Stepwise dissection and visualization of the catalytic mechanism of haloalkane dehalogenase LinB using molecular dynamics simulations and computer graphics

The different steps of the dehalogenation reaction carried out by LinB on three different substrates have been characterized using a combination of quantum mechanical calculations and molecular dynamics simulations. This has allowed us to obtain information in atomic detail about each step of the reaction mechanism, that is, substrate entrance and achievement of the near-attack conformation, transition state stabilization within the active site, halide stabilization, water molecule activation and subsequent hydrolytic attack on the ester intermediate with formation of alcohol, and finally product release. Importantly, no bias or external forces were applied during the whole procedure so that both intermediates and products were completely free to sample configuration space in order to adapt to the plasticity of the active site and/or search for an exit. Differences in substrate reactivity were found to be correlated with the ease of adopting the near-attack conformation and two different exit pathways were found for product release that do not interfere with substrate entrance. Additional support for the different entry and exit pathways was independently obtained from an examination of the enzyme's normal modes.     

Guidelines for the incremental identification of aspects in requirements specifications

The desired principle of separation of concerns in software development can be jeopardized by the so-called crosscutting concerns, which tend to be scattered over (and tangled with) the functionality of the modular units of a system. The correct identification of such concerns (and their encapsulation into separate artifacts) is thereby considered a way to improve software understanding and evolution. Pursuing a proper management of concerns from the requirements engineering stage can greatly benefit the entire software life-cycle. In this paper, we propose conceptual guidelines on how to perform the identification of crosscutting concerns in the process of building requirements specifications. We argue that the identification must be carried out in an incremental way, to encapsulate apart the crosscutting concerns even if they have not emerged completely yet.

Epoxidation of soybean oil by the methyltrioxorhenium-CH2Cl2/H2O2 catalytic biphasic system

We studied the methyltrioxorhenium (MTO)-CH₂Cl₂/H₂O₂ biphasic system for epoxidizing soybean oil. The reactions were optimized (reactant ratio, time, and temperature), which resulted in a better performance (higher conversion and selectivity) than those described in the literature. Total doublebond conversion and 95% selectivity were obtained in 2 h at room temperature. Furthermore, it was possible to reach desired epoxidation degrees by changing the oxidant and MTO amounts. The rhenium-epoxidized soybean oil remained stable in the absence of stabilizers for up to 30 d when stored at mild conditions.     

Computing the homology of groups: The geometric way

In this paper, we present several algorithms related with the computation of the homology of groups, from a geometric perspective (that is to say, carrying out the calculations by means of simplicial sets and using techniques of Algebraic Topology). More concretely, we have developed some algorithms which, making use of the effective homology   method, construct the homology groups of Eilenberg–MacLane spaces K(G,1)$K(G,1)$ for different groups G$G$, allowing one in particular to determine the homology groups of G$G$.     

SNR gap approximation for M-PSK-Based bit loading

Adaptive OFDM has the potential of providing bandwidth-efficient communications in hostile propagation environments. Currently, bit loading algorithms use M-ary quadrature amplitude modulation of the OFDM sub-carriers, where the number of bits per symbol modulating each of them is obtained in order to maximize the performance. SNR gap approximation for M-QAM signaling makes the algorithms simpler to implement. However, in some circumstances it may be preferable to use. M-ary phase shift keying. In this letter an approximation is derived for M-PSK similar to the SNR gap of M-QAM so that bit loading algorithms can be extended to this type of modulation. In addition, the performance obtained when using M-PSK is compared to that of M-QAM in a practical situation.     

Pollution Buildup on Road Surfaces

Samples of sediment found on an urban road in Aberdeen (Scotland) were collected by washing designated surfaces. This method, called the “wet” method, was capable of collecting sediment of the smallest particle size range that is normally left behind by traditional sampling techniques using dry vacuuming. Over 17 months (mainly on a weekly basis), 66 samples were collected and analyzed for sediment loading, particle size distribution, concentration of heavy metals (Zn, Cu, Pb, Cd) in four sediment size fractions, and several dissolved pollutants in the effluent collected from washing (NO3?,?SO42?,?PO43?,?Cl?,?F?,?NH4+, total organic carbon, total carbon). Standard statistical methods, including multiple regressions, were used to determine relationships amongst different sediment characteristics. It was found that sediment loading, as well as concentrations of Cl? and SO42?, were highest in the winter months, especially when snow was present on the road surface. It was observed that 66% of total road sediment loading was found within a 0.5 m strip next to the curb. The average sediment particle sizes found were smaller than those previously recorded in the literature. As expected, the concentrations of heavy metals were highest in the smallest particle size fraction analyzed (<63?μm), and this occurred during the summer months when less sediment was available on the street surface. The antecedent dry weather period had a very weak and negative influence on the loading rate of the smallest particle size fraction next to the curb.     

Influence diagnostics in regression with complex designs through conditional bias

One of the areas of Statistics in which the influence analysis has been widely studied is the multiple linear regression model. Nevertheless, the influence diagnostics proposed in this context cannot be applied to regression in complex survey, under randomized inference, since the i.i.d. case does not incorporate any probability weighting or population structure, such as clustering, stratification or measures of size into the analysis. In this paper we introduce some influence diagnostics in regression in complex survey. They are built on the conditional bias concept (Moreno-Rebollo et al., 1999). We emphasize the similarities and differences of the proposed measures with respect to the existing ones for the i.i.d. case. Research partly supported by the Spanish MCYT grant BFM2001-3844 and Spanish MEC grant MTM2004-0111433.     

Probabilistic Approach to Predict Cracking in Lightly Reinforced Microconcrete Panels

The ultimate strength of structures made of brittle materials—such as microconcrete—strongly depends on microstructural defects, the structure size, and the loading pattern. Probabilistic approaches allow one to take account of such dependencies. By using a Weibull model, cracking of ferrocement panels is analyzed. Provided the behavior of the reinforcement remains elastic, it is shown that the Weibull parameters identified on unreinforced microconcrete samples tested in flexure may be used to predict multiple cracking in ferrocement panels tested in tension. A key aspect of the analysis is related to the understanding and modeling of the stress heterogeneity effect on the local failure probability of unreinforced as well as reinforced microconcrete by the use of a so-called Weibull stress.     

A comparison of the tribological behaviour of steel/steel, steel/DLC and DLC/DLC contacts when lubricated with mineral and biodegradable oils

Diamond-like carbon (DLC) coatings, which can nowadays be applied to many highly loaded mechanical components, sometimes need to operate under lubricated conditions. It is reasonable to expect that in steel/DLC contacts, at least the steel counter body will behave according to conventional lubrication mechanisms and will interact with lubricants and additives in the contact. However, in DLC/DLC contacts, such mechanisms are still unclear. For example, the “inertness” of DLC coatings raises several questions about whether they are able to provide real boundary “lubrication” or whether they are just a “passive” member in these contacts. On the other hand, biodegradable oils, in particular vegetable base oils, possess a good lubricating ability, often much better than mineral or conventional synthetic oils as a result of the large amount of un-saturated and polar components that can promote the lubricity of DLC coatings. Accordingly, in this study, we present the results of experiments under severe boundary-lubrication conditions during reciprocating sliding. We look at the effect of the type of mating surfaces - steel/DLC, DLC/DLC and steel/steel - and the type of oil on the tribological performance of DLC coatings. We compare the wear and friction behaviours of two types of DLC coatings, i.e., a “pure” non-doped a-C:H DLC coating (denoted as a-DLC) and a WC-containing multilayer coating (denoted as W-DLC) tested with a mineral oil and a biodegradable vegetable oil. These oils, which have very different chemical compositions, were used as base oils and also with mild AW and strong EP additives. Among other things, the results confirm the following: (1) coating/coating lubricated contacts can resemble metal-lubrication mechanisms; (2) additives reduce wear in coating/coating contacts by up to 80%; (3) better wear and friction performance are obtained with oils that contain large amounts of polar and un-saturated molecules; (4) a coating/coating combination generally results in less wear than a steel/coating combination.