Correction: Dermatan sulfate in tunicate phylogeny: Order-specific sulfation pattern and the effect of [→4IdoA(2-Sulfate)β-1→3GalNAc(4-Sulfate)β-1→] motifs in dermatan sulfate on heparin cofactor II activity

After the publication of the work entitled "Dermatan sulfate in tunicate phylogeny: Order-specific sulfation pattern and the effect of [→4IdoA(2-Sulfate)β-1→3GalNAc(4-Sulfate)β-1→] motifs in dermatan sulfate on heparin cofactor II activity", by Kozlowski et al., BMC Biochemistry 2011, 12:29, we found that the legends to Figures 2 to 5 contain serious mistakes that compromise the comprehension of the work. This correction article contains the correct text of the legends to Figures 2 to 5.     

A method for predicting unsteady potential flow about an aerofoil

A new model is presented for the calculation of the incompressible, inviscid flow around an arbitrary aerofoil undergoing unsteady motion. The technique was developed from the steady flow algorithm of Leishman and Galbraith¹ in which use was made of a linear distribution of panel vorticity. The procedure is in the same class as that of Basu and Hancock² but, because of the particular approach to the manner of specifying the shed vorticity, only a set of linear simultaneous equations needs be solved, unlike the method of Reference 2, complicated by the necessary solution of a quadratic. A brief history of unsteady flow modelling is given in the introduction, followed by the mathematical details of the current method. Results are presented and discussed for a number of cases which clearly illustrate relevant characteristics of unsteady flow.     

Electrocatalytic Determination of Sulfite at Immobilized Microdroplet Liquid|Liquid Interfaces: The EIC′ Mechanism

Liquid|liquid interfaces provide a natural boundary and a reactive interface where an organic phase is in contact with an aqueous analyte. The selectivity of ion transfer processes at liquid|liquid interfaces can help to provide sensitivity, introduce reactive reagents, or allow analyte accumulation at the electrode surface. In this study, microdroplet deposits of the organic liquid 4‐(3‐phenylpropyl)‐pyridine (PPP) with the ferrocenylmethyl‐dodecyldimethylammonium⁺ (FDA⁺) redox system are deposited onto a basal plane pyrolytic graphite electrode and employed to transfer anions from the aqueous into the organic phase. A clear trend of more hydrophobic anions transferring more readily (at more negative potentials) is observed and an ESI‐mass spectrometry method is developed to confirm the transfer. Subsequently, the electrocatalytic oxidation of sulfite, SO₃^2?, within the organic phase and in the presence of different electrolyte anions is investigated. Competition between sulfite transfer and inert anion transfer occurs. The electrocatalytic sulfite oxidation is suppressed in the presence of PF₆^? and occurs most readily in the presence of the hydrophilic nitrate anion. The resulting process can be classified as an electrocatalytic EIC′‐process (E: electron transfer; I: ion transfer; C: chemical reaction step). The effectiveness of the electrocatalytic process is limited by i) competition during anion transfer and ii) the liquid|liquid interface acting as a diffusion barrier. The analytical sensitivity of the method is limited to ca. 100 μM SO₃^2? (or ca. 8 ppm) and potential approaches for improvement of this limit are discussed.     

Investigating the molecular mechanisms of in-plane mechanochemistry on cantilever arrays

Free-standing cantilevers, which directly translate specific biochemical reactions into micromechanical motion, have recently attracted much attention as label-free biosensors and micro/nano robotic devices. To exploit this mechanochemical sensing technology, it is essential to develop a fundamental understanding of the origins of surface stress. Here we report a detailed study into the molecular basis of stress generation in aqueous environments focusing on the pH titration of model mercaptohexadecanoic acid self-assembled monolayers (SAMs), using in situ reference cantilevers coated with nonionizable hexadecanethiol SAMs. Semiautomated data analysis and a statistical model were developed to quantify cyclic deprotonation/protonation reactions on multiple arrays. In-plane force titrations were found to have the sensitivity to detect ionic hydrogen bond formation between protonated and nonprotonated carboxylic acid groups in the proximity of the surface pK1/2, which generated a mean tensile differential surface stress of +1.2 +/- 0.3 mN/m at pH 6.0, corresponding to 1 pN attractive force between two adjacent MHA molecules. Conversely, the magnitude of compressive differential surface stress was found to increase progressively with pH >/= 7.0, reaching a maximum of -14.5 +/- 0.5 mN/m at pH 9.0, attributed to enhanced electrostatic repulsion between deprotonated carboxylic acid groups. However, striking differences were observed in the micromechanical responses to different ionic strength and ion species present in the aqueous environment, highlighting the critical role of counter- and co-ions on surface stress. Our findings provide fundamental insights into the molecular mechanisms of in-plane mechanochemistry, which may be exploited for biosensing and nanoactuation applications.     

Anion selectivity in zwitterionic amide-functionalised metal salt extractants

Amide-functionalised salen ligands capable of extracting metal salts have been synthesised and characterised. Single-crystal X-ray structure determinations of complexes of NiSO4, [Ni(L)(SO4)], confirm that the ionophores are in a zwitterionic form with Ni(II) bound in the deprotonated salen moiety and the SO4(2-) ion associated with protonated pendant N'-amidopiperazine groups. Treatment of [Ni(L)(SO4)] with base removes the protons from the pendant amido-amine group resulting in loss of the SO4(2-) ion and formation of metal-only complexes of type [Ni(L-2H)], which have been characterized by single-crystal X-ray diffraction. Three of the ligands with solubilities suitable for solvent extraction studies show loading and stripping pH-profiles that are suitable for the recovery of CuSO4 or CuCl2 from industrial leach solutions. The copper-only complexes, [Cu(L-2H)], are selective for Cl- over SO4(2-) in both solvent extraction and bulk liquid membrane transport experiments and were found to bind Cl- in two steps via the formation of a 1:1:1 [Cu(L-H)Cl] assembly, followed by a 1:1:2 [Cu(L)Cl2] assembly as the pH of the aqueous phase is lowered. The anion transport selectivity was evaluated for a number of other mono-charged anions and interestingly the ligands were found to display a preference for the Br- ion. To probe the influence of the Hofmeister bias on the selectivity of anion complexation, single-phase potentiometric titration experiments were employed to investigate the binding of SO4(2-) and Cl- by one of the copper only complexes, [Cu(L-2H)] in 95 %/5 % MeOH/water. Under these conditions selectivity was reversed (SO4(2-)>Cl-) confirming that the Hofmeister bias, which reflects the relative hydration energies of the anions, dominates the selectivity of anion extraction from aqueous media into CHCl3.     

NMR chemical shielding surface of N-Acetyl-N′-Methylalaninamide: A density functional study

The five energetically lowest minima on the potential energy surface of N-acetyl-N′-methylalaninamide were optimized at the Becke3LYP/DZd level of theory to compare these density functional theory results with the literature findings at restricted Hartree-Fock/3-21G. While the relative energies are very similar, the amide moiety is predicted to be much more flexible at Becke3LYP/DZd. As a consequence, the three minima that favor a nonplanar amide group differ by up to 14° in their ϕ and ψ values between the two levels. To compare the change in the density functional NMR chemical shifts with respect to ϕ and ψ with experimental results, Becke3LYP/DZd was employed to optimize a structure for N-acetyl-N′-methylalaninamide at each 30° interval on the (ϕ, ψ) surface in the regions that correspond to the α helix and the β-pleated sheet and at each 60° interval elsewhere. The corresponding NMR chemical shielding surface was computed with the density functional program deMon. The resultant NMR chemical shielding surfaces for N and C^β are in good agreement with the experiment, while the change in the NMR chemical shielding of C′ and C^α cannot be described only in terms of ϕ and ψ. The chemical shifts for those atoms also depend on the nonplanarity of the amide moiety. We evaluated this dependence for N-methylacetamide as a model system. Estimates of the parameters derived from N-methyl-acetamide allowed the NMR-shielding surfaces of C′ and C^α to be corrected for the nonplanar nitrogen influence. Although the effect is less pronounced with lower level theoretical geometries, due to the smaller degree of pyramidalization of the amide nitrogen, the (ϕ, ψ) NMR chemical shielding surfaces will need to be corrected. The agreement with the experiment was much better for the corrected surface of C′ when the nitrogen in the α helix had a nonplanar environment. © 1997 by John Wiley & Sons, Inc.     

Dynamics of fluorescence depolarisation in star-shaped oligofluorene-truxene molecules

Star-shaped molecules are of growing interest as organic optoelectronic materials. Here a detailed study of their photophysics using fluorescence depolarisation is reported. Fluorescence depolarisation dynamics are studied in branched oligofluorene-truxene molecules with a truxene core and well-defined three-fold symmetry, and are compared with linear fluorene oligomers. An initial anisotropy value of 0.4 is observed which shows a two-exponential decay with time constants of 500 fs and 3-8 ps in addition to a long-lived component. The femtosecond component is attributed to exciton localisation on one branch of the molecule and its amplitude reduces when the excitation is tuned to the low energy tail of the absorption spectrum. The picosecond component shows a weak dependence on the excitation wavelength and is similar to the calculated rate of the resonant energy transfer of the localised exciton between the branches. These assignments are supported by density-functional theory calculations which show a disorder-induced splitting of the two degenerate excited states. Exciton localisation is much slower than previously reported in other branched molecules which suggests that efficient light-harvesting systems can be designed using oligofluorenes and truxenes as building blocks.     

The interaction of iron pyrite with oxygen, nitrogen and nitrogen oxides: a first-principles study

Sulphide materials, in particular MoS(2), have recently received great attention from the surface science community due to their extraordinary catalytic properties. Interestingly, the chemical activity of iron pyrite (FeS(2)) (the most common sulphide mineral on Earth), and in particular its potential for catalytic applications, has not been investigated so thoroughly. In this study, we use density functional theory (DFT) to investigate the surface interactions of fundamental atmospheric components such as oxygen and nitrogen, and we have explored the adsorption and dissociation of nitrogen monoxide (NO) and nitrogen dioxide (NO(2)) on the FeS(2)(100) surface. Our results show that both those environmentally important NO(x) species chemisorb on the surface Fe sites, while the S sites are basically unreactive for all the molecular species considered in this study and even prevent NO(2) adsorption onto one of the non-equivalent Fe-Fe bridge sites of the (1 × 1)-FeS(2)(100) surface. From the calculated high barrier for NO and NO(2) direct dissociation on this surface, we can deduce that both nitrogen oxides species are adsorbed molecularly on pyrite surfaces.     

High-fidelity simulations of moving and flexible airfoils at low Reynolds numbers

The present paper highlights results derived from the application of a high-fidelity simulation technique to the analysis of low-Reynolds-number transitional flows over moving and flexible canonical configurations motivated by small natural and man-made flyers. This effort addresses three separate fluid dynamic phenomena relevant to small fliers, including: laminar separation and transition over a stationary airfoil, transition effects on the dynamic stall vortex generated by a plunging airfoil, and the effect of flexibility on the flow structure above a membrane airfoil. The specific cases were also selected to permit comparison with available experimental measurements. First, the process of transition on a stationary SD7003 airfoil section over a range of Reynolds numbers and angles of attack is considered. Prior to stall, the flow exhibits a separated shear layer which rolls up into spanwise vortices. These vortices subsequently undergo spanwise instabilities, and ultimately breakdown into fine-scale turbulent structures as the boundary layer reattaches to the airfoil surface. In a time-averaged sense, the flow displays a closed laminar separation bubble which moves upstream and contracts in size with increasing angle of attack for a fixed Reynolds number. For a fixed angle of attack, as the Reynolds number decreases, the laminar separation bubble grows in vertical extent producing a significant increase in drag. For the lowest Reynolds number considered (Re _c  = 10⁴), transition does not occur over the airfoil at moderate angles of attack prior to stall. Next, the impact of a prescribed high-frequency small-amplitude plunging motion on the transitional flow over the SD7003 airfoil is investigated. The motion-induced high angle of attack results in unsteady separation in the leading edge and in the formation of dynamic-stall-like vortices which convect downstream close to the airfoil. At the lowest value of Reynolds number (Re _c  = 10⁴), transition effects are observed to be minor and the dynamic stall vortex system remains fairly coherent. For Re _c  = 4 × 10⁴, the dynamic-stall vortex system is laminar at is inception, however shortly afterwards, it experiences an abrupt breakdown associated with the onset of spanwise instability effects. The computed phased-averaged structures for both values of Reynolds number are found to be in good agreement with the experimental data. Finally, the effect of structural compliance on the unsteady flow past a membrane airfoil is investigated. The membrane deformation results in mean camber and large fluctuations which improve aerodynamic performance. Larger values of lift and a delay in stall are achieved relative to a rigid airfoil configuration. For Re _c = 4.85 × 10⁴, it is shown that correct prediction of the transitional process is critical to capturing the proper membrane structural response.     

Efficient pairing computation on supersingular Abelian varieties

We present a general technique for the efficient computation of pairings on Jacobians of supersingular curves. This formulation, which we call the eta pairing, generalizes results of Duursma and Lee for computing the Tate pairing on supersingular elliptic curves in characteristic 3. We then show how our general technique leads to a new algorithm which is about twice as fast as the Duursma–Lee method. These ideas are applied to elliptic and hyperelliptic curves in characteristic 2 with very efficient results. In particular, the hyperelliptic case is faster than all previously known pairing algorithms.