Forced vibrations of a bubble in a liquid-filled elastic vessel

There is increasing demand for accurate characterization of the in vivo behavior of microbubble agents used for ultrasound imaging and therapy. This study examines bubble-vessel interaction, in particular the propagation of disturbances along the vessel wall. Finite element simulations of a 3 μm radius microbubble suspended in a viscous liquid and enclosed in a 4 μm radius elastic vessel were performed, and the results compared with existing analytical results for wave propagation in elastic liquid-filled tubes. The vessel wall was shown to have a significant effect upon the amplitude of bubble oscillation and hence acoustic radiation from it, as well as distension of the vessel wall. It was found that the most important factor was the ratio of the excitation frequency to the natural "ring" frequency of the vessel which in turn depends upon its dimensions and mechanical properties. As this ratio increases, the motion of the vessel wall becomes increasingly localized to the site of the bubble. It was also shown that the validity of the results obtained using the applied model of vessel elasticity is limited to frequencies below the ring frequency, and this should be taken into account in the development of protocols for ultrasound safety and/or therapeutic procedures.     

On the parameter choice in grad-div stabilization for the Stokes equations

Standard error analysis for grad-div stabilization of inf-sup stable conforming pairs of finite element spaces predicts that the stabilization parameter should be optimally chosen to be $\mathcal O(1)$ . This paper revisits this choice for the Stokes equations on the basis of minimizing the $H^{1}(\Omega )$ error of the velocity and the $L^{2}(\Omega )$ error of the pressure. It turns out, by applying a refined error analysis, that the optimal parameter choice is more subtle than known so far in the literature. It depends on the used norm, the solution, the family of finite element spaces, and the type of mesh. In particular, the approximation property of the pointwise divergence-free subspace plays a key role. With such an optimal approximation property and with an appropriate choice of the stabilization parameter, estimates for the $H^{1}(\Omega )$ error of the velocity are obtained that do not directly depend on the viscosity and the pressure. The minimization of the $L^{2}(\Omega )$ error of the pressure requires in many cases smaller stabilization parameters than the minimization of the $H^{1}(\Omega )$ velocity error. Altogether, depending on the situation, the optimal stabilization parameter could range from being very small to very large. The analytic results are supported by numerical examples. Applying the analysis to the MINI element leads to proposals for the stabilization parameter which seem to be new.     

Indirect detection of the 183W and 57Fe nuclei using 119Sn‐relayed 1H,X correlation spectroscopy

Recently reported triple‐resonance Y‐relayed ¹H,X correlation experiments have been utilized to characterize ¹⁸³W and ⁵⁷Fe chemical shifts using ¹¹⁹Sn as the Y‐relaying nucleus instead of the previously used ³¹P. Application of an adaptation of Gudat's original INEPT/HMQC sequence results in a significant enhancement of the signal‐to‐noise (S/N) ratio for two‐dimensional ¹¹⁹Sn‐relayed ¹H,¹⁸³W and ¹H, ⁵⁷Fe correlation spectra with efficient detection of the transition metal nucleus in tungsten and iron complexes lacking an observable direct scalar coupling between the transition metal and any hydrogen nuclei. Strengths and shortcomings of the novel sequence and the original sequences reported by Gudat are discussed in the context of ¹¹⁹Sn‐relayed proton detection of very low frequency transition metal nuclei. Copyright © 2010 John Wiley & Sons, Ltd.     

Phase Transitions of Ruthenium-Doped Iron Oxide Studied by 57Fe Mössbauer Spectroscopy at Elevated Temperatures

Hyperfine Interactions - The 57Fe Mössbauer spectra recorded in situ from 5% ruthenium-doped maghemite show parameters typical for maghemite up to 600 K and a hyperfine field distribution...     

Native-Like and Denatured Cytochrome <Emphasis Type="Italic">c</Emphasis> Ions Yield Cation-to-Anion Proton Transfer Reaction Products with Similar Collision Cross-Sections

The relationship between structures of protein ions, their charge states, and their original structures prior to ionization remains challenging to decouple. Here, we use cation-to-anion proton transfer reactions (CAPTR) to reduce the charge states of cytochrome c ions in the gas phase, and ion mobility to probe their structures. Ions were formed using a new temperature-controlled nanoelectrospray ionization source at 25 °C. Characterization of this source demonstrates that the temperature of the liquid sample is decoupled from that of the atmospheric pressure interface, which is heated during CAPTR experiments. Ionization from denaturing conditions yields 18+ to 8+ ions, which were each isolated and reacted with monoanions to generate all CAPTR products with charge states of at least 3+. The highest, intermediate, and lowest charge-state products exhibit collision cross-section distributions that are unimodal, multimodal, and unimodal, respectively. These distributions depend strongly on the charge state of the product, although those for the intermediate charge-state products also depend on that of the precursor. The distributions of the 3+ products are all similar, with averages that are less than half that of the 18+ precursor ions. Ionization of cytochrome c from native-like conditions yields 7+ and 6+ ions. The 3+ CAPTR products from these precursors have slightly more compact collision cross-section distributions that are indistinguishable from those for the 3+ CAPTR products from denaturing conditions. More broadly, these results indicate that the collision cross-sections of ions of this single domain protein depend strongly on charge state for charge states greater than ~4.

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pKas of the conjugate acids of N-heterocyclic carbenes in water

pK(a) values of 19.8-28.2 are reported for the conjugate acids of a large series of NHCs in water. The effects of ring size, N-substituent and C(4)-C(5) saturation on pK(a) are discussed.     

Comparison of a calculated and measured XANES spectrum of α-Fe2O3

Comparison and prediction of the experimental XANES spectrum is a good measurement of the quality of the electronic structure calculations employed, and their ability to predict electronic transitions in solids. Here we present a comparison between BLYP + U and hybrid-BLYP calculations regarding the geometric, magnetic and electronic structures of α-Fe(2)O(3) (hematite). Several values of U and different percentages of Fock-exchange have been screened to see how their contributions affect different properties of hematite, paying particular attention to the electronic structure. To estimate the quality of the various methods the calculated density-of-states were compared to the experimentally collected XANES spectrum of the iron K-edge, providing information about the orbitals describing the conduction band. We find that in agreement with previous studies DFT + U and hybrid-functional simulations can correctly predict the character of the valence band, but only Fock-exchange higher than 30% or U-values equal or larger than 6 eV properly reproduce the order between the t(g) and e orbitals in the conduction band, and can, therefore, be used to study and predict XANES spectra and electronic transitions in hematite.     

Scaffold hopping using clique detection applied to reduced graphs

Similarity-based methods for virtual screening are widely used. However, conventional searching using 2D chemical fingerprints or 2D graphs may retrieve only compounds which are structurally very similar to the original target molecule. Of particular current interest then is scaffold hopping, that is, the ability to identify molecules that belong to different chemical series but which could form the same interactions with a receptor. Reduced graphs provide summary representations of chemical structures and, therefore, offer the potential to retrieve compounds that are similar in terms of their gross features rather than at the atom-bond level. Using only a fingerprint representation of such graphs, we have previously shown that actives retrieved were more diverse than those found using Daylight fingerprints. Maximum common substructures give an intuitively reasonable view of the similarity between two molecules. However, their calculation using graph-matching techniques is too time-consuming for use in practical similarity searching in larger data sets. In this work, we exploit the low cardinality of the reduced graph in graph-based similarity searching. We reinterpret the reduced graph as a fully connected graph using the bond-distance information of the original graph. We describe searches, using both the maximum common induced subgraph and maximum common edge subgraph formulations, on the fully connected reduced graphs and compare the results with those obtained using both conventional chemical and reduced graph fingerprints. We show that graph matching using fully connected reduced graphs is an effective retrieval method and that the actives retrieved are likely to be topologically different from those retrieved using conventional 2D methods.