Linear compartmental systems. IV. A software,under MS-Windows,for obtaining the instantaneous species concentrations in enzyme systems

Software application is implemented in this work to take full advantage of the characteristics of current operating systems and to provide the optimized symbolic kinetic equations for both enzyme and ligand species involved in enzyme reactions. This software, called SKEE-w2013, is implemented using C# language and runs under all operating systems from Windows XP up to Windows 8. It is applicable to any enzyme reaction mechanism that fits the general reaction scheme proposed previously by our group. It can be downloaded, free of charge, from http://oretano.iele-ab.uclm.es/~BioChem-mg/software.php. Besides the optimized equations, the software can provide non-optimized equations, so that the user can compare the advantage of using optimized equations rather than the non-optimized ones, whenever they do not coincide. Moreover, the software circumvents the limitations of other existing previous software tools implemented with what are nowadays obsolete programming languages and that, moreover, are limited to non-optimized kinetic equations.     

Linear compartmental systems. III. Application to enzymatic reactions

In this paper we extend to enzyme systems the results previously obtained in paper I of this series for linear compartmental systems. We obtain the time course equations for both the enzyme and ligand species involved in the reaction mechanisms, which fit a general enzyme system model when the connections between the different enzyme species are of first or pseudofirst order. The kinetic equations obtained here for a given species, enzyme or ligand have the advantage over all previous equations described in the literature, in that they are in the most simplified form possible, since they only contain the kinetic parameters and initial concentrations of the enzymatic reaction which really have some influence on the time progress curves of the species under study. These kinetic equations are denominated optimized equation to distinguish them from the others, which shall call non-optimized equations. We discuss those cases when both types of equation coincide and we show how, when they do not coincide, the non-optimized equations can be simplified to the optimized ones. Therefore, we show that the optimized equations could be used in all cases to avoid the need of subsequent simplifications to eliminate the parameters that play no role in the corresponding time equations. To illustrate the use of this procedure we will apply it to two simple examples of enzymatic reactions.     

Characterization of Mercury Contamination Surrounding a Chloralkali Production Facility in Tuzla,Bosnia and Herzegovina

Tuzla is among the most polluted cities of Bosnia and Herzegovina. The main source of pollution in the area is soil heavily contaminated by mercury released from a former chloralkali plant. This paper is focused on the characterization of mercury contaminated soil and air surrounding the chloralkali plant. In soil, the mobility and transformation of mercury were investigated by sequential extraction, while the methylation and reduction potentials were determined by the use of a radioactive tracer. Mercury emission from soil was determined by laboratory and by flux chamber measurements in the field. In addition, mercury concentrations in air were estimated by the analysis of air and the transplanted lichen Hypogymnia physodes. Mercury in soils in the vicinity of the chloralkali plant exceeded the background value by a factor of more than 3000. The fractionation of mercury in surface soil by sequential extraction showed that the mercury in soil was primarily bound to organic matter and a fraction containing elemental mercury and mercury (I) chloride is also significant. The obtained methylation and reduction potentials are low. The mercury flux from soil was estimated by two approaches. Fluxes of up to 8000?ng/m²/day were measured at the most polluted site; evaporation from soil was shown to be the primary source of elevated mercury in air. Air concentration mapping also revealed other sources of mercury; the most likely is the 715 MW coal power plant in the vicinity of former chloralkali facility.     

Grid‐based algorithm to search critical points,in the electron density,accelerated by graphics processing units

Using a grid‐based method to search the critical points in electron density, we show how to accelerate such a method with graphics processing units (GPUs). When the GPU implementation is contrasted with that used on central processing units (CPUs), we found a large difference between the time elapsed by both implementations: the smallest time is observed when GPUs are used. We tested two GPUs, one related with video games and other used for high‐performance computing (HPC). By the side of the CPUs, two processors were tested, one used in common personal computers and other used for HPC, both of last generation. Although our parallel algorithm scales quite well on CPUs, the same implementation on GPUs runs around 10× faster than 16 CPUs, with any of the tested GPUs and CPUs. We have found what one GPU dedicated for video games can be used without any problem for our application, delivering a remarkable performance, in fact; this GPU competes against one HPC GPU, in particular when single‐precision is used. © 2014 Wiley Periodicals, Inc.     

From Wiener index to molecules

In this paper we present an algorithm for the generation of molecular graphs with a given value of the Wiener index. The high number of graphs for a given value of the Wiener index is reduced thanks to the application of a set of heuristics taking into account the structural characteristics of the molecules. The selection of parameters as the interval of values for the Wiener index, the diversity and occurrence of atoms and bonds, the size and number of cycles, and the presence of structural patterns guide the processing of the heuristics generating molecular graphs with a considerable saving in computational cost. The modularity in the design of the algorithm allows it to be used as a pattern for the development of other algorithms based on different topological invariants, which allow for its use in areas of interest, say as involving combinatorial databases and screening in chemical databases.     

Novel methodology for the study of mercury methylation and reduction in sediments and water using <Superscript>197</Superscript>Hg radiotracer

Mercury tracers are powerful tools that can be used to study mercury transformations in environmental systems, particularly mercury methylation, demethylation and reduction in sediments and water. However, mercury transformation studies using tracers can be subject to error, especially when used to assess methylation potential. The organic mercury extracted can be as low as 0.01% of the endogenous labeled mercury, and artefacts and contamination present during methylmercury (MeHg) extraction processes can cause interference. Solvent extraction methods based on the use of either KBr/H₂SO₄ or HCl were evaluated in freshwater sediments using ¹⁹⁷Hg radiotracer. Values obtained for the ¹⁹⁷Hg tracer in the organic phase were up to 25-fold higher when HCl was used, which is due to the coextraction of ¹⁹⁷Hg²⁺ into the organic phase during MeHg extraction. Evaluations of the production of MeHg gave similar results with both MeHg extraction procedures, but due to the higher Hg²⁺ contamination of the controls, the uncertainty in the determination was higher when HCl was used. The Hg²⁺ contamination of controls in the HCl extraction method showed a nonlinear correlation with the humic acid content of sediment pore water. Therefore, use of the KBr/H₂SO₄ method is recommended, since it is free from these interferences. ¹⁹⁷Hg radiotracer (T _1/2 = 2.673 d) has a production rate that is about 50 times higher than that of ²⁰³Hg (T _1/2 = 46.595 d), the most frequently used mercury radiotracer. Hence it is possible to obtain a similar level of performance to ²⁰³Hg when it is used it in short-term experiments and produced by the irradiation of ¹⁹⁶Hg with thermal neutrons, using mercury targets with the natural isotopic composition. However, if the 0.15% natural abundance of the ¹⁹⁶Hg isotope is increased, the specific activity of the ¹⁹⁷Hg tracer can be significantly improved. In the present work, ¹⁹⁷Hg tracer was produced from mercury 51.58% enriched in the ¹⁹⁶Hg isotope, and a 340-fold increase in specific activity with respect to natural mercury targets was obtained. When this high specific activity tracer is employed, mercury methylation and reduction experiments with minimum mercury additions are feasible. Tracer recovery in methylation experiments (associated with Me¹⁹⁷Hg production from ¹⁹⁷Hg²⁺ spike, but also with Hg²⁺ contamination and Me¹⁹⁷Hg artefacts) with marine sediments was about 0.005% g⁻¹ WS (WS: wet sediment) after 20 h incubation with mercury additions of 0.05 ng g⁻¹ WS, which is far below natural mercury levels. In this case, the amount of Hg²⁺ reduced to Hg⁰ (expressed as the percent ¹⁹⁷Hg⁰ recovered with respect to the ¹⁹⁷Hg²⁺ added) varied from 0.13 to 1.6% g⁻¹ WS. Me¹⁹⁷Hg production from ¹⁹⁷Hg²⁺ spike after 20 h of incubation of freshwater sediment ranged from 0.02 to 0.13% g⁻¹ WS with mercury additions of 2.5 ng g⁻¹ WS, which is also far below natural levels. ¹⁹⁷Hg⁰ recoveries were low, 0.0058 ± 0.0013% g⁻¹ WS, but showed good reproducibility in five replicates. Me¹⁹⁷Hg production from ¹⁹⁷Hg²⁺ spiked in freshwater samples ranged from 0.1 to 0.3% over a period of three days with mercury additions of 10 ng L⁻¹. A detection limit of 0.05% for Me¹⁹⁷Hg production from ¹⁹⁷Hg²⁺ spike was obtained in seawater in a 25 h incubation experiment with mercury additions of 12 ng L⁻¹.     

Iron oxide nanoparticles and VOx/Hexadecylamine nanotubes composite

In this work, we present the synthesis and characterization of a hybrid nanocomposite constituted by iron oxide nanoparticles and vanadium oxide/Hexadecylamine (VO_x/Hexa) nanotubes. Transmission Electron Microscopy (TEM) images show small particles (around 20 nm) in contact with the external wall of the multiwall tubes, which consist of alternate layers of VO_x and Hexa. By Energy Dispersive Spectroscopy (EDS), we detected iron ions within the tube walls and we have also established that the nanoparticles are composed of segregated iron oxide. The samples were studied by Electron Paramagnetic Resonances (EPR) and dc-magnetization as a function of the magnetic field. The analysis of the magnetization and EPR data confirms that a fraction of the V atoms are in the V⁴⁺ electronic state and that the nanoparticles exhibit a superparamagnetic behavior. The percentage of V and Fe present in the nanocomposite was determined using Instrumental Neutron Activation Analysis (INAA).     

Determination of the fission averaged cross sections of some threshold reactions induced on chlorine, potassium, and calcium, and their role in the development of self-validated methods of neutron activation analysis

The feasibility of validating data obtained in the determination of chlorine, potassium, and calcium by neutron capture activation analysis, through their determination using threshold reactions has been studied. To this purpose the authors experimentally determined the following fission neutron spectrum averaged cross sections (in mb):³⁷Cl(n,p)³⁷S, 0.234±0.015;⁴¹K(n,α)³⁸Cl, 0.740±0.044;⁴²Ca(n,p)⁴²K, 3.09±0.22;⁴³Ca(n,p)⁴³K, 2.27±0.12;⁴⁴Ca(n,p)⁴⁴K, 0.074±0.013. The application of these values to the analysis of some reference materials are presented. Also, the problem of mutual interferences has been addressed for the following pairs:³⁶S(n,Γ)³⁷S and³⁷Cl(n,p)³⁷S;³⁷Cl(n,Γ)³⁸Cl and⁴¹K(n,α)³⁸Cl;⁴¹K(n,ψ)⁴²K and⁴²Ca(n,p)⁴²K.     

The solid‐state 2:1 molecular complex of 1,5:3,7‐dimethano‐1,3,5,7‐benzotetrazonine with hydroquinone

The title compound, 1,5:3,7‐dimethano‐1,3,5,7‐benzotetrazonine–hydroquinone (2/1), 2C₁₁H₁₄N₄·C₆H₆O₂, crystallizes with the hydroquinone molecule located on a center of inversion. In contrast to other hydroquinone–adamanzane adducts, which form extended hydrogen‐bonded networks, in the present case, one hydroquinone molecule is linked to two 1,5:3,7‐dimethano‐1,3,5,7‐benzotetrazonine molecules, forming a 2:1 cluster through O—H...N hydrogen bonds.     

Geochemical characterization of volcanic ashes from recent events in Northern Patagonia Andean Range by INAA

Summary Volcanic ashes erupted by recent magmatic events were collected from one sedimentary sequence of lake Nahuel Huapi (Patagonia, Argentina) and then analyzed by Instrumental Neutron Activation Analysis. Primary volcanic components, including white and brownish pumice fragments, scoriae and glass shards, as well as bulk sediments from four tephra layers identified in the sedimentary sequence, were characterized by their major and trace element contents. The two tephra layers being in the upper section of the sequence can be linked to the eruptions of Cordon Caulle fissure (Puyehue-Cordon Caulle region) occurred in 1921-1922 and 1960, according to core dating. The third tephra layer, which is clearly associated to an event occurred in the 1890-1900 decade, has different compositional patterns showing a different source from those upper tephras. Whereas, the fourth, which could be associated to an event occurred at the end of the 18 th century, shows the same composition patterns as those registered for the Cordon Caulle fissure.