The role of electrostatic interactions in the mechanism of peptide bond hydrolysis by a Ser-Lys catalytic dyad

General-base catalysis in the active site of serine proteasesis carried out by the imidazole side chain of a histidine. Duringformation of the transition state, an adjacent carboxylic acidgroup stabilizes the positive charge that forms on the general-basecatalyst and as a result contributes several orders of magnitudeto the catalytic efficiency of these enzymes. In the recentlydiscovered family of self-cleaving proteins exemplified by theLexA repressor of Escherichia coli, instead of the imidazoleof a histidine, the active-site general-base catalyst was foundto be the -amino of a lysine. The considerably higher capacityof the lysine side chain for proton acceptance raises interestingquestions concerning the role of electrostatic interactionsin the mechanism of proton transfer by this highly basic group.The negative charge elimination studies described here and theireffects on the k_max and pK of LexA self-cleavage are consistentwith a model in which electrostatic interactions between anacidic side chain and the general-base catalyst form a barrierto proton transfer. The implications are that the -amino group,unlike the imidazole group, is capable of effecting proton transferwithout the intervention of a countercharge.     

Querying and creating visualizations by analogy

While there have been advances in visualization systems, particularly in multi-view visualizations and visual exploration, the process of building visualizations remains a major bottleneck in data exploration. We show that provenance metadata collected during the creation of pipelines can be reused to suggest similar content in related visualizations and guide semi-automated changes. We introduce the idea of query-by-example in the context of an ensemble of visualizations, and the use of analogies as first-class operations in a system to guide scalable interactions. We describe an implementation of these techniques in VisTrails, a publicly-available, open-source system.     

Beating the heat [CMOS hot-carrier reliability]

CMOS hot-carrier reliability at both transistor and circuit levels has been examined. Accurate reliability assessment requires defining suitable criteria for acceptable performance for both circuit and individual transistors. As device designers meet demands for greater speed and more complex circuitry accompanied by shrinking the size of transistor into the deep-submicron regime, they have to contend with increase in current densities and higher electric fields. Though in general a MOSFET's driving capability increases as the channel length decreases, the resulting high field will eventually limit the driving capability of the device. The authors discuss improving CMOS hot-carrier reliability through analysis, modelling and simulation     

Modelization of the whispering gallery mode in microgear resonators using the Floquet-Bloch formalism

In this paper, a two-dimensional (2-D) method describing the whispering gallery mode in a microgear resonator is presented. The microgear is a microdisk surrounded by a circular grating. The method, which is based on the Floquet-Bloch formalism, analytically describes the field within the disk and outside the grating. On the other hand, the field within the grating is calculated using a finite-difference scheme in polar coordinates. Matching the boundary conditions, it is possible to work in a forced oscillation regime or in a free oscillation regime (laser mode). The resonant wavelength and quality factor can then be deduced. Compared to the coupled mode theory and to 2-D finite-difference time-domain computations, the method is faster and more accurate. Moreover, a polarization effect of the microgear is demonstrated. The TE polarization experiences a Q-factor improvement contrary to TM polarization. Finally, microgear structures prove to be more efficient than micro flowers.     

Performance Bound for LDPC Coded Unitary Space–Time Modulation

This paper is concerned with the bit error probability (BEP) of coded unitary space–time modulation systems based on finite-length low density parity check (LDPC) codes. The union bound on the BEP of the maximum likelihood (ML) decoding is derived for any code rate, unitary space–time constellation and mapping. The tightness of the bound is checked with simulation results of the ordered statistic decoding (OSD). Numerical and simulation results show that the union bound is also close to the error performance of the sum–product (SP) decoding at low BEP levels when Gray mapping is employed. The derived bound is useful to benchmark the error performance of finite-length coded unitary space–time modulation systems, especially for those that employ short-to-medium length LDPC codes.

Poly(aryl-ether-ether-ketone) and its advanced composites: A review

Poly(aryl-ether-ether-ketone) or PEEK is a highly aromatic semi-crystalline thermoplastic. Its good mechanical properties and solvent resistances rank it as one of the most promising matrix polymers for high performance composites. This article attempts to provide an in-depth review of work on PEEK and fiber-reinforced PEEK composites. Discussions on various areas including synthesis, molecular weight determination, solution properties, structural hierarchy, morphology and mechanical properties of both neat polymer and composites, will be provided. In addition, environmental effects such as physical aging, thermal aging, moisture, solvents, and radiation will be summarized.     

Characterization of petroleum-degrading bacteria from oil-contaminated sites in Vietnam

Four petroleum-degrading bacterial strains, 2TN-NB, 6TBX-CL, MVK2-5, and XCK, were isolated from various oil-contaminated sites in Vietnam. Determination of the nucleotide sequence of the gene encoding 16S rRNA allowed 2TN-NB to be identified as Acinetobacter sp. and the other three stains as Pseudomonas sp. Among the four isolates, 2TN-NB was most effective in degrading crude oil: in 1 d, it degraded 95% of the crude oil in the culture medium (5%, v/v). The isolated strains could also degrade a sulfur-containing aromatic hydrocarbon, dibenzothiophene (DBT), with low efficiency. Except for MVK2-5, which degraded crude oil least efficiently, the isolates produced biosurfactants in amounts sufficient for structural analysis. FT-IR measurement suggested that strains 6TBX-CL and XCK produced glycolipid-type biosurfactants while that produced by 2TN-NB was of the polysaccharide type.     

Prediction Models for Debonding Failure Loads of Carbon Fiber Reinforced Polymer Retrofitted Reinforced Concrete Beams

This study focuses on debonding failure in reinforced concrete beams with carbon fiber reinforced polymer composite bonded on the soffit using the wet lay-up method. An experimental study, which involved 26 tests, was carried out. The experiments showed two failure modes: Intermediate span debond and end debond. The first failure is the result of the high bond stress near the tip of a flexure-shear crack, whereas the second type of failure is due to the high shear stress developed in the weakest concrete layer at the tension reinforcement level. The experiments have shown that U-straps can be effective in preventing intermediate span and end debond. Based on experimental observations, two simple and practical theoretical models were developed and verified with the experimental data, together with a large database of other existing tests.