Usage scenarios of a semantic-based digital shape workbench

Motivated by the undisputed emergence of 3D content, this paper presents cases where semantic technologies have the potential to be used to build robust real-life solutions out of the AIM@SHAPE Digital Shape Workbench both in its current and its future forms. We focus on understanding what makes semantic knowledge applications successful in operational environments which involve shapes and present existing and future scenarios on favoring ontology based integration that systematically resolves both syntactic and semantic heterogeneity, allowing scientists to concentrate more on their content. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Free-field dynamic response of an inhomogeneous half-space

In this work, elastic wave propagation in the inhomogeneous half-space is solved by an analytical approach based on plane wave decomposition in conjunction with appropriate functional transformations for the displacement vector. Specifically, free-field motions are recovered at the surface of a half-space with either quadratic or exponential type of depth-dependent material parameters. The incident wave is a time harmonic, planar pressure wave and the resulting free-field motions are obtained in closed form, first for the full-space and then for the half-space by adding the reflected waves. Parametric studies show marked differences in the results when compared against the corresponding ones for a homogeneous background. Finally, sensitivities of the free-field waves on the basic characteristics of the underlying inhomogeneous material and of the incoming wave are investigated.     

Optimization of parameters for coverage of low molecular weight proteins

Proteins with molecular weights of <25 kDa are involved in major biological processes such as ribosome formation, stress adaption (e.g., temperature reduction) and cell cycle control. Despite their importance, the coverage of smaller proteins in standard proteome studies is rather sparse. Here we investigated biochemical and mass spectrometric parameters that influence coverage and validity of identification. The underrepresentation of low molecular weight (LMW) proteins may be attributed to the low numbers of proteolytic peptides formed by tryptic digestion as well as their tendency to be lost in protein separation and concentration/desalting procedures. In a systematic investigation of the LMW proteome of Escherichia coli, a total of 455 LMW proteins (27% of the 1672 listed in the SwissProt protein database) were identified, corresponding to a coverage of 62% of the known cytosolic LMW proteins. Of these proteins, 93 had not yet been functionally classified, and five had not previously been confirmed at the protein level. In this study, the influences of protein extraction (either urea or TFA), proteolytic digestion (solely, and the combined usage of trypsin and AspN as endoproteases) and protein separation (gel- or non-gel-based) were investigated. Compared to the standard procedure based solely on the use of urea lysis buffer, in-gel separation and tryptic digestion, the complementary use of TFA for extraction or endoprotease AspN for proteolysis permits the identification of an extra 72 (32%) and 51 proteins (23%), respectively. Regarding mass spectrometry analysis with an LTQ Orbitrap mass spectrometer, collision-induced fragmentation (CID and HCD) and electron transfer dissociation using the linear ion trap (IT) or the Orbitrap as the analyzer were compared. IT-CID was found to yield the best identification rate, whereas IT-ETD provided almost comparable results in terms of LMW proteome coverage. The high overlap between the proteins identified with IT-CID and IT-ETD allowed the validation of 75% of the identified proteins using this orthogonal fragmentation technique. Furthermore, a new approach to evaluating and improving the completeness of protein databases that utilizes the program RNAcode was introduced and examined.     

Kinetics and Products of the Reactions of Ethyl and n‐Propyl Nitrates with OH Radicals

The kinetics of the reactions of ethyl (1) and n‐propyl (2) nitrates with OH radicals has been studied using a low‐pressure flow tube reactor combined with a quadrupole mass spectrometer. The rate constants of the title reactions were determined under pseudo–first‐order conditions from kinetics of OH consumption in high excess of nitrates. The overall rate constants, k₁ = 1.14 × 10^?13 (T/298)^2.45 exp(193/T) and k₂ = 3.00 × 10^?13 (T/298)^2.50 exp(205/T) cm³ molecule^?1 s^?1 (with conservative 15% uncertainty), were determined at a total pressure of 1 Torr of helium over the temperature range (248–500) and (263–500) K, respectively. The yields of the carbonyl compounds, acetaldehyde and propanal, resulting from the abstraction by OH of an α‐hydrogen atom in ethyl and n‐propyl nitrates, followed by α‐substituted alkyl radical decomposition, were determined at T = 300 K to be 0.77 ± 0.12 and 0.22 ± 0.04, respectively.     

Experimental Study of the Reaction of Isopropyl Nitrate with OH Radicals: Kinetics and Products

The kinetics of the reaction of isopropyl nitrate (IPN) with OH radicals has been studied using a low‐pressure flow tube reactor coupled with a quadrupole mass spectrometer: OH + (CH₃)₂CHONO₂ → products (2). The rate constant of the title reaction was determined using both the absolute method, monitoring the kinetics of OH radicals consumption in excess of IPN, and the relative rate method using the reaction of OH with Br₂ as reference one and following HOBr formation. As a result of the absolute and relative measurements, the overall rate coefficients, k₂ = (6.6 ± 1.2) × 10^?13 exp(–(233 ± 56)/) was determined at a pressure of 1 Torr of helium over the temperature range 268–355 K. Acetone, resulting from H‐atom abstraction from the tertiary C–H bond of IPN followed by 2‐nitroxy‐2‐propyl radical decomposition, was found to be a major reaction product with the yield of 0.82 ± 0.13, independent of temperature in the range 277–355 K.     

Temperature‐dependent rate coefficients and mechanism for the gas‐phase reaction of chlorine atoms with acetone

The rate coefficient for the gas‐phase reaction of chlorine atoms with acetone was determined as a function of temperature (273–363 K) and pressure (0.002–700 Torr) using complementary absolute and relative rate methods. Absolute rate measurements were performed at the low‐pressure regime (～2 mTorr), employing the very low pressure reactor coupled with quadrupole mass spectrometry (VLPR/QMS) technique. The absolute rate coefficient was given by the Arrhenius expression k(T) = (1.68 ± 0.27) × 10^?11 exp[?(608 ± 16)/T] cm³ molecule^?1 s^?1 and k(298 K) = (2.17 ± 0.19) × 10^?12 cm³ molecule^?1 s^?1. The quoted uncertainties are the 2σ (95% level of confidence), including estimated systematic uncertainties. The hydrogen abstraction pathway leading to HCl was the predominant pathway, whereas the reaction channel of acetyl chloride formation (CH₃C(O)Cl) was determined to be less than 0.1%. In addition, relative rate measurements were performed by employing a static thermostated photochemical reactor coupled with FTIR spectroscopy (TPCR/FTIR) technique. The reactions of Cl atoms with CHF₂CH₂OH (3) and ClCH₂CH₂Cl (4) were used as reference reactions with k₃(T) = (2.61 ± 0.49) × 10^?11 exp[?(662 ± 60)/T] and k₄(T) = (4.93 ± 0.96) × 10^?11 exp[?(1087 ± 68)/T] cm³ molecule^?1 s^?1, respectively. The relative rate coefficients were independent of pressure over the range 30–700 Torr, and the temperature dependence was given by the expression k(T) = (3.43 ± 0.75) × 10^?11 exp[?(830 ± 68)/T] cm³ molecule^?1 s^?1 and k(298 K) = (2.18 ± 0.03) × 10^?12 cm³ molecule^?1 s^?1. The quoted errors limits (2σ) are at the 95% level of confidence and do not include systematic uncertainties. © 2010 Wiley Periodicals, Inc. Int J Chem Kinet 42: 724–734, 2010     

Thionin-sensitized intrazeolite photooxygenation of trisubstituted alkenes: substituent effects on the regioselectivity as probed through isotopic labeling

The regioselectivity for the intrazeolite photooxygenation of several trisubstituted alkenes with geminal dimethyl groups was examined. The length of the alkyl chain at the lone position was varied, and as end groups, the phenyl or the cyclohexyl functionalities were chosen. The general trend for all alkenes is a significant increase of the reactivity at the twin position compared to the photooxygenation in solution. For the cyclohexyl-substituted alkenes, it was found that the regioselectivity is nearly independent of the alkyl chain length. However, for the phenyl-substituted alkenes, the ene reactivity of the allylic methylene hydrogen atoms at the lone position and the twix/twin regioselectivity depend significantly on the distance of the phenyl group from the double bond. These trends are discussed in terms of cation-pi interactions and conformational effects. Intramolecular and intermolecular isotope effects in the intrazeolite photooxygenation of deuterium-labeled alkenes suggest that a perepoxide-type intermediate is formed in the rate-determining step. Type I photooxygenation that involves reaction of the radical cations of the alkenes with superoxide ion are unlikely.