bluuebunny/crossref_metadata_2025 huggingface dataset:
Numerical analysis of pile behaviour under lateral loads in layered elastic–plastic soils
Authors: Yang Zhaohui , Jeremić Boris
Published: October 2002

This paper presents results from a finite element study on the behaviour of a single pile in elastic–plastic soils. Pile behaviour in uniform sand and clay soils as well as cases with sand layer in clay deposit and clay layer in sand deposit were analysed and cross compared to investigate layering effects. Finite element results were used to generate p–y curves and then compared with those obtained from methods commonly used in practice. Copyright © 2002 John Wiley & Sons, Ltd.
Elastic solutions for stresses in a transversely isotropic half‐space subjected to three‐dimensional buried parabolic rectangular loads
Authors: Wang Cheng‐Der , Liao Jyh‐Jong
Published: October 2002

In many areas of engineering practice, applied loads are not uniformly distributed but often concentrated towards the centre of a foundation. Thus, loads are more realistically depicted as distributed as linearly varying or as parabola of revolution. Solutions for stresses in a transversely isotropic half‐space caused by concave and convex parabolic loads that act on a rectangle have not been derived. This work proposes analytical solutions for stresses in a transversely isotropic half‐space, induced by three‐dimensional, buried, linearly varying/uniform/parabolic rectangular loads. Load types include an upwardly and a downwardly linearly varying load, a uniform load, a concave and a convex parabolic load, all distributed over a rectangular area. These solutions are obtained by integrating the point load solutions in a Cartesian co‐ordinate system for a transversely isotropic half‐space. The buried depth, the dimensions of the loaded area, the type and degree of material anisotropy and the loading type for transversely isotropic half‐spaces influence the proposed solutions. An illustrative example is presented to elucidate the effect of the dimensions of the loaded area, the type and degree of rock anisotropy, and the type of loading on the vertical stress in the isotropic/transversely isotropic rocks subjected to a linearly varying/uniform/parabolic rectangular load. Copyright © 2002 John Wiley & Sons, Ltd.
The fractional matching numbers of graphs
Authors: Liu Yan , Liu Guizhen
Published: October 2002

A fractional matching of a graph G is a function f that assigns to each edge a number in [0, 1] such that, for each vertex v, ∑ f(e) ≤ 1, where the sum is taken over all edges incident to v. The fractional matching number of G is the supremum of ∑e∈E(G) f(e) over all fractional matchings f. In this paper, we provide a new formula for calculating the fractional matching numbers of graphs using the Gallai–Edmonds Structure Theorem. Thus, we characterize graphs for which the fractional matching number equals the matching number and graphs for which the fractional matching number is the maximum possible (one‐half the number of vertices). © 2002 Wiley Periodicals, Inc.
Combinatorial algorithms for inverse network flow problems
Authors: Ahuja Ravindra K. , Orlin James B.
Published: October 2002

An inverse optimization problem is defined as follows: Let S denote the set of feasible solutions of an optimization problem P, let c be a specified cost vector, and x0 ∈ S. We want to perturb the cost vector c to d so that x0 is an optimal solution of P with respect to the cost vector d, and w∥d − c∥p is minimum, where ∥ · ∥p denotes some selected lp norm and w is a vector of weights. In this paper, we consider inverse minimum‐cut and minimum‐cost flow problems under the l1 normal (where the objective is to minimize ∑j∈Jwj|dj − cj| for some index set J of variables) and under the l∞ norm (where the objective is to minimize max{wj|dj − cj|: j ∈ J}). We show that the unit weight (i.e., wj = 1 for all j ∈ J) inverse minimum‐cut problem under the l1 norm reduces to solving a maximum‐flow problem, and under the l∞ norm, it requires solving a polynomial sequence of minimum‐cut problems. The unit weight inverse minimum‐cost flow problem under the l1 norm reduces to solving a unit capacity minimum‐cost circulation problem, and under the l∞ norm, it reduces to solving a minimum mean cycle problem. We also consider the nonunit weight versions of inverse minimum‐cut and minimum‐cost flow problems under the l∞ norm. © 2002 Wiley Periodicals, Inc.
Identification of novel protein‐coding genes from human fetal hippocampus ESTs database
Authors: Ding Keyue , Sun Xiaojing , Zhou Min , Cai Jingjing , Cai Tianjing , Zhang Yan , Zhu Tong , Zhang Zhengguo , Qiang Boqin , Shen Yan
Published: October 2002

We presented a procedure to identify novel protein‐coding genes from human fetal hippocampus ESTs database generated in our previous study. The protocol is involved in searching the GenBank non‐redundant (nr) protein database with ESTs coding regions query. We used ESTScan program to detect and reconstruct coding regions in the ESTs sequence data. With almost 10,000 raw ESTs analyzed, 4,061 coding regions were extracted. The corresponding amino acid sequences were then searched against the GenBank nr‐protein databases; all the similarity hits were parsed in a homology analysis workbench. 22 ESTs were identified as the “seed” ESTs, which might be the fragment of the novel protein‐coding genes. Indeed, further analysis of these ESTs in full‐length cDNA cloning in silico, as well as the mapping information in UCSC and the added experimental proof, verified the effectiveness of the strategy. Taking advantage of rare ESTs resources, and the effective strategy, we would explore more novel genes in the human genome.

[The ESTs sequence data described in this paper have been submitted to the GenBank data library (http://www.ncbi.nlm.nih.gov/dbEST) under accession nos. BM174886‐958, BM259607‐9; and the full length cDNA sequence can be obtained in http://www.chgb.org.cn/hippocampus.htm]
Effect of penicillin induced epilepsy seizure on granulare cell layer of dentate gyrus in rat: a stereological study
Authors: Adiguzel Esat , Akdogan Ilgaz , Duzcan S. Ender , Tufan A. Cevik
Published: October 2002

Nonstereological methods have been the prefrence of investigators in the field of neuron counting. Development of stereological methods in biological sciences improved the reliability of neuroscientific investigations. This study was designed to investigate the effect of penicillin induced epilepsy seizure on total cell number of granulare cell layer of dentate gyrus. Optical fractionator method, one of the unbiased stereological methods, was used to estimate the total cell number. Seizure was observed and recorded in EEG 3–4 minutes after intracortical injection of 500 IU penicillin‐G. Rat brains were removed one week later from penicillin‐G introduction. The number of neurons in the granulare cell layer of dentate gyrus was less in the experimental group (111728±14110) compared to that in the control group (120228±16718). This difference was not statistically significant (p>0.05).
Novel elastomeric polyurethanes with pendant epoxy groups as highly reactive auxiliary groups for further derivatizations
Authors: Alferiev Ivan S.
Published: October 2002

The introduction of pendant, reactive groups into polyurethane macromolecules is a challenging problem. A variant of the nondegradative modification of polyurethanes with epoxy groups attached to the urethane sites is proposed. Two types of commercial elastomeric segmented polyurethanes, represented by a poly(ether urethane) and a poly(urethane urea), were functionalized by base‐induced N‐glycidylation of the urethane hard segments with an excess of epibromohydrin in dimethylacetamide solutions at low temperatures. This resulted in the modification of polymers with 0.30–0.44 mmol/g of pendant epoxy groups. Lithium or potassium tert‐butoxides were used as bases to initiate the reaction. A nonpolymeric urethane model (ethyl N‐p‐tolylcarbamoate) was used to verify the course of glycidylation. One of the polymers was subjected to epoxy ring opening with 1‐propanethiol, demonstrating the versatility of pendant glycidyl groups as auxiliary groups for further bulk modifications of polyurethanes. These functionalized polyurethanes are useful for the further covalent attachment of suitable moieties (stabilizing or biocompatibility‐enhancing agents). © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 4378–4385, 2002
Characterization and degradation behavior of poly(butylene adipate‐co‐terephthalate)s
Authors: Herrera Ricard , Franco Lourdes , Rodríguez‐Galán Alfonso , Puiggalí Jordi
Published: October 2002

Random copolyesters based on 1,4‐butanediol and different ratios between adipic and terephthalic units were synthesized from thermal polycondensation of the appropriate mixture of monomers or by melt transesterification of the mixture of homopolymers. 1H NMR spectroscopy makes feasible the study of the average block lengths of polymers once synthesized and after degradation in different media. Calorimetric data are reported, including those referred to the study of isothermal and nonisothermal crystallizations. Degradability of samples was evaluated by different methods including NMR and thermal analysis, evaluation of molecular weight by gel permeation chromatography or from intrinsic viscosity measures, scanning electron micrographs, and changes in mechanical properties. Distilled water at 70 °C acidic conditions provided by a pH 2.3 aqueous medium and enzymatic media containing lipases from Pseudomonas cepacia or Candida cylindracea were considered in this study. The degradability of the studied copolyesters strongly depends on the terephthalate content and the degradation media. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 4141–4157, 2002
Fluorinated poly(arylene ether ketone)s bearing pentafluorostyrene moieties prepared by a modified polycondensation
Authors: Ding Jianfu , Liu Futian , Li Mei , Day Michael , Zhou Ming
Published: October 2002

The polycondensation of decafluorobenzophenone with hexafluorobisphenol A was modified by the addition of a molecular sieve dehydrating apparatus to the refluxing reaction system. This modification promoted the polymerization and enabled the reactions to be conducted in milder conditions and completed in a shorter time, thereby depressing side reactions such as branching and crosslinking. The resulting fluorinated poly(arylene ether ketone)s (FPAEK) were free of gel particles and possessed the designed molecular weights. This modified procedure was also suitable for introducing crosslinkable pentafluorostyrene (FSt) moieties into the polymers at the chain ends and/or inside the chain with the vinyl group of FSt being pendant. The resulting FSt containing fluorinated poly(arylene ether ketone)s (FPAEK‐FSt) can then be thermally crosslinked at 100 °C in the presence of 1% benzoyl peroxide (BPO) or at 250 °C without any initiator. The glass‐transition temperatures (Tg's) of FPAEK increased with increasing molecular weight and leveled off at about 147 °C for the polymer with a number‐average molecular weight of 18,600 Da, whereas the values were not apparently affected by the addition of FSt units. However, crosslinking of the FPAEK‐FSt resulted in an approximate 30 °C increase of the Tg. Spin‐coating FPAEK‐FSt onto silicon wafers followed by crosslinking gave films with excellent thermal stability, physical strength, and adhesion to the substrate as well as good reproducibility in terms of film preparation and optical properties. The refractive index and birefringence of the films measured at a wavelength of 1.55 μm were 1.502 and 2.5 × 10−3, respectively. © 2002 Government of Canada. Exclusive worldwide publication rights in the article have been transferred to Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 4205–4216, 2002
Thermally stable nonlinear optical polyurea functionalized by multiple charge‐transfer chromophore
Authors: Yang Zhou , Li Shaojun , Ye Cheng
Published: October 2002

A novel high glass‐transition temperature (272 °C) polyurea functionalized by a multiple charge‐transfer chromophore, 2‐{4‐[4,5‐bis(4‐nitrophenyl)imidazolyl]phenyl}‐4,5‐bis(4‐aminophenyl)imidazole, was synthesized. Simultaneous poling and polymerization and the in situ second‐harmonic generation (SHG) measurement technique was carried out to evaluate the thermal stability of the poling‐induced orientation. The nonlinear optical coefficient d33 of poled polyurea film was 24 pm/V at 1064 nm fundamental wavelength. The SHG signal of the poled polymer film was quite stable below 200 °C and still remained 80% of its initial value after heating at 250 °C. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 4297–4301, 2002
Knowledge‐based choice of the initiator type for monomer removal by postpolymerization
Authors: Ilundain Pedro , Alvarez Daniel , Da Cunha Louis , Salazar Rafael , Barandiaran María J. , Asua José M.
Published: October 2002

The mechanisms involved in monomer removal by postpolymerization were investigated to establish a criterion to select the most effective initiator systems. Three redox systems yielding radicals of different hydrophobicities were studied. Efficiency in monomer removal by postpolymerization increased with the hydrophobicity of the radical formed from the initiator system. This result was independent of the water solubility of the residual monomer. The mechanistic reasons for this finding are discussed. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 4245–4249, 2002
Synthesis and polymerization of 5‐(methacrylamido)tetrazole, a water‐soluble acidic monomer
Authors: Taden Andreas , Tait Alison H. , Kraft Arno
Published: October 2002

The reaction of methacryloyl chloride with 5‐aminotetrazole gave the polymerizable methacrylamide derivative 5‐(methacrylamido)tetrazole (4) in one step. The monomer had an acidic tetrazole group with a pKa value of 4.50 ± 0.01 in water methanol (2:1). Radical polymerization proceeded smoothly in dimethyl formamide or, after the conversion of monomer 4 into sodium salt 4‐Na, even in water. A superabsorbent polymer gel was obtained by the copolymerization of 4‐Na and 0.08 mol % N,N′‐methylenebisacrylamide. Its water absorbency was about 200 g of water/g of polymer, although the extractable sol content of the gel turned out to be high. The consumption of 4‐Na and acrylamide (as a model compound for the crosslinker) during a radical polymerization at 57 °C in D2O was followed by 1H NMR spectroscopy. Fitting the changes in the monomer concentration to the integrated form of the copolymerization equation gave the reactivity ratios r4‐Na = 1.10 ± 0.05 and racrylamide = 0.45 ± 0.02, which did not differ much from those of an ideal copolymerization. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 4333–4343, 2002
Synthesis and characterization of novel 3,6‐di[3′,5′‐bis(trifluoromethyl)phenyl]pyromellitic dianhydride for polyimide synthesis
Authors: Myung B. Y. , Kim J. J. , Yoon T. H.
Published: October 2002

A novel dianhydride monomer, 3,6‐di[3′,5′‐bis(trifluoromethyl)phenyl]pyromellitic dianhydride (12FPMDA), was synthesized via a three‐step process: (1) the preparation of 3,5‐bis(trifluoromethyl)benzene boronic acid (6FBB) and 3,6‐dibromo‐1,2,4,5‐tetramethylbenzene (2B4MB) via Grignard and bromination reactions, respectively; (2) the Suzuki cross‐coupling reaction of 6FBB and 2B4MB, resulting in 3,6‐di[3′,5′‐bis(trifluoromethyl)phenyl]tetramethylbenzene (12F4MB); and (3) the oxidation and cyclodehydration of 12F4MB to afford 12FPMDA. 12FPMDA was then characterized by Fourier transform infrared (FTIR), 1H NMR, 19F NMR, elemental analysis, and a melting‐point apparatus, and it was used to prepare polyimides with aromatic diamines such as 1,1‐bis(4‐aminophenyl)‐2,2,2‐trifluoroethane and 4,4′‐diaminodiphenylether. Polyimides were synthesized via a two‐step process: (1) the preparation of poly(amic acid) in p‐chlorophenol with isoquinoline and (2) solution imidization at the reflux temperature for 12 h. They were designed to have molecular weights of 20,000 g/mol via off‐stoichiometry. The resulting polyimides were characterized by FTIR, NMR, gel permeation chromatography, differential scanning calorimetry, and thermogravimetric analysis, and their solubility, solution viscosity, water absorption, coefficients of thermal expansion (CTEs), and dielectric constants were also evaluated. The polyimides exhibited excellent solubility even in acetone and toluene, high glass‐transition temperatures (>311 °C), good thermal stability (>518 °C in air), and well‐controlled molecular weights (19,000–21,000 g/mol). They also provided low CTEs (35–50 ppm/°C), water absorption (1.26–1.35 wt %), and dielectric constants (2.49–2.52). © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 4217–4227, 2002
Synthesis of highly crosslinked monodisperse polymer particles: Effect of reaction parameters on the size and size distribution
Authors: Choi J. , Kwak S.‐Y. , Kang S. , Lee S.‐S. , Park M. , Lim S. , Kim J. , Choe C. R. , Hong S. I.
Published: October 2002

Monodisperse polystyrene particles crosslinked with different concentrations of divinylbenzene were synthesized in the 3.2–9.1 μm size range by dispersion polymerization in an isopropyl alcohol/toluene mixed‐dispersion medium with poly(N‐vinylpyrrolidone) as a steric stabilizer and 2,2′‐azobisisobutyronitrile as a radical initiator. The effects of the reaction parameters such as the crosslinking agent concentration, media solvency (controlled by varying the amount of toluene addition), the initiator concentration, and the stabilizer concentration on the particle size and size distribution were investigated with reference particles with a monodisperse size distribution and crosslinked by 1.5 wt % divinylbenzene. The appropriate increase in media solvency was a prerequisite for preparing crosslinked particles without coagulated and/or odd‐shaped particles. The investigation of the effects of the polymerization parameters also shows that only specific sets of conditions produce particles with a monodisperse size distribution. The glass‐transition temperatures of the particles increased with increasing divinylbenzene concentration. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 4368–4377, 2002
Ultraviolet curing of acrylic systems: Real‐time Fourier transform infrared, mechanical, and fluorescence studies
Authors: Peinado Carmen , Salvador Enrique F. , Alonso Asunción , Corrales Teresa , Baselga Juan , Catalina Fernando
Published: October 2002

The photopolymerization of acrylic‐based adhesives has been studied by Fourier transform infrared and fluorescence analysis in real time. Real‐time infrared spectroscopy reveals the influence of the nature of the photoinitiator on the kinetics of the reaction. Furthermore, the incident light intensity dependence of the polymerization rate shows that primary radical termination is the predominant mechanism during the initial stages of the curing of the acrylic system with bis(2,4,6‐trimethylbenzoyl) phenyl phosphine oxide (TMBAPO) as a photoinitiator. The fluorescence intensity of selected probes increases during the ultraviolet curing of the adhesive, sensing microenvironmental viscosity changes. Depending on the nature of the photoinitiator, different fluorescence–conversion curves are observed. For TMBAPO, the fluorescence increases more slowly during the initial stage because of the delay in the gel effect induced by primary radical termination. Mechanical tests have been carried out to determine the shear modulus over the course of the acrylic adhesive ultraviolet curing. In an attempt to extend the applications of the fluorescence probe method, we have undertaken comparisons between the fluorescence changes and shear modulus. Similar features in both curves confirm the feasibility of the fluorescence method for providing information about microstructural changes during network formation. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 4236–4244, 2002
Luminescent polymeric ruthenium complexes with polystyrene‐b‐poly(methyl methacrylate) macroligands: The sequential activation of initiator sites for blocks generated by parallel polymerization mechanisms
Authors: Smith Adam P. , Fraser Cassandra L.
Published: October 2002

The synthesis of polystyrene‐b‐poly(methyl methacrylate) diblock copolymers with a luminescent ruthenium(II) tris(bipyridine) [Ru(bpy)3] complex at the block junction is described. The macroligand precursor, polystyrene bipyridine‐poly(methyl methacrylate) [bpy(PS–H)(PMMA)], was synthesized via the atom transfer radical polymerization of styrene and methyl methacrylate from two independent, sequentially activated initiating sites. Both polymerization steps resulted in the growth of blocks with sizes consistent with monomer loading and narrow molecular weight distributions (i.e., polydispersity index < 1.3). Subsequent reactions with ruthenium(II) bis(bipyridine) dichloride [Ru(bpy)2Cl2] in the presence of Ag+ generated the ruthenium tris(bipyridine)‐centered diblock, which is of interest for the imaging of block copolymer microstructures and for incorporation into new photonic materials. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 4250–4255, 2002
Characterization of the network properties of poly(ethylene glycol)–acrylate hydrogels prepared by variations in the ethanol–water solvent composition during crosslinking copolymerization
Authors: Ravi Nathan , Mitra Arpita , Hamilton Paul , Horkay Ferenc
Published: October 2002

The characteristics of poly(ethylene glycol) (PEG)–acrylate hydrogel networks were investigated as a function of the ethanol–water solvent composition during free‐radical crosslinking copolymerization. Macromonomer (88% ω‐methoxy‐PEG–acrylate and 10% ω‐phenoxy‐PEG–acrylate) and crosslinker (2% PEG–diacrylate) concentrations were kept constant. As the copolymerization progressed, the polymer solution in 100% ethanol became increasingly turbid, indicating the development of a heterogeneous network structure. In 100% water, however, the initially turbid polymer solution became increasingly transparent as the crosslinking copolymerization progressed. All the gels were optically clear upon equilibration in water. Kinetic studies, with attenuated total reflectance‐infrared, showed a long induction period, along with a lowered reaction rate, in 100% ethanol, and a decrease in conversion with an increase in ethanol content. These results agree with the UV analysis of the sol fractions, which indicated an increase in the amounts of unreacted PEG–acrylates with an increase in the ethanol content. The gels which were formed with a high ethanol concentration exhibited lower Young's modulus and higher swelling ability, suggesting that the network structure was significantly affected by the solvent composition during free‐radical crosslinking copolymerization. From the stress–strain and swelling experiments, the Flory–Huggins interaction parameter was evaluated. The creep characteristics of the hydrogels were modeled with two Kelvin elements. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 2677–2684, 2002
Spontaneous thinning/thickening deformation observed for plastic blend films and some factors affecting film deformation
Authors: Li Jianchun , He Yong , Inoue Yoshio
Published: October 2002

The fully amorphous films of highly syndiotactic poly[(R,S)‐3‐hydroxybutyrate] (s‐PHB)/atactic poly(4‐vinylphenol) (PVPh) blends show reversible thinning/thickening phenomena at 37 °C in aqueous medium. On the other hand, isotactic poly[(R)‐3‐hydroxybutyrate] (i‐PHB)/PVPh blend film, in which i‐PHB blend component was partially crystalline, did not show any thinning/thickening phenomena under the same conditions. To elucidate the factors influencing these phenomena, the structure and molecular interaction in these blends were characterized by Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry, and wide‐angle X‐ray diffraction. The FTIR spectra indicated that the ester carbonyl of PHB and the phenolic hydroxyl of PVPh formed hydrogen bonds in both the thinned and thickened s‐PHB/PVPh blend films. The blend composition, intermolecular hydrogen‐bonding interaction, crystallization behavior, miscibility, and the glass‐transition temperature of the blends affected the thinning/thickening phenomena. Some other polyesters such as poly(ϵ‐caprolactone), poly (L‐lactic acid), atactic poly(D,L‐lactic acid), and poly(ethylene terephthalate) had no ability to exhibit thinning/thickening phenomena in water at 37 °C when they were blended with PVPh. This result implies that s‐PHB/PVPh is the rare example with the ability to show reversible thinning/thickening phenomena. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 2736–2743, 2002
Polyaniline emeraldine base in N‐methyl‐2‐pyrrolidinone containing secondary amine additives: A rheological investigation of solutions
Authors: Yang Dali , Mattes B. R.
Published: October 2002

From a rheological study of emeraldine base (EB)/N‐methyl‐2‐pyrrolidinone (NMP)/2‐methyl‐aziridine (2MA) solutions, a correlation between the solution concentration and solution viscosity was found. We investigated the rheokinetic mechanism of the EB dissolution process and determined the reaction rate, activation energy, equilibrium constant, and Gibbs free energy (ΔGo) for the complexation between 2MA and EB tetrameric molecules ({EB}). The low rate constant (∼3.0 × 10−4 mol−2 L2 min−1 at 298 K) indicates that the process of EB/NMP/2MA solution formation is slow. The {EB} and 2MA molecules need approximately 76 kJ/mol energy to form the complexes, and this implies that stable bonds may need to be broken before the complexes can form. Therefore, increasing the temperature can accelerate solution formation. The equilibrium constant increases with temperature, and this indicates that EB · 2MA complexation is endothermic. A positive value of ΔGo (5.26 kJ/mol) indicates that EB · 2MA complexation is a thermodynamically unfavorable reaction; therefore, the concentrated EB/NMP/2MA solutions eventually gel. Furthermore, we find that the activation energy of EB/NMP viscous flow is 80 kJ/mol, which is about 3–4 times the energy of NH hydrogen bonding. This suggests that at least three hydrogen bonds can form between two {EB} molecules, which might be responsible for the poor solubility of EB in organic solvents. The effects of the temperature, EB concentration, and 2MA:{EB} molar ratio on the gelation process have also been investigated. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 2702–2713, 2002
Multivariable structural characterization of semicrystalline polymer blends by small‐angle light scattering
Authors: Akpalu Yvonne A. , Lin Youyu
Published: October 2002

A new multi‐variable‐measurement approach for characterizing and correlating the nanoscale and microscale morphology of crystal‐amorphous polymer blends with melt‐phase behavior is described. A vertical small‐angle light scattering (SALS) instrument optimized for examining the scattering and light transmitted from structures ranging from 0.5 to 50 μm, thereby spanning the size range characteristic of the initial‐to‐late stages of thermal‐phase transitions (e.g., melt‐phase separation and crystallization) in crystal‐amorphous polymer blends, was constructed. The SALS instrument was interfaced with differential scanning calorimetry (DSC), and simultaneous SALS/DSC/transmission measurements were performed. We show that the measurement of transmitted light and SALS underHV(cross‐polarized) optical alignments during melting can be used to reliably measure the thermodynamic (e.g., crystal melting and melt‐phase separation temperatures) and structural variables (e.g., crystalline fraction within the superstructures and volume fraction of superstructures) necessary for describing the multiphase behavior of crystal‐amorphous blends in one combined measurement. We also evaluate the orientation correlations of crystalline volume elements within the superstructures. Our results indicate that simultaneous measurement of transmitted light can provide a reliable estimate of the total scattering from density and orientation fluctuations and the melt‐phase separation temperature of polymer blends. For solution‐cast poly(ϵ‐caprolactone)/poly(D,L‐lactic acid) blends, our multivariable measurements during melting provide the parameters necessary to generate a crystal–liquid and liquid–liquid phase diagram and characterize the solid‐state morphology. This opens up the challenge to explore use of our vertical SALS instrument as a rapid and convenient method for developing structure–property relationships for crystal‐amorphous polymer blends. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 2714–2727, 2002
Excluded‐volume effects on the chain dimensions and transport coefficients of sodium poly(styrene sulfonate) in aqueous sodium chloride
Authors: Yashiro Junko , Norisuye Takashi
Published: October 2002

Fifteen samples of sodium poly(styrene sulfonate) with weight‐average molecular weights of 3 × 104 to 8 × 105 have been studied by static and dynamic light scattering and viscometry in 0.05 and 0.5 M aqueous NaCl at 25 °C. The measured radii of gyration, translational diffusion coefficients, and intrinsic viscosities at the lower salt concentration exhibit molecular weight dependencies stronger than those predictable for uncharged flexible chains in the good solvent limit. These data and those at the higher NaCl concentration are analyzed, along with previous intrinsic viscosity data covering a broad molecular weight range, in the framework of the quasi‐two‐parameter (QTP) theory with the wormlike chain as the model. It is shown that the relevant theories for the expansion factors in the QTP scheme combined with these theories for the unperturbed wormlike chain are capable of describing the experimental data with a degree of accuracy similar to that known for nonionic flexible polymers. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 2728–2735, 2002
Coil extension stage in the cold drawing of glassy polymers
Authors: Yang Xiao‐Zhen , Sun Juan
Published: October 2002

Cold drawing is known as a thermodynamically reversible process for glassy polymers. In the extension process, there might be a stage in which the global structure of chain coils extends in the drawing direction. This extension stage has not been clearly identified because of the lack of a quantitative relationship between the global structure evolution and the local structure reorientation. We have developed a theoretical method to elucidate the relationship, which is based on a simulated chain conformational distribution and a relationship between the chain conformations and the extension. Any local structure, such as the fraction of trans conformations of ethylene glycol of poly(ethylene terephthalate) (PET), can then be calculated with an ensemble average as a function of the system extension. Combined with infrared conformational band measurements, the coil extension stage has been characterized in the cold drawing of amorphous PET. This stage does not start from the yielding point but instead begins nearly at the end of the stress softening. In the recovery process, the experimental measurements and theoretical predictions are well correlated. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 2646–2652, 2002
Interfacial structure and properties in polystyrene/epoxy bilayer films
Authors: Jeon H. S. , Dixit P. S. , Yim H. , Kent M. S. , Shin K. , Satija S.
Published: October 2002

The interfacial structure and properties of immiscible deuterated polystyrene (dPS)/epoxy bilayer films were investigated with neutron reflectivity as functions of the composition of the epoxy layer, the thickness of the dPS layer, and the annealing time. We have found that the interfacial width and its growth rate depend strongly on the compositions of the epoxy layer but only weakly on the thickness of the dPS layer. The effect of the resin/crosslinker composition on the interfacial width and its growth rate is likely due to the different near‐surface structures that result for different epoxy stoichiometries. For an ultra‐thin dPS film (thickness = 2Rg), the data suggest a slight suppression of the growth of the interfacial width that could be due to confinement effects for the long‐chain molecules such as have been previously reported for a thickness of less than approximately 4Rg, where Rg is the radius of gyration of polymer molecules. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 2653–2660, 2002
Synthesis and characterization of silica‐graft‐polystyrene hybrid nanoparticles: Effect of constraint on the glass‐transition temperature of spherical polymer brushes
Authors: Savin Daniel A. , Pyun Jeffrey , Patterson Gary D. , Kowalewski Tomasz , Matyjaszewski Krzysztof
Published: October 2002

The effect of the chain constraint on the glass‐transition temperature of polystyrene (pS) was studied in the context of polymer tethering to curved surfaces. The synthesis and characterization of silica‐graft‐polystyrene (SiO2‐g‐pS) hybrid nanoparticles is reported. Silica nanoparticles possessing covalently bound pS chains were prepared by the atom transfer radical polymerization of styrene from functionalized colloidal surfaces. These hybrid nanoparticles serve as interesting examples of spherical polymer brushes, as a high density of grafted pS was achieved on the inorganic colloid. The confirmation of a brushlike extension of immobilized chains in a good solvent was obtained with dynamic light scattering in toluene of SiO2‐g‐pS colloids possessing various molar masses of tethered pS. The solid‐state morphology of SiO2‐g‐pS ultrathin films was assessed with transmission electron microscopy, and this confirmed that the silica colloids were well‐dispersed in a matrix of the tethered polymer. Differential scanning calorimetry was used to study the effects of tethering and chain immobilization on the glass‐transition temperature of pS. The measured glass‐transition temperature of annealed bulk films of the hybrid nanoparticles was elevated with respect to the value for pure bulk pS. The enhancements ranged from 13 to 2 K for SiO2‐g‐pS brushes possessing tethered pS with number‐average molecular weights of 5230 and 32,670 g/mol, respectively. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 2667–2676, 2002
Effects of melt‐processing conditions on the quality of poly(ethylene terephthalate) montmorillonite clay nanocomposites
Authors: Davis Cher H. , Mathias Lon J. , Gilman Jeffrey W. , Schiraldi David A. , Shields J. Randy , Trulove Paul , Sutto Tom E. , Delong Hugh C.
Published: October 2002

Organically modified montmorillonite was synthesized with a novel 1,2‐dimethyl‐3‐N‐alkyl imidazolium salt or a typical quaternary ammonium salt as a control. Poly(ethylene terephthalate) montmorillonite clay nanocomposites were compounded via melt‐blending in a corotating mini twin‐screw extruder operating at 285 °C. The nanocomposites were characterized with thermal analysis, X‐ray diffraction, and transmission electron microscopy to determine the extent of intercalation and/or exfoliation present in the system. Nanocomposites produced with N,N‐dimethyl‐N,N‐dioctadecylammonium treated montmorillonite (DMDODA‐MMT), which has a decomposition temperature of 250 °C, were black, brittle, and tarlike resulting from DMDODA degradation under the processing conditions. Nanocomposites compounded with 1,2‐dimethyl‐3‐N‐hexadecyl imidazolium treated MMT, which has a decomposition temperature of 350 °C, showed high levels of dispersion and delamination. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 2661–2666, 2002
Ethylene/1‐hexene copolymers synthesized with a single‐site catalyst: Crystallization analysis fractionation, modeling, and reactivity ratio estimation
Authors: Sarzotti Deborah M. , Soares João B. P. , Penlidis Alexander
Published: October 2002

A series of poly(ethylene‐co‐1‐hexene) samples made with rac‐ethylene bis(indenyl)zirconium dichloride/methylaluminoxane were analyzed by crystallization analysis fractionation (CRYSTAF). The nine samples had comonomer contents of 0–4.2 mol % 1‐hexene with a narrow range of molecular weights (34,000–39,000 g/mol). Because all the copolymer samples had narrow, unimodal chemical composition distributions, they were ideal as calibration standards for CRYSTAF. A linear calibration curve was constructed relating the peak crystallization temperature from CRYSTAF operated at a cooling rate of 0.1 °C/min and the comonomer content as determined by 13C NMR. Reactivity ratios for ethylene and 1‐hexene were estimated by the fitting of reactant liquid‐phase compositional data to the Mayo–Lewis equation. It was found that a value of the 1‐hexene reactivity ratio could not be unequivocally determined from the set of samples analyzed because the range of comonomer incorporation was too narrow. Stockmayer's bivariate distribution was used to model the fractionation process in CRYSTAF, and although a good fit to experimental CRYSTAF profiles was attained, the model did not fully describe the underlying crystallization phenomena. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 2595–2611, 2002
Equilibrium and kinetic folding of hen egg‐white lysozyme under acidic conditions
Authors: Sasahara Kenji , Demura Makoto , Nitta Katsutoshi
Published: October 2002

The equilibrium and kinetic folding of hen egg‐white lysozyme was studied by means of circular dichroism spectra in the far‐ and near‐ultraviolet (UV) regions at 25°C under the acidic pH conditions. In equilibrium condition at pH 2.2, hen lysozyme shows a single cooperative transition in the GdnCl‐induced unfolding experiment. However, in the GdnCl‐induced unfolding process at lower pH 0.9, a distinct intermediate state with molten globule characteristics was observed. The time‐dependent unfolding and refolding of the protein were induced by concentration jumps of the denaturant and measured by using stopped‐flow circular dichroism at pH 2.2. Immediately after the dilution of denaturant, the kinetics of refolding shows evidence of a major unresolved far‐UV CD change during the dead time (<10 ms) of the stopped‐flow experiment (burst phase). The observed refolding and unfolding curves were both fitted well to a single‐exponential function, and the rate constants obtained in the far‐ and near‐UV regions coincided with each other. The dependence on denaturant concentration of amplitudes of burst phase and both rate constants was modeled quantitatively by a sequential three‐state mechanism, U↔I↔N, in which the burst‐phase intermediate (I) in rapid equilibrium with the unfolded state (U) precedes the rate‐determining formation of the native state (N). The role of folding intermediate state of hen lysozyme was discussed. Proteins 2002;49:472–482. © 2002 Wiley‐Liss, Inc.
All‐atom fast protein folding simulations: The villin headpiece
Authors: Shen Min‐yi , Freed Karl F.
Published: October 2002

We provide a fast folding simulation using an all‐atom solute, implicit solvent method that eliminates the need for treating solvent degrees of freedom. The folding simulations for the 36‐residue villin headpiece exhibit close correspondence with the landmark all‐atom explicit solvent molecular dynamics simulations by Duan and Kollman (Duan & Kollman, Science 1998;282:740–744; Duan, Wang, & Kollman, Proc Natl Acad Sci USA 1998;95:9897–9902). Our implicit solvent approach uses only an entry‐level single CPU PC with comparable throughput (∼4 nsec/day) to the DK supercomputer simulation. The native state is shown to be stable. Our 200‐nsec folding trajectory agrees with the DK simulation in displaying a burst phase, a rapid initial shrinkage, a highly native‐like binding site structure, and more. Proteins 2002;49:439–445. © 2002 Wiley‐Liss, Inc.
FROST: A filter‐based fold recognition method
Authors: Marin Antoine , Pothier Joël , Zimmermann Karel , Gibrat Jean‐François
Published: October 2002

To assess the reliability of fold assignments to protein sequences, we developed a fold recognition method called FROST (Fold Recognition‐Oriented Search Tool) based on a series of filters and a database specifically designed as a benchmark for this new method under realistic conditions. This benchmark database consists of proteins for which there exists, at least, another protein with an extensively similar 3D structure in a database of representative 3D structures (i.e., more than 65% of the residues in both proteins can be structurally aligned). Because the testing of our method must be carried out under conditions similar to those of real fold recognition experiments, no protein pair with sequence similarity detectable using standard sequence comparison methods such as FASTA is included in the benchmark database. While using FROST, we achieved a coverage of 60% for a rate of error of 1%. To obtain a baseline for our method, we used PSI‐BLAST and 3D‐PSSM. Under the same conditions, for a 1% error rate, coverages for PSI‐BLAST and 3D‐PSSM were 33 and 56%, respectively. Proteins 2002;49:493–509. © 2002 Wiley‐Liss, Inc.
A new test set for validating predictions of protein–ligand interaction
Authors: Nissink J. Willem M. , Murray Chris , Hartshorn Mike , Verdonk Marcel L. , Cole Jason C. , Taylor Robin
Published: October 2002

We present a large test set of protein–ligand complexes for the purpose of validating algorithms that rely on the prediction of protein–ligand interactions. The set consists of 305 complexes with protonation states assigned by manual inspection. The following checks have been carried out to identify unsuitable entries in this set: (1) assessing the involvement of crystallographically related protein units in ligand binding; (2) identification of bad clashes between protein side chains and ligand; and (3) assessment of structural errors, and/or inconsistency of ligand placement with crystal structure electron density. In addition, the set has been pruned to assure diversity in terms of protein–ligand structures, and subsets are supplied for different protein‐structure resolution ranges. A classification of the set by protein type is available. As an illustration, validation results are shown for GOLD and SuperStar. GOLD is a program that performs flexible protein–ligand docking, and SuperStar is used for the prediction of favorable interaction sites in proteins. The new CCDC/Astex test set is freely available to the scientific community (http://www.ccdc.cam.ac.uk). Proteins 2002;49:457–471. © 2002 Wiley‐Liss, Inc.
Docking of non‐nucleoside inhibitors: Neotripterifordin and its derivatives to HIV‐1 reverse transcriptase
Authors: Zhou Zhigang , Madrid Marcela , Madura Jeffry D.
Published: October 2002

The docking of small molecules to proteins has played an important role in the understanding of drug/receptor interactions. An important drug/receptor interaction is between non‐nucleoside inhibitors of HIV‐1 RT and the non‐nucleoside binding pocket. We report the results of docking calculations in which we have docked known and proposed non‐nucleoside reverse transcriptase inhibitors to the type 1 virus. The proposed NNRTIs dock in a similar position and orientation as known inhibitors. In addition, we observe a linear correlation between the calculated interaction energy and EC50 for the inhibitors, suggesting that the docked structure orientation and the interaction energies are reasonable. Two hydrogen bonds between nevirapine and RT (3HVT and 1VRT) are observed and are reproduced across different docking schemes. Since we used two different HIV‐1 RT crystal structures (3HVT and 1VRT), which are at different levels of resolution (2.9 and 2.2 Å, respectively), we propose that structures with resolutions better than 3 Å can be used to produce reasonable docking results. Proteins 2002;49:529–542. © 2002 Wiley‐Liss, Inc.
Ligand specificity and ligand‐induced conformational change in gal repressor
Authors: Chatterjee Sumana , Ghosh Kajari , Dhar Amlanjyoti , Roy Siddhartha
Published: October 2002

Gal repressor (GalR) binds D‐galactose, which is responsible for lifting of repression of the gal operon. Proton T1 measurements of α‐ and β‐anomers of galactose as a function of gal repressor show preferential binding of the β‐anomer. The β‐anomer was isolated by high‐performance liquid chromatography and was shown to bind tightly to GalR. Calorimetry was used to determine enthalpy changes at several temperatures. Heat capacity change was found to be positive, indicating that a significant amount of hydrophobic surface area was exposed upon galactose binding. Bis‐ANS binding to GalR is significantly enhanced in the presence of a saturating amount of galactose, indicating additional exposure of hydrophobic surfaces. We propose that the galactose‐induced conformational change involves the opening of the two subdomains, which may disrupt protein–protein interactions responsible for repression. Proteins 2002;49:554–559. © 2002 Wiley‐Liss, Inc.
Stability scale and atomic solvation parameters extracted from 1023 mutation experiments
Authors: Zhou Hongyi , Zhou Yaoqi
Published: October 2002

The stability scale of 20 amino acid residues is derived from a database of 1023 mutation experiments on 35 proteins. The resulting scale of hydrophobic residues has an excellent correlation with the octanol‐to‐water transfer free energy corrected with an additional Flory–Huggins molar‐volume term (correlation coefficient r = 0.95, slope = 1.05, and a near zero intercept). Thus, hydrophobic contribution to folding stability is characterized remarkably well by transfer experiments. However, no corresponding correlation is found for hydrophilic residues. Both the hydrophilic portion and the entire scale, however, correlate strongly with average burial accessible surface (r = 0.76 and 0.97, respectively). Such a strong correlation leads to a near uniform value of the atomic solvation parameters for atoms C, S, O/N, O−0.5, and N+0.5,1. All are in the range of 12–28 cal mol−1 Å−2, close to the original estimate of hydrophobic contribution of 25–30 cal mol−1 Å−2 to folding stability. Without any adjustable parameters, the new stability scale and new atomic solvation parameters yielded an accurate prediction of protein–protein binding free energy for a separate database of 21 protein–protein complexes (r = 0.80 and slope = 1.06, and r = 0.83 and slope = 0.93, respectively). Proteins 2002;49:483–492. © 2002 Wiley‐Liss, Inc.
Influence of induced fit in the interaction of Bacillus subtilis trp RNA‐binding attenuator protein and its RNA antiterminator target oligomer
Authors: Flynn Peter F. , Wendt Alice , Gollnick Paul
Published: October 2002

In the presence of excess tryptophan, tryptophan‐activated TRAP (trp RNA‐binding attenuator protein) binds to a specific target in the trp‐leader transcript, which induces the formation of a transcription terminator and transcription halts in the leader region. In the absence of tryptophan, TRAP does not bind RNA, an antiterminator forms, and the operon is expressed. Although the ternary complex involving TRAP (Bacillus stearothermophilus), tryptophan, and the RNA target has recently been crystallized, efforts to obtain structural data for the apo‐form of TRAP (in any species) have not been successful. We have used multidimensional/multinuclear nuclear magnetic resonance (NMR) spectroscopy to probe the structure–function relationship in the TRAP‐activated system, and have obtained high‐resolution multidimensional/multinuclear NMR spectra of TRAP in all three of its functional states: tryptophan‐free or apo‐TRAP, tryptophan‐activated TRAP, and tryptophan‐activated TRAP‐RNA ternary complex. Chemical shift perturbation analysis of the NMR data clarifies the interpretation of results obtained from previous crystal studies. Results presented herein demonstrate that tryptophan binding induces an essential structural change in TRAP that supports high‐affinity binding of the RNA target oligonucleotide. Proteins 2002;49:432–438. © 2002 Wiley‐Liss, Inc.