bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thermo‐oxidative degradation of HDPE as a function of its crystalline content
Authors: Avalos‐Belmontes Felipe , Zapata‐Gonzalez Ivan , Ramos‐De Valle Luis F. , Zitzumbo‐Guzman Roberto , Alonso‐Romero Sergio 
Published: August 2009

AbstractThe composition, the thermal properties, and the kinetics of the thermo‐oxidative degradation of high‐density polyethylene (HDPE) were studied as a function of the increasing crystalline fraction, which resulted from the selective extraction of the amorphous part, through digestion by immersion in fuming nitric acid (HNO3) for different periods of time. The chemical and thermodynamic changes in HDPE, brought about by digestion in nitric acid for different periods of time, are discussed. Changes in the chemistry and microstructure of the HDPE, as a function of acid treatment for different periods of time, were studied using infra‐red spectroscopy (FTIR), gel permeation chromatography (GPC), and thermal analysis (DSC and TGA), as well as scanning electron microscopy (SEM). These studies were carried out as a function of the extracted amorphous fraction of HDPE samples via digestion in HNO3. These studies showed that in the first stages of the acid chemical attack, the amorphous part first undergoes a chemical modification and then dissolves into the strong acid medium. The total crystalline fraction apparently decreases during the first stages of the chemical attack and then increases as the amorphous part is extracted. TGA results show that as the selective extraction of the amorphous part occurs, there is a displacement of the thermo‐oxidative degradation toward higher temperatures. The kinetics of the thermo‐oxidative degradation as a function of the extraction of the amorphous part was followed according to the Horowitz‐Metzger method, and it was found that as the concentration of the crystalline fraction increases, the activation energy for the thermo‐oxidative degradation increases. SEM studies show that the extraction of the amorphous part does not affect the size of the crystalline lamellar thickness of HDPE. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 1906–1915, 2009
Noncovalent functionalization of multiwalled and double‐walled carbon nanotubes: Positive effect of the filler functionalization on high glass transition temperature epoxy resins
Authors: Prado L. A. S. de A. , De La Vega A. , Sumfleth J. , Schulte K. 
Published: August 2009

AbstractDouble‐walled carbon nanotubes (DWCNTs) and multiwalled carbon nanotubes (MWCNTs) were modified using melamine to attach NH2 to the surface of these fillers, without previous oxidation of their graphene layers. FT‐Raman, elemental (chemical) and thermogravimetric analysis, confirmed the modification, which was more extensive for DWCNTs. The potential of this modification was evaluated by adding the melamin‐modified nanotubes to thermosets based on diglycidyl ether of bisphenol A (resin) and polycyclic amine (hardener). Broadening of the glass transition interval and an increase between 7 and 8 °C of the glass transition temperatures show better filler/matrix interaction for the nanocomposites based on melamine‐modified nanotubes. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 1860–1868, 2009
Effect of postcasting heat‐treatment on the structure and properties of semicrystalline phase‐inversion poly(vinylidene fluoride) membranes
Authors: Lin Dar‐Jong , Chang Hsu‐Hsien , Beltsios Konstantinos , Don Trong‐Ming , Jeng Yi‐Su , Cheng Liao‐Ping 
Published: August 2009

AbstractMicroporous PVDF membranes were prepared by immersion‐precipitation in 1‐octanol of casting dopes dissolved at different temperatures, with dissolution temperature affecting strongly the membrane microstructure. The effect of postcoagulation thermal annealing, which is an additional thermal parameter, on membrane microstructure and properties is probed herein. Membranes obtained were annealed at temperatures up to 160 °C, which is close to the melting point of PVDF polymer. Annealing leads to a substantial modification of the nano‐scale fine structure of the membranes, while the overall‐microporous structure is preserved. At elevated annealing temperatures, nano‐grains, fibrils, and stick‐like crystalline entities gradually eclipse, while globules develop more robust connections based on wide bands of crystal elements. Probing by X‐ray diffraction and dynamic scanning calorimetry shows that crystallinity increases when annealing temperature and time are increased. As regards mechanical properties, the tensile strength of the membranes can be enhanced substantially, up to about 10 times, upon appropriate high temperature prolonged annealing. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 1880–1893, 2009
Nylon‐6 nanocomposites, study of the influence of the nanofiller nature on morphology and material properties
Authors: Tabuani Daniela , Ceccia Simona , Camino Giovanni 
Published: August 2009

AbstractIn this article we investigated the influence of various nanofilllers' aspect ratio, chemical nature, and organic modification on some selected nylon‐6 properties, such as crystallinity, thermal and mechanical resistance, and fire behavior. Materials were prepared by twin‐screw extrusion and characterized by means of scanning and transmission electron microscopy, X‐ray diffraction, thermogravimetric analysis, tensile tests, and cone calorimeter. Fillers characteristics were found to influence at different extents the material final properties. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 1935–1948, 2009
Temperature and urea induced denaturation of the TRP‐cage mini protein TC5b: A simulation study consistent with experimental observations
Authors: Gattin Z. , Riniker S. , Hore P. J. , Mok K. H. , van Gunsteren W. F. 
Published: August 2009

AbstractThe effects of temperature and urea denaturation (6M urea) on the dominant structures of the 20‐residue Trp‐cage mini‐protein TC5b are investigated by molecular dynamics simulations of the protein at different temperatures in aqueous and in 6M urea solution using explicit solvent degrees of freedom and the GROMOS force‐field parameter set 45A3. In aqueous solution at 278 K, TC5b is stable throughout the 20 ns of MD simulation and the trajectory structures largely agree with the NMR‐NOE atom–atom distance data available. Raising the temperature to 360 K and to 400 K, the protein denatures within 22 ns and 3 ns, showing that the denaturation temperature is well below 360 K using the GROMOS force field. This is 40–90 K lower than the denaturation temperatures observed in simulations using other much used protein force fields. As the experimental denaturation temperature is about 315 K, the GROMOS force field appears not to overstabilize TC5b, as other force fields and the use of continuum solvation models seem to do. This feature may directly stem from the GROMOS force‐field parameter calibration protocol, which primarily involves reproduction of condensed phase thermodynamic quantities such as energies, densities, and solvation free energies of small compounds representative for protein fragments. By adding 6M urea to the solution, the onset of denaturation is observed in the simulation, but is too slow to observe a particular side‐chain side‐chain contact (Trp6‐Ile4) that was experimentally observed to be characteristic for the denatured state. Interestingly, using temperature denaturation, the process is accelerated and the experimental data are reproduced.
Crystal structure of a trimeric form of the KV7.1 (KCNQ1) A‐domain tail coiled‐coil reveals structural plasticity and context dependent changes in a putative coiled‐coil trimerization motif
Authors: Xu Qiang , Minor Daniel L. 
Published: August 2009

AbstractCoiled‐coils are widespread protein–protein interaction motifs typified by the heptad repeat (abcdefg)n in which “a” and “d” positions are hydrophobic residues. Although identification of likely coiled‐coil sequences is robust, prediction of strand order remains elusive. We present the X‐ray crystal structure of a short form (residues 583–611), “Q1‐short,” of the coiled‐coil assembly specificity domain from the voltage‐gated potassium channel Kv7.1 (KCNQ1) determined at 1.7 Å resolution. Q1‐short lacks one and half heptads present in a previously studied tetrameric coiled‐coil construct, Kv7.1 585–621, “Q1‐long.” Surprisingly, Q1‐short crystallizes as a trimer. In solution, Q1‐short self‐assembles more poorly than Q1‐long and depends on an R‐h‐x‐x‐h‐E motif common to trimeric coiled‐coils. Addition of native sequences that include “a” and “d” positions C‐terminal to Q1‐short overrides the R‐h‐x‐x‐h‐E motif influence and changes assembly state from a weakly associated trimer to a strongly associated tetramer. These data provide a striking example of a naturally occurring amino sequence that exhibits context‐dependent folding into different oligomerization states, a three‐stranded versus a four‐stranded coiled‐coil. The results emphasize the degenerate nature of coiled‐coil energy landscapes in which small changes can have drastic effects on oligomerization. Discovery of these properties in an ion channel assembly domain and prevalence of the R‐h‐x‐x‐h‐E motif in coiled‐coil assembly domains of a number of different channels that are thought to function as tetrameric assemblies raises the possibility that such sequence features may be important for facilitating the assembly of intermediates en route to the final native state.
Computational design of Candida boidinii xylose reductase for altered cofactor specificity
Authors: Khoury George A. , Fazelinia Hossein , Chin Jonathan W. , Pantazes Robert J. , Cirino Patrick C. , Maranas Costas D. 
Published: August 2009

AbstractIn this study we introduce a computationally‐driven enzyme redesign workflow for altering cofactor specificity from NADPH to NADH. By compiling and comparing data from previous studies involving cofactor switching mutations, we show that their effect cannot be explained as straightforward changes in volume, hydrophobicity, charge, or BLOSUM62 scores of the residues populating the cofactor binding site. Instead, we find that the use of a detailed cofactor binding energy approximation is needed to adequately capture the relative affinity towards different cofactors. The implicit solvation models Generalized Born with molecular volume integration and Generalized Born with simple switching were integrated in the iterative protein redesign and optimization (IPRO) framework to drive the redesign of Candida boidinii xylose reductase (CbXR) to function using the non‐native cofactor NADH. We identified 10 variants, out of the 8,000 possible combinations of mutations, that improve the computationally assessed binding affinity for NADH by introducing mutations in the CbXR binding pocket. Experimental testing revealed that seven out of ten possessed significant xylose reductase activity utilizing NADH, with the best experimental design (CbXR‐GGD) being 27‐fold more active on NADH. The NADPH‐dependent activity for eight out of ten predicted designs was either completely abolished or significantly diminished by at least 90%, yielding a greater than 104‐fold change in specificity to NADH (CbXR‐REG). The remaining two variants (CbXR‐RTT and CBXR‐EQR) had dual cofactor specificity for both nicotinamide cofactors.
Structure‐based design of novel Chlamydomonas reinhardtii D1‐D2 photosynthetic proteins for herbicide monitoring
Authors: Rea Giuseppina , Polticelli Fabio , Antonacci Amina , Scognamiglio Viviana , Katiyar Prashant , Kulkarni Sudhir A. , Johanningmeier Udo , Giardi Maria Teresa 
Published: August 2009

AbstractThe D1‐D2 heterodimer in the reaction center core of phototrophs binds the redox plastoquinone cofactors, QA and QB, the terminal acceptors of the photosynthetic electron transfer chain in the photosystem II (PSII). This complex is the target of the herbicide atrazine, an environmental pollutant competitive inhibitor of QB binding, and consequently it represents an excellent biomediator to develop biosensors for pollutant monitoring in ecosystems. In this context, we have undertaken a study of the Chlamydomonas reinhardtii D1‐D2 proteins aimed at designing site directed mutants with increased affinity for atrazine. The three‐dimensional structure of the D1 and D2 proteins from C. reinhardtii has been homology modeled using the crystal structure of the highly homologous Thermosynechococcus elongatus proteins as templates. Mutants of D1 and D2 were then generated in silico and the atrazine binding affinity of the mutant proteins has been calculated to predict mutations able to increase PSII affinity for atrazine. The computational approach has been validated through comparison with available experimental data and production and characterization of one of the predicted mutants. The latter analyses indicated an increase of one order of magnitude of the mutant sensitivity and affinity for atrazine as compared to the control strain. Finally, D1‐D2 heterodimer mutants were designed and selected which, according to our model, increase atrazine binding affinity by up to 20 kcal/mol, representing useful starting points for the development of high affinity biosensors for atrazine.
How strong are side chain interactions in the folding intermediate?
Authors: Samatova Ekaterina N. , Katina Natalia S. , Balobanov Vitaly A. , Melnik Bogdan S. , Dolgikh Dmitry A. , Bychkova Valentina E. , Finkelstein Alexei V. 
Published: August 2009

AbstractInfluence of 12 nonpolar amino acids residues from the hydrophobic core of apomyoglobin on stability of its native state and folding intermediate was studied. Six of the selected residues are from the A, G and H helices; these are conserved in structure of the globin family, although nonfunctional, that is, not involved in heme binding. The rest are nonconserved hydrophobic residues that belong to the B, C, D, and E helices. Each residue was substituted by alanine, and equilibrium pH‐induced transitions in apomyoglobin and its mutants were studied by circular dichroism and fluorescent spectroscopy. The obtained results allowed estimating changes in their free energy during formation of the intermediate state. It was first shown that the strength of side chain interactions in the apomyoglobin intermediate state amounts to 15–50% of that in its native state for conserved residues, and practically to 0% for nonconserved residues. These results allow a better understanding of interactions occurring in the intermediate state and shed light on involvement of certain residues in protein folding at different stages.
Differential stability of the bovine prion protein upon urea unfolding
Authors: Julien Olivier , Chatterjee Subhrangsu , Thiessen Angela , Graether Steffen P. , Sykes Brian D. 
Published: August 2009

AbstractPrion diseases, or transmissible spongiform encephalopathies, are a group of infectious neurological diseases associated with the structural conversion of an endogenous protein (PrP) in the central nervous system. There are two major forms of this protein: the native and noninfectious cellular form, PrPC; and the misfolded, infectious, and proteinase K‐resistant form, PrPSc. The C‐terminal domain of PrPC is mainly α‐helical in structure, whereas PrPSc in known to aggregate into an assembly of β‐sheets, forming amyloid fibrils. To identify the regions of PrPC potentially involved in the initial steps of the conversion to the infectious conformation, we have used high‐resolution NMR spectroscopy to characterize the stability and structure of bovine recombinant PrPC (residues 121 to 230) during unfolding with the denaturant urea. Analysis of the 800 MHz 1H NMR spectra reveals region‐specific information about the structural changes occurring upon unfolding. Our data suggest that the dissociation of the native β‐sheet of PrPC is a primary step in the urea‐induced unfolding process, while strong hydrophobic interactions between helices α1 and α3, and between α2 and α3, stabilize these regions even at very high concentrations of urea.
Characterization of the SRP68/72 interface of human signal recognition particle by systematic site‐directed mutagenesis
Authors: Iakhiaeva Elena , Hinck Cynthia S. , Hinck Andrew P. , Zwieb Christian 
Published: August 2009

AbstractThe signal recognition particle (SRP) is a ribonucleoprotein complex which is crucial for the delivery of proteins to cellular membranes. Among the six proteins of the eukaryotic SRP, the two largest, SRP68 and SRP72, form a stable SRP68/72 heterodimer of unknown structure which is required for SRP function. Fragments 68e′ (residues 530 to 620) and 72b′ (residues 1 to 166) participate in the SRP68/72 interface. Both polypeptides were expressed in Escherichia coli and assembled into a complex which was stable at high ionic strength. Disruption of 68e′/72b′ and SRP68/72 was achieved by denaturation using moderate concentrations of urea. The four predicted tetratricopeptide repeats (TPR1 to TPR4) of 72b′ were required for stable binding of 68e′. Site‐directed mutagenesis suggested that they provide the structural framework for the binding of SRP68. Deleting the region between TPR3 and TPR4 (h120) also prevented the formation of a heterodimer, but this predicted alpha‐helical region appeared to engage several of its amino acid residues directly at the interface with 68e′. A 39‐residue polypeptide (68h, residues 570–605), rich in prolines and containing an invariant aspartic residue at position 585, was found to be active. Mutagenesis scanning of the central region of 68h demonstrated that D585 was solely responsible for the formation of the heterodimer. Coexpression experiments suggested that 72b′ protects 68h from proteolytic digestion consistent with the assertion that 68h is accommodated inside a groove formed by the superhelically arranged four TPRs of the N‐terminal region of SRP72.
Towards low energy physics from the heterotic string
Authors: Ramos‐Sánchez S. 
Published: August 2009

AbstractWe investigate orbifold compactifications of the heterotic string, addressing in detail their construction, classification and phenomenological potential. We present a strategy to search for models resembling the minimal supersymmetric extension of the standard model (MSSM) in ℤ6‐II orbifold compactifications. We find several MSSM candidates with the gauge group and the exact spectrum of the MSSM, and supersymmetric vacua below the compactification scale. They also exhibit the following realistic features: R‐parity, seesaw suppressed neutrino masses, and intermediate scale of supersymmetry breakdown. In addition, we find that similar models also exist in other ℤN orbifolds and in the SO(32) heterotic theory.
Parametric self pulsing in a quantum opto‐mechanical system
Authors: Holmes C.A. , Milburn G.J. 
Published: August 2009

AbstractWe describe an opto‐mechanical system in which the coupling between optical and mechanical degrees of freedom takes the form of a fully quantised third‐order parametric interaction. Two physical realisations are proposed: a harmonically trapped atom in a standing wave and the ‘membrane in the middle’ model. The dominant resonant interaction corresponds to a stimulated Raman process in which two phonons are converted into a single cavity photon. We show that this system can exhibit a stable limit‐cycle in which energy is periodically exchanged between optical and mechanical degrees of freedom. This is equivalently described as a parametric self‐pulsing.
Initial charge carrier dynamics in porous silicon revealed by time‐resolved fluorescence and transient reflectivity
Authors: Juška Gediminas , Medvids Arturs , Gulbinas Vidmantas 
Published: August 2009

AbstractNonequilibrium charge carrier relaxation dynamics in porous silicon was investigated by means of time‐resolved photoluminescence and ultrafast transient reflectance. Fluorescence band shift to the low energy side and intensity decay were observed during several initial nanoseconds under porous silicon excitation at 3.3 eV, and attributed to the spectral diffusion and trapped carrier recombination. Ultrafast transient reflectance pump–probe technique reveals reflectance dynamics on a several ps time scale present with 3.1 eV excitation, but absent with excitation at 1.77 eV.
Disorder effects on electronic and optical properties of the ternary GaxIn1−xP (x = 0.25, 0.50, and 0.75) alloy
Authors: Kumar S. , Parashari Satyam S. , Auluck S. 
Published: August 2009

AbstractWe have performed first‐principles calculations for the electronic and optical properties of GaxIn1−xP alloys for compositions x = 25, 50, and 75%. The effects of Ga composition on the electronic density of states, dielectric functions, and pressure coefficients are discussed in detail using a simple cubic structure and a special quasi‐random structure. Effective masses are calculated along the Γ(000) symmetry point. Overall, the calculated properties are in agreement with the available experimental data. Our calculations show that the direct band gap and the electron effective masses vary nonlinearly with concentration x.
Oxide glasses with magnetic nanoparticles: transparent magnets (Faraday rotation and electron magnetic resonance studies)
Authors: Edelman Irina , Kliava Janis 
Published: August 2009

AbstractIn the first part of this paper we outline the state of the art in the field of magnetic nanoparticles in oxide glasses. We describe the theoretical background of two complementary techniques used for the studies of the state of paramagnetic ions, clusters and magnetic particles in a diamagnetic matrix, viz., magnetooptical Faraday rotation (FR) and electron magnetic resonance (EMR) and we overview previous results obtained with these techniques for several glass systems. In the second part, we highlight the case of potassium‐alumina‐borate glasses – a glassy system where doping with paramagnetic oxides results in formation of magnetic particles at very low contents of paramagnetic additions: Fe2O3 and MnO. In the special case when the ratio of the iron and manganese oxides in the charge is 3/2, magnetic nanoparticles with characteristics close to those of manganese ferrite are formed already at the first stage of the glass preparation. After thermal treatment all glasses show FR and EMR spectra attesting to the presence of superparamagnetic nanoparticles, characterized by relatively broad size and shape distributions. The formation of magnetic nanoparticles confers to these glasses magnetic and magneto‐optical properties typical of magnetically ordered substances. At the same time, the glasses remain transparent in a part of the visible and near infrared spectral range and display a high FR value. Such properties make them particularly interesting for use as new media for various magneto‐optical devices.
Analysis of Raman modes in Mn‐doped ZnO nanocrystals
Authors: Guo Shuxia , Du Zuliang , Dai Shuxi 
Published: August 2009

AbstractMn‐doped ZnO was synthesized using a co‐precipitation technique. X‐ray diffraction (XRD) measurements and photoluminescence (PL) spectra show that Mn ions are doped into the lattice positions of ZnO. The modes at 202, 330, and 437 cm−1 in the Raman spectrum are assigned as 2E2 (low), E2 (high)–E2 (low), and E2 (high) modes of ZnO base, respectively. The mode at 528 cm−1 is ascribed to a local vibrational mode related to Mn. The mode at 580 cm−1 should be an intrinsic mode of ZnO and assigned to E1 longitudinal optical (LO). Its reinforcement should result from a combination of resonance at the excitation wavelength and impurity‐induced scattering.