Rod-climbing effect in Newtonian fluids

When a rotating rod is brought into a polymer melt or concentrated polymer solution, the meniscus climbs the rod. This spectacular rod climbing is due to the normal stresses present in the polymer fluid and is thus a purely non-Newtonian effect. A similar rod climbing of an interface between two fluids has therefore been taken as a signature that one of the fluids exhibits normal stress effects. We show here, however, that the effect can occur with simple Newtonian fluids: it occurs when a Taylor-Couette instability happens in the less viscous of the two liquids but not in the more viscous one.     

Real-Time Detection of Polymerase Activity Using Supercritical Angle Fluorescence

We investigated the incorporation efficiencies of different fluorescently labelled dNTPs with polymerases by complementary strand synthesis. For this reason single stranded DNA was immobilized on a coverslip and the increase of fluorescence due to the synthesis of the corresponding strand with tagged dNTPs was detected with a supercritical angle fluorescence biosensor in real-time. By comparison of the observed signal intensities it was possible to conclude that the system Cy5-dCTP-Klenow (exonuclease free) fragment gives the best incorporation yield of the investigated enzymes and dNTPs.     

Global observables at PHENIX

We present PHENIX recent results on charged particle and transverse energy densities measured at mid-rapidity in Au?Au collisions at $\sqrt {s_{NN} } = 130$ GeV and 200 GeV over a broad range of centralities. The mean transverse energy per charged particle is derived. The first PHENIX measurements at $\sqrt {s_{NN} } = 19.6$ GeV are also presented. A comparison with calculations from various theoretical models is performed.     

Structure determination of aligned samples of membrane proteins by NMR spectroscopy

The paper briefly reviews the process of determining the structures of membrane proteins by NMR spectroscopy of aligned samples, describes the integration of recent developments in the interpretation of spectra of aligned proteins and illustrates the application of these methods to the trans-membrane helical domain of a protein. The emerging methods of interpreting the spectral parameters from aligned samples of isotopically labeled proteins provide opportunities for simultaneously assigning the spectra and determining the structures of the proteins, and also for comparing the results from solid-state NMR experiments on completely aligned samples with those of solution NMR experiments on weakly aligned samples.     

Synthesis and stereochemical properties of chiral square complexes of iron(II)

The hexadentate, and ditopic ligand 2,5-bis([2,2']bipyridin-6-yl)pyrazine yields a chiral, tetrameric, square-shaped, self-assembled species upon complexation with Fe2+ ions. The racemate of this complex was resolved with antimonyl tatrate as the chiral auxiliary. The purity of the enantiomer was determined by NMR spectroscopy, by using a chiral, diamagnetic shift reagent, and by circular dichroism (CD). The CD spectrum was also calculated by time-dependent density functional theory, and the correlation that was found between CD spectrum and configuration was confirmed by X-ray cristallography. When a "chiralised" version of the ligand was used instead, the corresponding iron complex was obtained in diastereomerically pure form.     

Biliverdin reduction by cyanobacterial phycocyanobilin:ferredoxin oxidoreductase (PcyA) proceeds via linear tetrapyrrole radical intermediates

Cyanobacterial phycocyanobilin:ferredoxin oxidoreductase (PcyA) catalyzes the four electron reduction of biliverdin IXalpha (BV) to phycocyanobilin, a key step in the biosynthesis of the linear tetrapyrrole (bilin) prosthetic groups of cyanobacterial phytochromes and the light-harvesting phycobiliproteins. Using an anaerobic assay protocol, optically detected bilin-protein intermediates, produced during the PcyA catalytic cycle, were shown to correlate well with the appearance and decay of an isotropic g approximately 2 EPR signal measured at low temperature. Absorption spectral simulations of biliverdin XIIIalpha reduction support a mechanism involving direct electron transfers from ferredoxin to protonated bilin:PcyA complexes.     

Microchip capillary electrophoresis with a boron-doped diamond electrochemical detector for analysis of aromatic amines

The attractive features of a boron-doped diamond (BDD) thin-film detector for microchip capillary electrophoretic (CE) separations of dye-related amino-substituted aromatic compounds are described. The diamond electrode was employed in the end-column amperometric detection of 4-aminophenol (4-AP), 1,2-phenylenediamine (1,2-PDA), 2-aminonaphthalene (2-AN), 2-chloroaniline (2-CA), and o-aminobenzoic acid (o-ABA), and its attractive behavior was compared to commonly used screen-printed carbon and glassy-carbon electrodes. These conventional electrode materials exhibit a significant degree of passivation and low sensitivity to the above-mentioned environmental pollutants. The diamond-based electrochemical detection system displayed a favorable analytical performance, including lower noise levels, higher peak resolution with enhanced sensitivity, and improved resistance against electrode passivation. Factors influencing the on-chip analysis were assessed and optimized. The diamond detector displayed detection limits of 2.0 and 1.3 microM for 4-AP and 2-AN, respectively, and a wide linear response for these compounds over the 2-50 microM range. The enhanced stability was demonstrated by relative standard deviation (RSD) values of 1.4% and 4.7% for 100 microM 1,2-PDA and 200 microM 2-CA, respectively, for repetitive detections (n = 7). Besides, the simultaneously observed current decrease was 2.4 and 9.1% for 1,2-PDA and 2-CA, respectively (compared to 21.8 and 41.0% at the screen-printed carbon electrode and 28.3 and 34.1% at the glassy carbon electrode, respectively). The favorable properties of the diamond electrode indicate great promise for environmental applications in CE and other microchip devices.     

Development of the force field parameters for phosphoimidazole and phosphohistidine

Phosphorylation of histidine-containing proteins is a key step in the mechanism of many phosphate transfer enzymes (kinases, phosphatases) and is the first stage in a wide variety of signal transduction cascades in bacteria, yeast, higher plants, and mammals. Studies of structural and dynamical aspects of such enzymes in the phosphorylated intermediate states are important for understanding the intimate molecular mechanisms of their functioning. Such information may be obtained via molecular dynamics and/or docking simulations, but in this case appropriate force field parameters for phosphohistidine should be explicitly defined. In the present article we describe development of the GROMOS96 force field parameters for phosphoimidazole molecule--a realistic model of the phosphohistidine side chain. The parameterization is based on the results of ab initio quantum chemical calculations with subsequent refinement and testing using molecular mechanics and molecular dynamics simulations. The set of force constants and equilibrium geometry is employed to derive force field for the phosphohistidine moiety. Resulting parameters and topology are incorporated into the molecular modeling package GROMACS and used in molecular dynamics simulations of a phosphohistidine-containing protein in explicit solvent.