Generalized Contour Dynamics: A Review

Contour dynamics is a computational technique to solve for the motion of vortices in incompressible inviscid flow. It is a Lagrangian technique in which the motion of contours is followed, and the velocity field moving the contours can be computed as integrals along the contours. Its best-known examples are in two dimensions, for which the vorticity between contours is taken to be constant and the vortices are vortex patches, and in axisymmetric flow for which the vorticity varies linearly with distance from the axis of symmetry. This review discusses generalizations that incorporate additional physics, in particular, buoyancy effects and magnetic fields, that take specific forms inside the vortices and preserve the contour dynamics structure. The extra physics can lead to time-dependent vortex sheets on the boundaries, whose evolution must be computed as part of the problem. The non-Boussinesq case, in which density differences can be important, leads to a coupled system for the evolution of both mean interfacial velocity and vortex sheet strength. Helical geometry is also discussed, in which two quantities are materially conserved and whose evolution governs the flow.     

Thermal stability and thermodynamic properties of hybrid proton-conducting polyaryl etherketones

The thermal and structural stability of sulfonated cross-linked PEEK (polyether ether ketone) and its silicon-containing class II hybrid derivatives were characterized by combination of mass spectrometry, infrared spectroscopy, X-ray diffraction, thermogravimetric analysis, and differential scanning calorimetry. Thermodynamic properties of the hybrids were determined, including glass-transition temperature, degree of crystallinity, and thermal stability. The decomposition processes of the hybrid polymers could be consistently interpreted and their energetics quantitatively determined. The introduction of inorganic silanol moieties improves the thermal stability compared to sulfonated products.     

Molecular dynamics simulation of the cation motion upon adsorption of CO2 in Faujasite zeolite systems

Molecular Dynamics simulations have been carried out in NaX and NaY Faujasite systems to deepen understanding of the cation rearrangement during the CO2 adsorption process suggested by our recent diffusivity measurements. This study is a major contribution since the rearrangement of the cations in Faujasite, the most promising adsorbent for CO2 storage, can represent a significant breakthrough in understanding the adsorption and diffusion processes at the mircroscopic scale. For NaY, it has been shown that at low and intermediate loadings, SII cations can migrate toward the center of the supercage due to strong interactions with the adsorbates, followed by a hopping of SI'cation from the sodalite cage into the supercage to fill the vacant SII site. The SI cations are only displaced at a higher loading, leading to cation de-trapping out of the double six rings into the vacant SI' sites. For NaX, the SIII' cations which occupy the most accessible adsorption sites move significantly upon coordination to the carbon dioxide molecules. The SI' and SII cations remain consistently located in their initial sites whatever the loading. Indeed, the most probable migration mechanism involves SIII' cation displacements into nearby vacant SIII' sites.     

PRESSURE-VELOCITY EQUILIBRIUM HYDRODYNAMIC MODELS

This article describes mathematical models for phase separated mixtures of materials that are in pressure and velocity equilibrium but not necessarily temperature equilibrium. General conditions for constitutive models for such mixtures that exhibit a single mixture sound speed are discussed and specific examples are described.     

Robust cross-validation of linear regression QSAR models

A quantitative structure-activity relationship (QSAR) model is typically developed to predict the biochemical activity of untested compounds from the compounds' molecular structures. "The gold standard" of model validation is the blindfold prediction when the model's predictive power is assessed from how well the model predicts the activity values of compounds that were not considered in any way during the model development/calibration. However, during the development of a QSAR model, it is necessary to obtain some indication of the model's predictive power. This is often done by some form of cross-validation (CV). In this study, the concepts of the predictive power and fitting ability of a multiple linear regression (MLR) QSAR model were examined in the CV context allowing for the presence of outliers. Commonly used predictive power and fitting ability statistics were assessed via Monte Carlo cross-validation when applied to percent human intestinal absorption, blood-brain partition coefficient, and toxicity values of saxitoxin QSAR data sets, as well as three known benchmark data sets with known outlier contamination. It was found that (1) a robust version of MLR should always be preferred over the ordinary-least-squares MLR, regardless of the degree of outlier contamination and that (2) the model's predictive power should only be assessed via robust statistics. The Matlab and java source code used in this study is freely available from the QSAR-BENCH section of www.dmitrykonovalov.org for academic use. The Web site also contains the java-based QSAR-BENCH program, which could be run online via java's Web Start technology (supporting Windows, Mac OSX, Linux/Unix) to reproduce most of the reported results or apply the reported procedures to other data sets.     

Chemoenzymatic acylation of aminoglycoside antibiotics

The chemoenzymatic installation of the clinically valuable (S)-4-amino-2-hydroxybutyryl side chain onto a number of 2-deoxystreptamine-containing aminoglycosides is described using the purified Bacillus circulans biosynthetic enzymes BtrH and BtrG in combination with a synthetic acyl-SNAC surrogate substrate.     

Prediction of the conditions for breathing of metal organic framework materials using a combination of X-ray powder diffraction, microcalorimetry, and molecular simulation

The adsorption of C1 to C4 linear hydrocarbons in the flexible metal organic framework MIL-53(Cr) has been followed by adsorption manometry coupled with microcalorimetry and Synchrotron X-ray powder diffraction. This experimental investigation was completed by molecular modeling. In the case of methane, the solid remains rigid whatever the adsorbate amount. However for the C2-C4 series, an increasing flexibility of the structure is observed, which is ascribed first to a breathing of the material from a large pore to a narrow pore form followed by a further expansion at high pressure. The collected thermodynamic and structural information suggests that a minimum adsorption enthalpy of ca. 20 kJ mol (-1) in the initial large pore structure of MIL-53(Cr) is required to induce the structural transition "large to narrow pore". Further, the enthalpy of adsorption can be used to predict the pressure at which the structure reopens. Finally, the magnitude of the breathing can be related to the size of the probe molecule via the van der Waals volume. The above trends have been successfully verified in the case of water and carbon dioxide. This combined experimental and theoretical approach gives the first elements for the prediction of whether or not the MIL53 and similar flexible structures will respond to gas loading and what would be the pressure required and further the amplitude of the induced breathing.     

Biosynthesis of butirosin: transfer and deprotection of the unique amino acid side chain

Butirosin, an aminoglycoside antibiotic produced by Bacillus circulans, bears the unique (S)-4-amino-2-hydroxybutyrate (AHBA) side chain, which protects the antibiotic from several common resistance mechanisms. The AHBA side chain is advantageously incorporated into clinically valuable antibiotics such as amikacin and arbekacin by synthetic methods. Therefore, it is of significant interest to explore the biosynthetic origins of this useful moiety. We report here that the AHBA side chain of butirosin is transferred from the acyl carrier protein (ACP) BtrI to the parent aminoglycoside ribostamycin as a gamma-glutamylated dipeptide by the ACP:aminoglycoside acyltransferase BtrH. The protective gamma-glutamyl group is then cleaved by BtrG via an uncommon gamma-glutamyl cyclotransferase mechanism. The application of this pathway to the in vitro enzymatic production of novel AHBA-bearing aminoglycosides is explored with encouraging implications for the preparation of unnatural antibiotics via directed biosynthesis.