange‐correlation functionals has been achieved. The symmetry of the hardness tensor is maintained, even though its elements are computed differently, using either the left side (occupied) or right side (unoccupied) derivative of the one‐particle energies with respect to the orbital occupation numbers. The diagonal elements of the atomic hardness tensors are used as parameters in semi‐empirical and tight‐binding methods, and the total atomic hardnesses could be used to study reactivity indices for very large systems within the electronegativity equalization scheme. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Multipole moments and polarizability of molecular systems with D3h symmetry in orbitally degenerate states
Authors: Ogurtsov I. Ya. , Balan I. , Munteanu G.
Published: December 2005

It was proved, by ab initio studies, that the electronic ground states of the molecules MF3 (MV, Cr, Mn), M3 (MLi, Na, K), and C3H3, with D3h symmetry, have orbital degeneracy. It was shown that in the base functions of these degenerate states, the reduced matrix elements of the in‐plane E′‐type components of the dipole moment, of the quadrupole moments and of the nontotal symmetric components of the (hyper)polarizability are nonzero. The computed values of the dipole and quadrupole moments of the polarizability and hyperpolarizabilities are comparable to those of the molecular systems of the lower than D3h symmetry. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Theory of tip‐dependent imaging of adsorbates in the STM: CO on Cu(111)
Authors: Drakova D. , Nedjalkova M. , Doyen G.
Published: December 2005

The processes of local electron injection or extraction in the scanning tunneling microscopy (STM) and spectroscopy (STS) lead to the creation of short‐lived excited states localized at the electrode surfaces. The dynamic relaxation of the transient negative or positive ion resonances, due to both local and long‐range interactions, is the clue to the understanding of numerous phenomena in STM/STS ranging from the “anomalously” large tip height corrugation amplitudes on clean metal surfaces to the observation of quantum mirages and features in the STS, which are not observed with the help of other surface spectroscopies. Quantum nanodynamics theory (QND) has been applied to calculate the interaction potential of a single CO molecule with the Cu(111) surface, with a transient negative ion resonance formed when an electron is injected from the tip, and the tunneling conductance on the clean and CO covered Cu(111) surface using a clean metal tip Al/Al(111) and a Pt(111) tip with an adsorbed CO molecule at the apex. Within QND and three‐dimensional scattering theory, regarding the tunneling as an excited‐state problem, we provide the explanation of the tip‐dependent STM image of a single CO molecule on Cu(111). The appearance of the CO molecule as an indentation, using a clean metal tip and as a protrusion with a tip terminated by a CO molecule, is understood as a result of tunneling through two competing channels. Tunneling via adsorbate‐induced ion resonances enhances the tunneling conductance. In contrast, tunneling via metal ion resonances only leads to attenuation of the conductance in the presence of the adsorbate. The current in the vicinity of the adsorbed CO molecule is reduced when a clean metal tip is used; i.e., CO appears dark in the STM image, because metal ion resonances on Cu(111) derive from the surface states with image state components coupling to plasmons and are therefore very diffuse. With a CO‐terminated tip, the major current channel is, for symmetry reasons, from the 2π‐derived orbital of the tip CO molecule, via the diffuse 2π‐derived orbital of the CO molecule on the sample, hence adsorbed CO appears bright. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Neural network‐based modeling for semi‐batch and nonisothermal free radical polymerization
Authors: Curteanu Silvia , Petrila Corneliu
Published: December 2005

In this study, neural network models were developed and used to make predictions under different operation conditions: batch and semi‐batch, isothermal and nonisothermal. Different neural networks were projected for conversion and polymerization degrees, but the same networks were used for all tested reaction conditions. Simple architecture neural networks and simple methods of establishing the networks' structure are proposed for polymerization process modeling: feedforward networks with two hidden layers. This approach also shows how an intermediate addition of initiator (semi‐batch operation) or a temperature program consisting of a series of isothermal steps (nonisothermal polymerization) can prevent the dead‐end polymerization and also control some properties of the polystyrene (molecular weight, polydispersity) and reaction time. The semi‐batch operation has a significant influence on the reaction parameters when performed before the gel effect. The neural network modeling methodology presented has general validity and gives a very good representation of the polymerization processes. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Topological characteristics of random triangulated surfaces
Authors: Pippenger Nicholas , Schleich Kristin
Published: December 2005

We consider the topological characteristics of orientable surfaces generated by randomly gluing n triangles together. Our results are most conveniently expressed in terms of a parameter h = n / 2 + χ, where χ is the Euler characteristic of the surface. Simulations and results for similar models suggest that Ex [h] = log(3n) + γ + o(1) and Var [h] = log(3n) + γ ‐ π2 / 6 + o(1). We prove that Ex [h] = log n + O(1) and Var [h] = O(log n). We also derive results concerning a number of other topological invariants and combinatorial characteristics of these random surfaces. © 2005 Wiley Periodicals, Inc. Random Struct. Alg., 2006
A phase transition for avoiding a giant component
Authors: Bohman Tom , Kim Jeong Han
Published: December 2005

Let c be a constant and (e1,f1),(e2,f2),…,(ecn,fcn) be a sequence of ordered pairs of edges from the complete graph Kn chosen uniformly and independently at random. We prove that there exists a constant c2 such that if c > c2, then whp every graph which contains at least one edge from each ordered pair (ei,fi) has a component of size Ω(n), and, if c < c2, then whp there is a graph containing at least one edge from each pair that has no component with more than O(n1−ϵ vertices, where ϵ is a constant that depends on c2 − c. The constant c2 is roughly 0.97677. © 2005 Wiley Periodicals, Inc. Random Struct. Alg., 2006
Random cutting and records in deterministic and random trees
Authors: Janson Svante
Published: December 2005

We study random cutting down of a rooted tree and show that the number of cuts is equal (in distribution) to the number of records in the tree when edges (or vertices) are assigned random labels.

Limit theorems are given for this number, in particular when the tree is a random conditioned Galton–Watson tree. We consider both the distribution when both the tree and the cutting (or labels) are random and the case when we condition on the tree.

The proofs are based on Aldous' theory of the continuum random tree. © 2005 Wiley Periodicals, Inc. Random Struct. Alg., 2006
Data structures with dynamical random transitions
Authors: Dombry C. , Guillotin‐Plantard N. , Pinçon B. , Schott R.
Published: December 2005

We present a (non‐standard) probabilistic analysis of dynamic data structures whose sizes are considered dynamic random walks. The basic operations (insertion, deletion, positive and negative queries, batched insertion, lazy deletion, etc.) are time‐dependent random variables. This model is a (small) step toward the analysis of these structures when the distribution of the set of histories is not uniform. As an illustration, we focus on list structures (linear lists, priority queues, and dictionaries) but the technique is applicable as well to more advanced data structures. © 2005 Wiley Periodicals, Inc. Random Struct. Alg., 2006
Asymptotics in Knuth's parking problem for caravans
Authors: Bertoin Jean , Miermont Grégory
Published: December 2005

We consider a generalized version of Knuth's parking problem, in which caravans consisting of a random number of cars arrive at random on the unit circle. Then each car turns clockwise until it finds a free space to park. Extending a recent work by Chassaing and Louchard Random Struct Algor 21(1) (2002), 76–119, we relate the asymptotics for the sizes of blocks formed by occupied spots with the dynamics of the additive coalescent. According to the behavior of the caravans' size tail distribution, several qualitatively different versions of the eternal additive coalescent are involved. © 2005 Wiley Periodicals, Inc. Random Struct. Alg., 2006
Slow mixing of Glauber dynamics for the hard‐core model on regular bipartite graphs
Authors: Galvin David , Tetali Prasad
Published: December 2005

Let ∑ = (V,E) be a finite, d‐regular bipartite graph. For any λ > 0 let πλ be the probability measure on the independent sets of ∑ in which the set I is chosen with probability proportional to λ|I| (πλ is the hard‐core measure with activity λ on ∑). We study the Glauber dynamics, or single‐site update Markov chain, whose stationary distribution is πλ. We show that when λ is large enough (as a function of d and the expansion of subsets of single‐parity of V) then the convergence to stationarity is exponentially slow in |V(∑)|. In particular, if ∑ is the d‐dimensional hypercube {0,1}d we show that for values of λ tending to 0 as d grows, the convergence to stationarity is exponentially slow in the volume of the cube. The proof combines a conductance argument with combinatorial enumeration methods. © 2005 Wiley Periodicals, Inc. Random Struct. Alg., 2006
Minors in lifts of graphs
Authors: Drier Yotam , Linial Nathan
Published: December 2005

We study here lifts and random lifts of graphs, as defined by Amit and Linial (Combinatorica 22 (2002), 1–18). We consider the Hadwiger number η and the Hajós number σ of ℓ‐lifts of Kn and analyze their extremal as well as their typical values (that is, for random lifts). When ℓ = 2, we show that ${n \over 2} \leq \eta \leq n$, and random lifts achieve the lower bound (as n → ∞). For bigger values of ℓ, we show $\Omega({n \over {\sqrt{\log n}}}) \leq \eta \leq n\sqrt{\ell}$. We do not know how tight these bounds are, and in fact, the most interesting question that remains open is whether it is possible for η to be o(n). When ℓ < O(log n), almost every ℓ‐lift of Kn satisfies η = Θ(n) and for $\Omega(\log{n}) \leq \ell \leq n^{{1 \over 3} - \varepsilon}$, almost surely $\eta = \Theta({n\sqrt{\ell} \over {\sqrt{\log{n}}}})$. For bigger values of ℓ, $\Omega({n\sqrt{\ell} \over {\sqrt{\log{\ell}}}}) \leq \eta \leq n\sqrt{\ell}$ almost always. The Hajós number satisfies $\Omega(\sqrt{n}) \leq \sigma \leq n$, and random lifts achieve the lower bound for bounded ℓ and approach the upper bound when ℓ grows. © 2005 Wiley Periodicals, Inc. Random Struct. Alg., 2006
Some conditional correlation inequalities for percolation and related processes
Authors: van den Berg J. , Häggström O. , Kahn J.
Published: December 2005

Consider ordinary bond percolation on a finite or countably infinite graph. Let s, t, a, and b be vertices. An earlier paper (J. Van den Berg and J. Kahn, Ann Probab 29 (2001), 123–126) proved the (nonintuitive) result that, conditioned on the event that there is no open path from s to t, the two events ”there is an open path from s to a” and “there is an open path from s to b” are positively correlated. In the present paper we further investigate and generalize the theorem of which this result was a consequence. This leads to results saying, informally, that, with the above conditioning, the open cluster of s is conditionally positively (self‐) associated and that it is conditionally negatively correlated with the open cluster of t.

We also present analogues of some of our results for (a) random‐cluster measures and (b) directed percolation and contact processes and observe that the latter lead to improvements of some of the results in a paper of Belitsky et al. (Stoch Proc Appl 67 (1997), 213–225). © 2005 Wiley Periodicals, Inc. Random Struct. Alg., 2006
On random points in the unit disk
Authors: Ellis Robert B. , Jia Xingde , Yan Catherine
Published: December 2005

Let n be a positive integer and λ > 0 a real number. Let Vn be a set of n points in the unit disk selected uniformly and independently at random. Define G(λ, n) to be the graph with vertex set Vn, in which two vertices are adjacent if and only if their Euclidean distance is at most λ. We call this graph a unit disk random graph. Let
$\lambda = c \sqrt {\ln n/n}$
and let X be the number of isolated points in G(λ, n). We prove that almost always X ∼ n when 0 ≤ c < 1. It is known that if $\lambda = \sqrt {(\ln n + \phi (n))/n}$
where ϕ(n) → ∞, then G(λ, n) is connected. By extending a method of Penrose, we show that under the same condition on λ, there exists a constant K such that the diameter of G(λ, n) is bounded above by K · 2/λ. Furthermore, with a new geometric construction, we show that when $\lambda = c \sqrt {\ln n/n}$
and c > 2.26164 …, the diameter of G(λ, n) is bounded by (4 + o(1))/λ; and we modify this construction to yield a function c(δ) > 0 such that the diameter is at most 2(1 + δ + o(1))/λ when c > c(δ). © 2005 Wiley Periodicals, Inc. Random Struct. Alg., 2006