AstroGK: Astrophysical gyrokinetics code

The gyrokinetic simulation code AstroGK is developed to study fundamental aspects of kinetic plasmas and for applications mainly to astrophysical problems. AstroGK is an Eulerian slab code that solves the electromagnetic gyrokinetic-Maxwell equations in five-dimensional phase space, and is derived from the existing gyrokinetics code GS2 by removing magnetic geometry effects. Algorithms used in the code are described. The code is benchmarked using linear and nonlinear problems. Serial and parallel performance scalings are also presented.     

A novel approach towards the production of luminescent silicon nanoparticles: sputtering, gas aggregation and co-deposition with H2O

Silicon clusters were produced by sputtering of a p-doped Si target and aggregation of the Si atoms in an argon gas atmosphere. The clusters were deposited in ultra high vacuum onto either (i) carbon transmission electron microscope (TEM) grids or (ii) a liquid nitrogen cooled finger on which a thick layer of ice was co-deposited during the exposure to the cluster beam. The ice layer containing the clusters was melted to form a liquid sample which showed luminescence peaking at 421 nm when excited at 307.5 nm. The luminescence is attributed to electron-hole recombination in oxygen deficient defects in the Si–SiO₂ interface region. TEM images of the nanoparticles deposited on the carbon grids show spherical particles with diameters ranging from 4 to 50 nm, flake-like structures or nanotube-like shapes. Grids with higher deposited densities reveal clusters that are agglomerated into chains, TEM images of the dried liquid sample show a network of fibres indicating that growth into fibres is further promoted when the clusters gain mobility in the melted ice.     

Ultra-high resolution 17O solid-state NMR spectroscopy of biomolecules: a comprehensive spectral analysis of monosodium L-glutamate·monohydrate

Monosodium L-glutamate monohydrate, a multiple oxygen site (eight) compound, is used to demonstrate that a combination of high-resolution solid-state NMR spectroscopic techniques opens up new possibilities for (17)O as a nuclear probe of biomolecules. Eight oxygen sites have been resolved by double rotation (DOR) and multiple quantum (MQ) NMR experiments, despite the (17)O chemical shifts lying within a narrow shift range of <50 ppm. (17)O DOR NMR not only provides high sensitivity and spectral resolution, but also allows a complete set of the NMR parameters (chemical shift anisotropy and electric-field gradient) to be determined from the DOR spinning-sideband manifold. These (17)O NMR parameters provide an important multi-parameter comparison with the results from the quantum chemical NMR calculations, and enable unambiguous oxygen-site assignment and allow the hydrogen positions to be refined in the crystal lattice. The difference in sensitivity between DOR and MQ NMR experiments of oxygen in bio/organic molecules is also discussed. The data presented here clearly illustrates that a high resolution (17)O solid-state NMR methodology is now available for the study of biomolecules, offering new opportunities for resolving structural information and hence new molecular insights.     

Impurity analysis of gentamicin bulk samples by improved liquid chromatography-ion trap mass spectrometry

Several gentamicin bulk samples from different origins were investigated using an LC/MS method.LC equipped with ion trap MS with positive ionization was performed on a Capcell Pak C18(AQ) column with the mobile phase containing 50 mM trifluoroacetic(TFA) and methanol.Impurities present in batches of gentamicin bulk samples were elucidated and compared according to their fragmentation behavior.In total seventeen impurities present in samples,five impurities were not elucidated and two compounds were identifi...     

Unified syntheses of cavicularin and riccardin C: addressing the synthesis of an arene adopting a boat configuration

Concise syntheses of the natural products cavicularin (ten steps) and riccardin C (seven steps) are reported. Key features of the new synthetic route are a convergent strategy to assemble acyclic precursors and a sequence of regioselective reduction and halogenation steps to facilitate Wittig macrocyclisation and transannular ring contraction reactions.     

An analytical treatment of the formation of one-dimensional steady shock waves in uniform and diverging ducts

Singular perturbation techniques are used to study boundary value problems whose solutions model the behavior of one-dimensional steady shock waves in ducts of constant and variable cross-sectional area.     

Monte Carlo simulation of mixed lennard-jones nonionic surfactant adsorption at the liquid/vapor interface

New Monte Carlo simulations are presented for nonionic surfactant adsorption at the liquid/vapor interface of a monatomic solvent specifically investigating the roles of tail attraction and binary mixtures of different tail lengths. Surfactant molecules consist of an amphiphilic chain with a solvophilic head and a solvophobic tail. All molecules in the system, solvent and surfactant, are characterized by the Lennard-Jones (LJ) potential. Adjacent atoms along the surfactant chain are connected by finitely extensible harmonic springs. Solvent molecules move via the Metropolis random-walk algorithm, whereas surfactant molecules move according to the continuum configurational bias Monte Carlo (CBMC) method. We generate thermodynamic adsorption and surface-tension isotherms and compare results quantitatively to single-surfactant adsorption (Langmuir, 2007, 23, 1835). Surfactant tail groups with attractive interaction lead to cooperative adsorption at high surface coverage and higher maximum adsorption at the interface than those without. Moreover, adsorption and surface-tension isotherms with and without tail attraction are identical at low concentrations, deviating only near maximum coverage. Simulated binary mixtures of surfactants with differing lengths give intermediate behavior between that of the corresponding single-surfactant adsorption and surface-tension isotherms both with and without tail attraction. We successfully predict simulated mixture results with the thermodynamically consistent ideal adsorbed solution (IAS) theory for binary mixtures of unequal-sized surfactants using only the simulations from the single surfactants. Ultimately, we establish that a coarse-grained LJ surfactant system is useful for understanding actual surfactant systems when tail attraction is important and for unequal-sized mixtures of amphiphiles.     

Monte Carlo simulations of Lennard-Jones nonionic surfactant adsorption at the liquid/vapor interface

We present Monte Carlo simulations of nonionic surfactant adsorption at the liquid/vapor interface of a monatomic solvent. All molecules in the system, solvent and surfactant, are characterized by the Lennard-Jones (LJ) potential using differing interaction parameters. Surfactant molecules consist of an amphiphilic chain with a solvophilic head and a solvophobic tail. Adjacent atoms along the surfactant chain are connected by finitely extensible harmonic springs. Solvent molecules move via the Metropolis random-walk algorithm, whereas surfactant molecules move according to the continuum configurational bias Monte Carlo (CBMC) method. We generate quantitative thermodynamic adsorption and surface tension isotherms in addition to surfactant radius of gyration, tilt angles, and potentials of mean force. Surface tension simulations compared to those calculated from the simulated adsorbed amounts and the Gibbs adsorption isotherm agree confirming equilibrium in our simulations. We find that the classical Langmuir isotherm is obeyed for our LJ surfactants over the range of head and tail lengths studied. Although simulated surfactant chains in the bulk solution exhibit random orientations, surfactant chains at the interface orient roughly perpendicular and the tails elongate compared to bulk chains even in the submonolayer adsorption regime. At a critical surfactant concentration, designated as the critical aggregation concentration (CAC), we find aggregates in the solution away from the interface. At higher concentrations, simulated surface tensions remain practically constant. Using the simulated potential of mean force in the submonolayer regime and an estimate of the surfactant footprint at the CAC, we predict a priori the Langmuir adsorption constant, KL, and the maximum monolayer adsorption, Gammam. Adsorption is driven not by proclivity of the surfactant for the interface, but by the dislike of the surfactant tails for the solvent, that is by a "solvophobic" effect. Accordingly, we establish that a coarse-grained LJ surfactant system mimics well the expected equilibrium behavior of aqueous nonionic surfactants adsorbing at the air/water interface.     

The determination of 17O NMR parameters of hydroxyl oxygen: a combined deuteration and DOR approach

The direct detection of hydroxyl oxygen (O-H) by (17)O double-rotation (DOR) NMR is very challenging because of the strong O-H dipole interaction. It is shown that deuteration of the hydroxyl site overcomes this using glycine.HCl as an illustration. Two well-separated sets of narrow (linewidth approximately 80-100 Hz) resonances with their spinning-sidebands are observed for the carboxyl and hydroxyl oxygens in the DOR spectrum of [(17)O,(2)H]glycine.HCl. The chemical shift anisotropy of these sites is obtained from a simulation of the DOR spinning-sideband intensities. The chemical shift span (Omega) for the carboxyl oxygen is found to be much larger than that of the hydroxyl oxygen, with Omega values of 540 +/- 15 and 210 +/- 10 ppm, respectively.