Quantification of secondary structure prediction improvement using multiple alignments

The use of multiple sequence alignments for secondary structurepredictions is analysed. Seven different protein families, containingonly sequences of known structure, were considered to providea range of alignment and prediction conditions. Using alignmentsobtained by spatial superposition of main chain atoms in knowntertiary protein structures allowed a mean of 8% in secondarystructure prediction accuracy, when compared to those obtainedfrom the individual sequences. Substitution of these alignmentsby those determined directly from an automated sequence alignmentalgorithm showed variations in the prediction accuracy whichcorrelated with the quality of the multiple alignments and distanceof the primary sequence. Secondary structure predictions canbe reliably improved using alignments from an automatic alignmentprocedure with a mean increase of 6.87percnt;, giving an overallprediction accuracy of 68.5%, if there is a minimum of 25% sequenceidentity between all sequences in a family.     

THE “UCKRON-1” TEST PROBLEM FOR REACTION ENGINEERING MODELING

Testing kinetic models against a “true” and detailed kinetic expression was the aim of the Workshop on Kinetic Model Development at the Denver AIChE Meeting in August, 1983. For this purpose an artificial reaction mechanism was created, based on the known thermodynamics of the methanol synthesis as a framework. The kinetic rate laws, that were derived from this mechanism, were made thermodynamically consistent by achieving agreement between equilibrium constants calculated at various temperatures from the given, real original thermodynamic relationship and those calculated from the detailed reversible kinetic expressions.

Using the artificial kinetics as the "true" one, CSTR experiments were simulated. The results of a statistically designed set of experiments were published after 5% random error was added to the data. Participation was invited for all interested to correlate the data, develop kinetic models and to calculate the performance of the specified reactor.

The results of 19 submitted entries are summarized with the conclusion that the models had more differences than were expected, but their predictive values were not as different as was anticipated, if the extreme high production rates due to thermal runaways are not considered. This in turn points out the necessity to check models experimentally, in pilot plant, not only for predicted optimum, but also for calculated runaway conditions. Models which did not capture the true character of this reaction failed to predict the onset of runaway reactions.     

Microstructure and morphology of amine-cured epoxy coatings before and after outdoor exposures—An AFM study

Atomic force microscopy (AFM) has been used to study the morphology and microstructure of an amine-cured epoxy before and after outdoor exposure. Measurements were made from samples prepared in an essentially CO₂-free, H₂O-free glove box and from samples prepared in ambient conditions. For those prepared in a CO₂-free glove box, AFM imaging was conducted on (1) an unexposed air/coating surface, (2) an unexposed coating bulk, (3) an unexposed coating/substrate interface, and (4) a field exposed air/coating surface. For samples prepared in ambient conditions, only the unexposed air/coating surface was investigated. The same regions of the exposed samples were scanned periodically by the AFM to monitor changes in the surface morphology of the coating as UV exposure progressed. Small angle neutron scattering and Fourier transform infrared spectroscopy (FTIR) studies were performed to verify the microstructure and to follow chemical changes during outdoor exposure, respectively. The results have shown that amine blushing, which occurs only under ambient conditions, had a significant effect on the surface morphology and microstructure of the epoxy. The surface morphology of the samples prepared under CO₂-free, dry conditions was generally smooth and homogeneous. However, the interface and the bulk samples clearly revealed a two-phase structure consisting of bright nodular domains and dark interstitial regions, indicating an inhomogeneous microstructure. Such heterogeneous structure of the bulk was in good agreement with results obtained by small angle neutron scattering of unexposed samples and by AFM phase imaging of the degraded sample surface. The relationship between submicrometer physical changes and molecular chemical degradation is discussed. Presented at the 82nd Annual Meeting of the Federation of Societies for Coatings Technology, October 27–29, 2004, in Chicago, IL.     

An accelerated algorithm for full band electron–phonon scattering rate computation

Computing scattering rates of electrons and phonons stands at the core of studies of electron transport properties. In the high field regime, the interactions between all electron bands with all phonon bands need to be considered. This full band interaction implies a huge computational burden in calculating scattering rates. In this study, a new accelerated algorithm is presented for this task, which speeds up the computation by two orders of magnitude (100 times) and dramatically simplifies the coding. At the same time, it visually demonstrates the physical process of scattering more clearly.     

FA composition and regiospecific analysis of Acer saccharum (sugar maple tree) and Acer saccharinum (silver maple tree) seed oils

GC analysis was performed to determine regiospecific distribution and FA composition in seed oils of the Aceraceae species, Acer saccharum and A. saccharinum. The oil content in the seeds was low at 5.0% in A. saccharum and 5.8% in A. saccharinum, and the main FA were linoleic (30.8 and 29.4%), oleic (21.3 and 27.6%), palmitic (10.1 and 10.5%), and cis-vaccenic (9.4 and 7.9%) acids, respectively. In addition, both oils contained long-chain monoenes of the n−9 and n−7 groups, including 11-eicosenoic, 13-docosenoic, 15-tetracosenoic, 13-eicosenoic, and 15-docosenoic acids, whereas γ-linolenic acid accounted for 0.8% of total FA in A. saccharum, and 0.5% in A. saccharinum. Regiospecific analysis, performed using the methodology of dibutyroyl derivatives of MAG, indicated that linoleic, oleic, and linolenic acids were mainly esterified at the internal position of TAG in both seed oils, whereas long-chain monoenes of the n−7 group were almost exclusively esterified on the external positions.     

阳极氧化铝的表面参数对硅酮结构的装锒密封胶长期黏结性的影响(连载一)

硅酮密封胶对阳极氧化铝的黏结质量千差万别.影响黏结性的关键因素是铝材表面的封孔程度、氧化层的着色情况、清洁剂的特性以及基材表面清洁与打胶之间允许的时间间隔.由于清洁剂将有机污染物从阳极氧化铝表面去除的效果不同,所以此效果并不和黏结质量有必然联系.据猜测,吸附在阳极氧化铝表面的清洁溶剂会改善基材表面从而提高硅酮胶的黏结性,但这种改善效果会随着清洁溶剂随时间的的挥发而降低.对于给定的溶剂,最佳的黏结效果取决于材料表面的封孔程度.依照ISO 2143酸刻蚀方法测量材料表面的封孔程度,可以预测未着色的阳极氧化铝基材的黏结性.对于着色的阳极氧化铝表面,依照ISO 2931的测试标准,用电相位漂移方法可以用来预测黏结质量.一种控制阳极氧化铝表面的方法被提了出来,此方法是测量不同频率下基材的电阻抗并将它成功地和硅酮密封胶与该材料表面的长期黏接性联系起来.     

Stability of ruthenium catalysts supported on TiO2 or ZrO2 in catalytic wet air oxidation

The stability of ruthenium catalysts supported on TiO₂ and ZrO₂ were studied in the wet air oxidation of aqueous solution of succinic and p-hydroxybenzoic acids taken as model effluent and on real effluents from the paper-pulp industry. Catalyst recycling experiments were conducted in batch reactor and long-term stability tests were conducted in trickle-bed reactor. In all experiments, ruthenium and support materials were perfectly stable to leaching, sintering and fouling. Ruthenium catalysts experienced a weak deactivation as they were exposed to air, e.g., in recycling experiments however the loss of activity occurred only after the first exposure and was completely reversible upon catalyst reduction. The deactivation was attributed to an over-oxidation of the catalyst surface particularly noticeable in the case of very small Ru-clusters (1 nm).     

A generalist herbivore in a specialist mode Metabolic,sequestrative, and defensive consequences

Adults of a generalist herbivore, the lubber grasshopper,Romalea guttata, can be converted to functional specialists by feeding them exclusively on catnip,Nepeta cataria. No obvious adverse effects on adult development resulted from this enforced monophagy. Notwithstanding the fact thatR. guttata has had no coevolutionary relationship with this Eurasian mint, it readily sequesters compounds that are identical to or derived from the terpenoid lactones that are characteristic ofN. cataria. R. guttata appears to both biomagnify minor allelochemicals and to sequester metabolites of theNepeta terpenes in its paired defensive glands. The levels of autogenously produced phenolics are not affected by feeding onN. cataria and the defensive secretions of catnip-fed grasshoppers are more repellent to ants than those of wild-fed acridids. Metabolites of theN. cataria monoterpenes are sequestered in the defensive glands when catnip is added to the natural diet ofR. guttata. The ability of a generalist,R. guttata, to facilely bioaccumulate a potpourri of foreign allelochemicals when feeding in a specialist mode is analyzed in terms of its biochemical, physiological, and functional significance. Sequestration is examined as a response to the enteric effronteries represented by the phytochemicals that can be characteristic of the overload in a monophagous diet.     

Esterification and Transesterification of Renewable Chemicals

An overview is given of newly developed Lewis or Brønsted acid and base catalysts for esterification, transesterification and ester interchange reactions. The most relevant applications of these catalysts and reactions in the domain of renewable resources, in particular, oils and fats, are discussed.     

Optimization of an herbicide release from ethylcellulose microspheres

Summary The herbicide 2,4-D was microencapsulated using ethyl cellulose to develop controlled release formulations that protect it from photodegradation and evaporation and to reduce the environment pollution. Ethyl cellulose microspheres loaded with 2,4-D were prepared by the emulsion solvent-evaporation technique. We have obtained the desired microspheres with higher drug entrapment and encapsulation yield by varying certain conditions as stirring speed, polymer-solvent ratio, drug-polymer ratio, pH of continuous phase and organic phase solvent. The shape and size of microspheres were analysed by scanning electron microscopy. The herbicide release was studied at 25 °C and the release data were analysed according to Fick’s Law. The results demonstrate that we can control the release rate by modifying the process parameters.