Accurate free energy calculation along optimized paths

The path‐based methods of free energy calculation, such as thermodynamic integration and free energy perturbation, are simple in theory, but difficult in practice because in most cases smooth paths do not exist, especially for large molecules. In this article, we present a novel method to build the transition path of a peptide. We use harmonic potentials to restrain its nonhydrogen atom dihedrals in the initial state and set the equilibrium angles of the potentials as those in the final state. Through a series of steps of geometrical optimization, we can construct a smooth and short path from the initial state to the final state. This path can be used to calculate free energy difference. To validate this method, we apply it to a small 10‐ALA peptide and find that the calculated free energy changes in helix‐helix and helix‐hairpin transitions are both self‐convergent and cross‐convergent. We also calculate the free energy differences between different stable states of β‐hairpin trpzip2, and the results show that this method is more efficient than the conventional molecular dynamics method in accurate free energy calculation. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Effect of pumping methods on transmembrane pressure, fluid balance and relative recovery in microdialysis

There is a growing interest in using large pore size probes for microdialysis of macromolecular markers to monitor cell and tissue functions. Fluid balance could be an important issue when using large pore size microdialysis probes, which are affected by the mode of operation. In this study, the effect of pumping systems, push, pull, push-and-pull, and the resulting transmembrane pressure on the fluid balance, as well as, the relative recovery of small molecular nutrients and metabolites and macromolecules (proteins) were examined. The validity of the internal reference in situ calibration was examined in detail. It is concluded that a push-and-pull system is the only effective method of eliminating fluid loss or gain. The relative recovery of small solutes is not affected much by the applied pumping methods; however, the relative recovery of macromolecules is significantly influenced by them. The in situ calibration technique using Phenol Red can provide reliable results for small molecules including glucose and lactic acid. Using 10 and 70-kDa fluorescent dextrans as the internal standard for large molecules in situ calibration of similar size does not work for the pull pump system, but does work well when using a push-and-pull pumping method.     

Sampling and Analysis of Odorous Compounds in Water Treatment Plants

Abstract

The following analytical method has been used to identify some odorous compounds in the air of the water treatment plant Werdholzli, Zurich: sampling of contaminated air with the help of activated carbon, desorption by the solvents carbon disulphide and methylene chloride, separation of the carbon disulfide extract into a polar and a nonpolar fraction by adsorption column chromatography on silica. Hereafter gaschromatographic analysis of the polar fraction on glass capillary column (Ucon HB 5100); detection and identification were achieved by flame ionisation, thermoionic nitrogen selective detector and computerized mass spectrometry (Finnigan 3200 F, data system 6110).

The results show the presence of sulfur compounds: thiophenes, thiazoles; nitrogen compounds: pyrazines; oxygen compounds: phenols, alcohols and some unsatured hydrocarbons. The malodorous compounds were sulfur and nitrogen compounds in the range of 0.01-0.1 ppm.     

Use Of Diffusion Controlled Preconcentration Systems With Chemically Immobilized Coatings For The Determination Of Atmospheric Nitric Acid

Abstract

A new coating procedure for different diffusion controlled preconcentration methods (tubular denuder, annular denuder, diffusion screen) is described for the determination of nitric acid in air. In this study, a silanization reaction is applied to obtain a chemically fixed coating with an end placed functional NH₂-group, which can be used as a sink to collect acidic compounds from air. This coating must be carried out only once and can be used for a long time. The denuders, coated with this procedures, were compared with conventionally coated NaF denuders.     

Measurements Of Biogenic Hydrocarbons And Their Atmospheric Degradation In Forests

Abstract

An analytical procedure for the sampling and quantitative determination of biogenic hydrocarbons in the atmosphere is presented. The method is based on the adsorptive preconcentration of the hydrocarbons using Tenax TA/Carbopack B filled sampling tubes followed by thermodesorption of the trapped compounds and gas chromatographic analysis. To avoid losses of the biogenic alkenes as a consequence of their reaction with ozone on the adsorbents during the sampling step, an ozone scrubber is used in front of the adsorption tubes. Diurnal variations of the monoterpene- and ozone-concentrations are determined at different heights in and above a forest stand (coniferous and deciduous trees) in the Vosges (Col du Donon, 760 m a.s.l.) in order to elucidate the importance of terpene-oxidation reactions on the formation of peroxidic products in forest air.     

Automatic Headspace Sampling for Determination of Ethylene Dibromide Residues in Cereals

Abstract

The possibility was investigated to apply a commercially available automatic head-space sampler in trace analysis of ethylene dibromide (EDB, 1,2-dibromoethane), in cereals.

Samples of rice and wheat flour were thermostatted in closed vials at 70[ddot]C for 30min. The top gas was then automatically introduced into a gas chromatograph equipped with an electron capture detector. Quantitation was performed using external standards (untreated samples spiked with solutions of EDB in N,N′-dimethylacetamide).

The relative standard deviation of the method was 3.4% for rice and 4.5% for wheat flour, at a residue level of 0.008 mg/kg. The detection limit was 0.001 mg/kg (the official EC residue tolerance is 0.01 mg/kg).

Preliminary experiments with other fumigants were carried out as well.

The headspace technique in question has the following advantages over other methods for determining EDB residues in cereals: 1. No sample pre-treatment like extraction, steam distillation, purge and trap etc.; 2. Automated sample handling; 3. “Clean” chromatograms.     

Residual‐based artificial viscosity for simulation of turbulent compressible flow using adaptive finite element methods

In this paper, we present a finite element method with a residual‐based artificial viscosity for simulation of turbulent compressible flow, with adaptive mesh refinement based on a posteriori error estimation with sensitivity information from an associated dual problem. The artificial viscosity acts as a numerical stabilization, as shock capturing, and as turbulence capturing for large eddy simulation of turbulent flow. The adaptive method resolves parts of the flow indicated by the a posteriori error estimates but leaves shocks and turbulence under‐resolved in a large eddy simulation. The method is tested for examples in 2D and 3D and is validated against experimental data. Copyright © 2012 John Wiley & Sons, Ltd.     

On the signal degradation induced by the interpolation and the sampling rate reduction in aeroacoustics hybrid methods

Taking place within more extensive work that focuses on hybrid methods in aeroacoustics, the present study is devoted to the data transfer operations that are to be performed between two stages of a hybrid calculation. More precisely, the article focuses on two typical operations that usually accompany such data transfer, which are (i) the sampling rate reduction and (ii) the interpolation of the unsteady perturbations to be transmitted from one stage to the other. First part of the paper analyzes the two main issues of such operations, which are the spuriousing and the aliasing phenomena. For doing so, the usual notions of the interpolation theory are revisited before they are synthesized within an original approach. The here proposed formalism allows to understand better both the spuriousing and the aliasing phenomena, as well as to accurately predict the impact of the latter on the data to be transmitted in terms of signal degradation. Second part of the paper provides an illustration and a validation of these theoretical developments via a direct application to a typical aerodynamic noise problem (aeroacoustic emission by a 2D cylinder cross flow). There, it is further shown how the here proposed formalism can help in improving aeroacoustics hybrid calculations by predicting (and thus possibly minimizing) the bias to be induced on the acoustic extrapolation stage because of the aliasing and/or spuriousing effects inherited from the sampling rate reduction and/or interpolation of CFD data—which is likely to occur in any hybrid scenario. Copyright © 2012 John Wiley & Sons, Ltd.     

A simplified adaptive Cartesian grid system for solving the 2D shallow water equations

This paper presents a new simplified grid system that provides local refinement and dynamic adaptation for solving the 2D shallow water equations (SWEs). Local refinement is realized by simply specifying different subdivision levels to the cells on a background uniform coarse grid that covers the computational domain. On such a non‐uniform grid, the structured property of a regular Cartesian mesh is maintained and neighbor information is determined by simple algebraic relationships, i.e. data structure becomes unnecessary. Dynamic grid adaptation is achieved by changing the subdivision level of a background cell. Therefore, grid generation and adaptation is greatly simplified and straightforward to implement. The new adaptive grid‐based SWE solver is tested by applying it to simulate three idealized test cases and promising results are obtained. The new grid system offers a simplified alternative to the existing approaches for providing adaptive mesh refinement in computational fluid dynamics. Copyright © 2011 John Wiley & Sons, Ltd.     

An improved Sampling Strategy for the Measurement of VOCs in Air,Based on Cooled Sampling and Analysis by Thermodesorption-GC-MS/FID

Abstract

Reliable and comprehensive sampling methods are required to obtain accurate data for VOC concentrations in air samples. The major drawback of the adsorption tube sampling method, widely employed in environmental studies, is the fact that C₂ compounds are usually not trapped quantitatively.

The focus of this work was thus to improve sampling based on adsorption tubes packed with Molsieve and Carbosieve. To improve the sampling efficiency for the C₂ compounds, a cooling device, based on Peltier cooling was constructed, which could be operated at a temperature down to ?30°C.

Experiments under laboratory and field conditions were carried out to study the influence of the sampling temperatuie on the recovery of ethane and ethene as the most volatile VOCs. The results clearly demonstrate the need for a cooled sampling device for the analysis of C₂ compounds in air. Under the investigated conditions, the recoveries with ambient temperature sampling were only in the range of 38–46% for ethane and 33–59% for ethene respectively, in comparison to the cooled sampling device. These findings are only valid for the described conditions and can change significantly with temperature and concentration. A generalisation of the recovery is thus very difficult to give.

The use of the sampling device for a field study is reported, where samples were collected simultaneously at three different altitudes in a diurnal profile on the slope of the Schulterberg mountain in Tyrol (Austria).