A general framework for ADMM acceleration

Numerical Algorithms - The Alternating Direction Multipliers Method (ADMM) is a very popular algorithm for computing the solution of convex constrained minimization problems. Such problems are...     

89Y magic-angle spinning NMR of Y2Ti2-xSnxO7 pyrochlores

The yttrium local environment in the series of pyrochlores Y2Ti2-xSnxO7 was studied using 89Y NMR. Oxides with the pyrochlore structure exhibit a range of interesting physical and chemical properties, resulting in many technological applications, including the encapsulation of lanthanide- and actinide-bearing radioactive waste. The use of the nonradioactive Y3+ cation provides a sensitive probe for any changes in the local structure and ordering with solid solution composition, through 89Y (I = 1/2) NMR. We confirm that a single pyrochlore phase is formed over the entire compositional range, with Y found only on the eight-coordinated A site. A significant (approximately 15 ppm) chemical shift is observed for each Sn substituted into the Y second neighbor coordination environment. The spectral signal intensities of the possible combinations of Sn/Ti neighbors match those predicted statistically assuming a random distribution of Sn4+/Ti4+ on the six-coordinated pyrochlore B site.     

Complementary Lidstone interpolation on scattered data sets

Recently we have introduced a new technique for combining classical bivariate Shepard operators with three point polynomial interpolation operators (Dell’Accio and Di Tommaso, On the extension of the Shepard-Bernoulli operators to higher dimensions, unpublished). This technique is based on the association, to each sample point, of a triangle with a vertex in it and other ones in its neighborhood to minimize the error of the three point interpolation polynomial. The combination inherits both degree of exactness and interpolation conditions of the interpolation polynomial at each sample point, so that in Caira et al. (J Comput Appl Math 236:1691–1707, 2012) we generalized the notion of Lidstone Interpolation (LI) to scattered data sets by combining Shepard operators with the three point Lidstone interpolation polynomial (Costabile and Dell’Accio, Appl Numer Math 52:339–361, 2005). Complementary Lidstone Interpolation (CLI), which naturally complements Lidstone interpolation, was recently introduced by Costabile et al. (J Comput Appl Math 176:77–90, 2005) and drawn on by Agarwal et al. (2009) and Agarwal and Wong (J Comput Appl Math 234:2543–2561, 2010). In this paper we generalize the notion of CLI to bivariate scattered data sets. Numerical results are provided.     

Structural analysis of leukotriene C<Subscript>4</Subscript> isomers using collisional activation and 157 nm photodissociation

The fragmentation of 5-hydroxy-6-glutathionyl-7,9,11,14-eicosatetraenoic acid [leukotriene C4 or LTC4 (5, 6)] and its isomeric counterpart LTC4 (14, 15) were studied by low and high-energy collisional induced dissociation (CID) and 157 nm photofragmentation. For singly charged protonated LTC4 precursors, photodissociation significantly enhances the signal intensities of informative fragment ions that are very important to distinguish the two LTC4 isomers and generates a few additional fragment ions that are not usually observed in CID experiments. The ion trap enables MSn experiments on the fragment ions generated by photodissociation. Photofragmentation is found to be suitable for the structural identification and isomeric differentiation of cysteinyl leukotrienes and is more informative than low or high-energy CID. We describe for the first time the structural characterization of the LTC4 (14, 15) isomer by mass spectrometry using CID and 157 nm light activation methods.     

Effect of random on-site energies on the critical temperature of a lattice Bose gas

We study the effect of random on-site energies on the critical temperature of a non-interacting Bose gas on a lattice. In our derivation the on-site energies are distributed according a Gaussian probability distribution function having vanishing average and variance ν ₀ ² . By using the replicated action obtained by averaging on the disorder, we perform a perturbative expansion for the Green functions of the disordered system. We evaluate the shift of the chemical potential induced by the disorder and we compute, for ν ₀ ² ? 1, the critical temperature for condensation. We find that, for large filling, disorder slightly enhances the critical temperature for condensation.     

Mass spectrometric analysis of the S-layer proteins from Clostridium difficile demonstrates the absence of glycosylation

Like many other bacterial cell surfaces, the cell wall of Clostridium difficile is also encapsulated by a proteinaceous paracrystalline layer, the surface (S)-layer. In many bacterial species, the S-layer proteins (SLPs) have been shown to be glycosylated, whereas in other species glycosylation is absent. Unusually, the S-layer of C. difficile is composed of two distinct proteins, the high-molecular weight (HMW) and low-molecular-weight (LMW) SLPs. Previous investigations have reported that one or both of these SLPs are glycosylated, though no definitive study has been conducted. We have used a variety of mass spectrometric approaches to analyse SLPs from a number of strains of C. difficile for the presence of associated glycans. Analysis of intact SLPs by matrix assisted laser desorption/ionisation time of flight (MALDI-ToF) mass spectrometry demonstrated that the observed molecular masses matched the predicted masses of the LMW and HMW SLPs. Furthermore, analysis of Cyanogen bromide (CNBr) and tryptic peptides displayed no evidence of post-translational modification. In the first in-depth study of its kind, we unequivocally demonstrate that the S-layer proteins from the C. difficile strains investigated are not glycosylated.     

Ab initio molecular dynamics simulations of the liquid/vapor interface of sulfuric acid solutions

Ab initio molecular dynamics simulations of the liquid-vapor interface are presented for thin slabs of 72 water molecules containing a single molecule of sulfuric acid. Trajectories in the 306-330 K range are calculated for two functionals with double- and triple-ζ quality basis sets. Comparisons are made between BLYP and HCTH/120 results for the slab simulations and for bulk simulations of one H(2)SO(4) in a periodic box with 63 waters. Good agreement is found with the available experimental data and the results of other relevant AIMD studies with respect to ionization of the acid, size of the coordination shells, partitioning of the ions with the hydronium exhibiting a surface preference and the anions in the interior, and the orientational distributions for the hydronium ions and for the surface/subsurface water molecules. The major differences in the performance of the two functionals are attributable to the greater basicity of the anion oxygen atoms with the HCTH functional and the more structured aqueous solution with BLYP. The enhanced basicity results in larger aqueous coordination shells for the anion oxygens. The structuring of the BLYP aqueous solution is observed in the corrugation of the water density profile, the higher first peak in g(OO)(r), and a smaller water self-diffusion constant. This structuring with the BLYP functional yields anion hydrogen bonds that endure longer and where the dissociated ions more rapidly and directly segregate in the slab. The simulations indicate that aqueous surfaces containing ionizable diprotic acids can be modeled with rather modest sized systems and be informative.     

Capillary size exclusion chromatography with picogram sensitivity for analysis of monoclonal antibodies purified from harvested cell culture fluid

Size exclusion chromatography (SEC) is widely used in the characterization and quality control of therapeutic proteins to detect aggregates. Aggregation is a carefully monitored quality attribute from the earliest stages of clinical development owing to the possibility of eliciting an immunogenic response in the patient. During early stage molecule assessment for cell culture production, small-scale screening experiments are performed to permit rapid turn-around of results so as to not delay timelines. We report the development of a capillary SEC methodology for preliminary molecule assessment to support the evaluation of therapeutic candidates at an early stage of development. By making several key modifications to a commercially available liquid chromatography system, we demonstrate a platform process to perform capillary SEC with excellent precision, picogram sensitivity and good ruggedness. The limit of quantitation was determined to be approximately 15 pg; picogram sensitivity for SEC analysis of monoclonal antibodies had not been achieved prior to this work. In addition, we have developed a method to capture low levels of antibody (1 μg/mL) from harvested cell culture fluid (HCCF) for capillary SEC analysis. Up to 40% recovery efficiency was achieved using this micro-recovery method on 3 mL HCCF samples. Using early stage cell culture transient transfection samples, which typically have much lower titers than stable cell line samples, we demonstrate a consistent method for analyzing aggregates in low protein concentration HCCF samples for molecule assessment and early stage candidate screening.     

Acetylation of a heterocyclic enaminonitrile: Unambiguous structural assignment using NMR methods

Using a combination of nmr techniques, the structure of the acetylation product of methyl 3-[2-amino-3-cyano-9-methoxy-4H-5,6-dihydronaphtho[1,2-b]pyran-4-yl] benzoate 2b has been shown to be the N-acetyl derivative 5a , rather than the rearranged 2-acetoxydihydropyridine 6a.