bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modelling inter‐yarn friction in woven fabric armour
Authors: Zeng X. S. , Tan V. B. C. , Shim V. P. W. 
Published: December 2005

AbstractThe 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

AbstractThe 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.
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

AbstractThis 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

AbstractPhotogrammetric 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

AbstractThe 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

AbstractTheThe 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

AbstractKnowing 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

AbstractThe 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

AbstractGlycation 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

AbstractEnergies 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

AbstractStructural 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

AbstractThe 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

AbstractPolyaniline (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

AbstractA 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

AbstractIt 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

AbstractThe 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

AbstractIn 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

AbstractWe 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

AbstractLet 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

AbstractWe 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