A comparison between parallelization approaches in molecular dynamics simulations on GPUs

We test the relative performances of two different approaches to the computation of forces for molecular dynamics simulations on graphics processing units. A “vertex‐based” approach, where a computing thread is started per particle, is compared to an “edge‐based” approach, where a thread is started per each potentially non‐zero interaction. We find that the former is more efficient for systems with many simple interactions per particle while the latter is more efficient if the system has more complicated interactions or fewer of them. By comparing computation times on more and less recent graphics processing unit technology, we predict that, if the current trend of increasing the number of processing cores—as opposed to their computing power—remains, the “edge‐based” approach will gradually become the most efficient choice in an increasing number of cases. © 2014 Wiley Periodicals, Inc.     

Label-free immunosensor for monitoring vitellogenin as a biomarker for exogenous oestrogen compounds in amphibian species

A label-free, optical waveguide lightmode spectroscopy based immunosensor was developed for frog (Bombina orientalis) vitellogenin (Vtg) determination in biological samples as a biomarker for exogenous oestrogen compounds. Antibody against Vtg was produced in rabbits immunised with purified lipovitellin (Lpv), a precursor of Vtg, from the homogenised ovary of oriental fire-bellied toads (B. orientalis). The purified protein and Lpv/Vtg-specific serum were applied in both competitive and direct immunoassay formats using optical waveguide lightmode spectroscopy immunosensor. When measuring Vtg in direct manner, the Lpv antibody (1.76 µg mL^?1) was immobilised on the sensor surface, and the linear measuring range for Vtg was 0.1–10 µg mL^?1. During the competitive measurement, 100 ng mL^?1 Lpv was applied for the immobilisation. The linear measuring range for Vtg was 0.5–50 ng mL^?1. We studied the relative substrate specificity of the antibody, and it was concluded that the method is suitable for the sensitive and selective determination of Vtg levels in toads. Heart, liver and gonad samples from male animals were spiked with Vtg and were analysed using the newly developed method, and female toads and spawn samples were tested and compared to the calibration curve obtained by the spiked samples.     

13C SPE MAS measurement of ligand concentration in compressible chromatographic beads

A method for measuring the ligand concentration in heterogeneous materials like chromatography media is described. In this method, ¹³C single pulse excitation magic angle spinning NMR experiment with broadband ¹H decoupling is used to determine the peak integrals for a butyl ligand in the spectrum of a dried chromatography medium. Within a carefully controlled protocol, those integrals compared with that of the internal reference compound dimethyl sulfone provide the required volume concentration with an accuracy of ca 2%. The effects of temperature, degree of hydration, and other experimental parameters are discussed. Copyright © 2015 The Authors. Magnetic Resonance in Chemistry published by John Wiley & Sons Ltd.     

Thionation of a cyanoxime derivative to form the sulphur-containing derivative,a novel ligand for complexation with transitional metal ions

Structural Chemistry - 2-Cyano-2-(hydroxyimino)dithioacetic acid was prepared starting from cyanoacetic acid methylester via 2-cyano-2-(hydroxyimino)acetic acid methylester. Before thionation, the...     

Synthesis and characterisation of alkaline earth-iron(III) double hydroxides

Double hydroxides containing alkaline earth and iron(III) ions were synthesised by the co-precipitation method. The solid materials obtained were characterised by a range of instrumental methods (powder X-ray diffractometry, thermogravimetry, scanning electron microscopy, energy dispersive X-ray fluorescence spectrometry, elemental maps, and infrared spectroscopy). It was found that the Ca(II)Fe(III), Mg(II)Fe(III), and Ba(II)Fe(III) double hydroxides had layered structures, while Sr(II)Fe(III) had not. The optimum conditions for synthesis of Ca(II)Fe(III)-layered double hydroxides (materials to be used in further studies) were also elaborated.     

Synthesis and in vitro antiproliferative activity of novel androst-5-ene triazolyl and tetrazolyl derivatives

A straightforward and reliable method for the regioselective synthesis of steroidal 1,4-disubstituted triazoles and 1,5-disubstituted tetrazoles via copper(I)-catalyzed cycloadditions is reported. Heterocycle moieties were efficiently introduced onto the starting azide compound 3β-acetoxy-16β-azidomethylandrost-5-en-17β-ol through use of the "click" chemistry approach. The antiproliferative activities of the newly-synthesized triazoles were determined in vitro on three human gynecological cell lines (HeLa, MCF7 and A2780) using the microculture tetrazolium assay.     

Efficient approach to novel 1α-triazolyl-5α-androstane derivatives as potent antiproliferative agents

Stereoselective 1,4-Michael addition of azoimide to 17β-acetoxy-5α-adrost-1-en-3-one was carried out to furnish a 1α-azido-3-ketone, which was reduced to give the 3β- and 3α-hydroxy epimers in a ratio of 5 : 2. The Cu(I)-catalyzed 1,3-dipolar cycloaddition of the major isomer to terminal alkynes afforded 1α-triazolyl derivatives, which were deacetylated to the corresponding 3β,17β-diols or oxidized to the analogous 3-ketones. However, the ability of the minor 1α,3α-azidoalcohol to undergo similar cyclization was found to be affected significantly by the steric bulk of the substituents on the alkyne reaction partner. All triazolyl compounds were tested in vitro on three malignant gynecological cell lines (HeLa, MCF7 and A2780).