Dynamical fermions in lattice gauge theories: Metropolis and Langevin techniques in two dimensions

A variety of techniques for the inclusion of dynamical fermions in lattice gauge theory is examined. Three pseudo-fermionic techniques that have the characteristics desirable for an unquenched simulation of four-dimensional QCD are studied in detail. Langevin and Metropolis pseudo-fermionic techniques are implemented for a 64×64 lattice on the Distributed Array Processor and their relative merits examined both for free fermions and the lattice Schwinger model.     

Aromatic polyamides. II. Thermal degradation of some aromatic polyamides and their model diamides

Thermal degradation behavior of poly(1,3-phenylene isophthalamide) and poly(chloro-2,4-phenylene isophthalamide) was investigated with the aid of some appropriate model compounds. The pyrolysis products of these materials were identified by gas chromatography (GC), gas chromatography/Fourier transform infrared spectroscopy (GC/FT-IR), and gas chromatography/mass spectrometry (GC/MS). The residual chars were characterized by IR spectroscopy. Thermogravimetric analysis (TGA) was applied to study the effect of end-group concentration on the degradation characteristics of the two polyamides. Kinetic parameters that describe the thermal degradation of the polyamides were also evaluated by TGA. The results of this investigation suggest that the thermal decomposition of these aromatic polyamides involves homolytic as well as hydrolytic cleavages of the amide units.     

Assessment of the repeatability and reproducibility of hydrogen/deuterium exchange mass spectrometry measurements

A system to perform automated hydrogen/deuterium exchange mass spectrometry measurements was constructed using an XYZ robotic autosampler that was capable of performing solvent manipulations and a 4.7 T Fourier transform ion cyclotron resonance (FT‐ICR) mass spectrometer. The system included features such as the first demonstration of a ‘dual column’ high‐performance liquid chromatography (HPLC) setup, and a novel digestion strategy. The performance of the system, in terms of the repeatability and reproducibility of the measurement of protein hydrogen/deuterium exchange, was assessed over a 2‐month period. The sensitivity of the measurement of hydrogen exchange towards several parameters was assessed, which allowed their impact on the reproducibility to be discussed. The parameters assessed were the temperature of the HPLC columns and switching valves, the temperature of the quench solutions, the pH of the mobile phase, the pH of the quenched solution, the acid used in the mobile phase and the analytical column used. Copyright © 2008 John Wiley & Sons, Ltd.     

Pitfalls in the Use of Common Luminescent Probes for Oxidative and Nitrosative Stress

Lucigenin (LC²⁺, bis-N-methylacridinium) and 2,7-dichlorofluorescin (DCFH₂) are widely used as chemiluminescent or fluorescent probes for cellular oxidative stress, to reflect levels of superoxide (O₂ ^·–) and hydrogen peroxide, respectively. We report mechanistic studies that add to the growing evidence for the unsuitability of either probe except in very well-defined circumstances. The ability for lucigenin to generate superoxide via reduction of LC²⁺ to LC^·+ and redox cycling with oxygen depends on the reduction potential of the LC²⁺/LC^·+ couple. Redox equilibrium between LC^·+ and the redox indicator benzyl viologen is established in microseconds after generation of the radicals by pulse radiolysis and indicated E(LC²⁺/LC^·+) –0.28 V vs. NHE. Reaction of LC^·+ with O₂ to generate O₂ ^·– was also observed directly similarly, occurring in milliseconds, with a rate constant k 3 × 10⁶ M ^–1 s^–1. Quinones act as redox mediators in LC^·+/O₂ redox cycling. Oxidation of DCFH₂ to fluorescent DCF is not achieved by O₂ ^·– or H₂O₂, but NO₂ ^·) reacts rapidly: k 1 × 10⁷ M ^–1 s^–1. Oxidation by H₂O₂ requires a catalyst: cytochrome c (released into the cytosol in apoptosis) is very effective (even 10 nM). Fluorescence reflects catalyst level as much as O₂ ^·–) production.     

Principles of Fourier transform ion cyclotron resonance mass spectrometry and its application in structural biology

Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry has become increasingly significant within recent years. The inherently ultra-high resolution and mass accuracy allow unequivocal assignments of chemical formulae to be made and further structural elucidation can be conducted through the utilization of tandem mass spectrometry techniques. With the advent of electrospray ionization (ESI), FT-ICR mass spectrometry has become a powerful tool for the investigation of biological macromolecules, such as the study of non-covalent interactions of proteins. In this article, the basic principles are highlighted, some of the techniques employed are described and examples of applications are provided, with particular respect being paid to the field of characterization of biomolecules.     

Small angle neutron scattering studies on micellar systems part 1. Ammonium octanoate,ammonium decanoate and ammonium perfluoroocatanoate

Small angle neutron scattering has been used to examine the size and shape of micelles of ammonium octanoate, ammonium decanoate and ammonium perfluoro-octanoate. Ammonium octanoate was found to form micelles with a micellar weight of 1640 and ammonium decanoate with a micellar weight of 12,576; both materials appeared to form spherical micelles. Ammonium perfluoro-octanoate formed micelles with a micellar weight of 17,610. Evidence from the scattering experiments suggested that the micelles were cylindrical and a model for the micelle is proposed.     

EPR spin-trapping evidence for the direct,one-electron reduction of tert-butylhydroperoxide to the tert-butoxyl radical by copper(II): paradigm for a previously overlooked reaction in the initiation of lipid peroxidation

Lipid peroxidation is often initiated using Cu(II) ions. It is widely assumed that Cu(II) oxidizes preformed lipid hydroperoxides to peroxyl radicals, which propagate oxidation of the parent fatty acid via hydrogen atom abstraction. However, the oxidation of alkyl hydroperoxides by Cu(II) is thermodynamically unfavorable. An alternative means by which Cu(II) ions could initiate lipid peroxidation is by their one-electron reduction of lipid hydroperoxides to alkoxyl radicals, which would be accompanied by the generation of Cu(III). We have investigated by EPR spectroscopy, in conjunction with the spin trap 5,5-dimethyl-1-pyrroline N-oxide, the reactions of various Cu(II) chelates with tert-butylhydroperoxide. Spectra contained signals from the tert-butoxyl, methyl, and methoxyl radical adducts. In many previous studies, the signal from the methoxyl adduct has been assigned incorrectly to the tert-butylperoxyl adduct, which is now known to be unstable, releasing the tert-butoxyl radical upon decomposition. This either is trapped by 5,5-dimethyl-1-pyrroline N-oxide or undergoes beta-scission to the methyl radical, which either is trapped or reacts with molecular oxygen to give, ultimately, the methoxyl radical adduct. By using metal chelates that are known to be specific in either their oxidation or reduction of tert-butylhydroperoxide (the Cu(II) complex of bathocuproine disulfonic acid and the Fe(II) complex of diethylenetriaminepentaacetic acid, respectively) for comparison, we have been able to deduce, from the relative concentrations of the three radical adducts, that the Cu(II) complexes tested each reduce tert-butylhydroperoxide directly to the tert-butoxyl radical. These findings suggest that a previously overlooked reaction, namely the direct reduction of preformed lipid hydroperoxides to alkoxyl radicals by Cu(II), may be responsible for the initiation of lipid peroxidation by Cu(II) ions.     

Small angle neutron scattering studies on micellar systems part 2. Mixed systems of ammonium decanoate and ammonium perfluoro-octanoate

Mixtures of ammonium decanoate (AmDec) and ammonium perfluoro-octanoate (APFO), in ammonium chloride: ammonium hydroxide buffer at pH 8.8 and an ionic strength of 0.1, were examined by small angle neutron scattering with varying proportions of the two surface active agents. The results indicated that mixed micelles were formed and it is suggested from analysis of the data that these were cylindrical in shape at APFO: AmDec ratios of 21, 11 and 12. At 21 and 11 the micelles were found to contain more APFO than expected on the basis of ideal mixing of the surface active agents in the micelle. At a ratio of 19 the micelles were found to be spherical but larger than those formed from AmDec alone. A speculative model is proposed for the mixed micelle which still, however, allows for segregation between hydrocarbon and fluorocarbon chains within the micelle.