A comparison of feasible direction methods for the stochastic transportation problem

The feasible direction method of Frank and Wolfe has been claimed to be efficient for solving the stochastic transportation problem. While this is true for very moderate accuracy requirements, substantially more efficient algorithms are otherwise diagonalized Newton and conjugate Frank–Wolfe algorithms, which we describe and evaluate. Like the Frank–Wolfe algorithm, these two algorithms take advantage of the structure of the stochastic transportation problem. We also introduce a Frank–Wolfe type algorithm with multi-dimensional search; this search procedure exploits the Cartesian product structure of the problem. Numerical results for two classic test problem sets are given. The three new methods that are considered are shown to be superior to the Frank–Wolfe method, and also to an earlier suggested heuristic acceleration of the Frank–Wolfe method.     

A high‐performance parallel‐generalized born implementation enabled by tabulated interaction rescaling

Implicit solvent representations, in general, and generalized Born models, in particular, provide an attractive way to reduce the number of interactions and degrees of freedom in a system. The instantaneous relaxation of the dielectric shielding provided by an implicit solvent model can be extremely efficient for high‐throughput and Monte Carlo studies, and a reduced system size can also remove a lot of statistical noise. Despite these advantages, it has been difficult for generalized Born implementations to significantly outperform optimized explicit‐water simulations due to more complex functional forms and the two extra interaction stages necessary to calculate Born radii and the derivative chain rule terms contributing to the force. Here, we present a method that uses a rescaling transformation to make the standard generalized Born expression a function of a single variable, which enables an efficient tabulated implementation on any modern CPU hardware. The total performance is within a factor 2 of simulations in vacuo. The algorithm has been implemented in Gromacs, including single‐instruction multiple‐data acceleration, for three different Born radius models and corresponding chain rule terms. We have also adapted the model to work with the virtual interaction sites commonly used for hydrogens to enable long‐time steps, which makes it possible to achieve a simulation performance of 0.86 μs/day for BBA5 with 1‐nm cutoff on a single quad‐core desktop processor. Finally, we have also implemented a set of streaming kernels without neighborlists to accelerate the non‐cutoff setup occasionally used for implicit solvent simulations of small systems. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Separation of neoglycoproteins with different degrees of glycosylation by boronate chromatography

Summary The separation of glycoproteins as glycoforms with specific degrees of glycosylation has been a problem until now. A technique involving boronate affinity chromatography has been developed to separate a heterogeneous sample of neoglycoprotein, chymotrypsin modified with maltose via reductive amination, into individual fractions with different degrees of glycosylation. Low-molecular-mass polyhydroxyl compounds, such as tris(hydroxymethyl)aminomethane (Tris), pentaerythritol, and triethanolamine proved efficient eluents due to their ability to form strong tridentate complexes with the boronate ligand. Compounds leading to either; too strong interaction with the boronate ligand (e. g. D-sorbitol and polyvinly alcohol), or too weak or no interaction (e. g. dextran) were not suitable eluents. The study provided the opportunity to probe further into the effect of glycosylation on the function of glycoproteins.     

Separation of mistletoe lectins based on the degree of glycosylation using boronate affinity chromatography

A mixture of two mistletoe lectins (MLs) has been separated according to the degree of glycosylation using boronate affinity chromatography. The mistletoe lectins, mistletoe lectin I (MLI) and mistletoe lectin III (MLIII) with degrees of glycosylation of 6.1 and 3.8%, respectively, were used in the investigation. MLI exhibited a higher retention time than MLIII due to its higher degree of glycosylation. Separation was confirmed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The developed method may lead to new applications for the boronate affinity technique, as well as provide an alternative separation method for MLs.     

A comparative CP/MAS 13C-NMR study of cellulose structure in spruce wood and kraft pulp

CP/MAS ¹³C-NMR spectroscopy in combination with spectral fitting was used to study the supermolecular structure of the cellulose fibril in spruce wood and spruce kraft pulp. During pulping, structures contributing to inaccessible surfaces in the wood cellulose are converted to the cellulose I allomorph, that is, the degree of order is increased. This increase is also accompanied by a conversion of cellulose I to cellulose I. Cellulose from wood composed of different cell types, that is, compression wood, juvenile wood, earlywood, latewood and normal wood exhibited a similar supermolecular structure. Assignments were made for signals from hemicellulose which contribute significantly to the spectral C-4 region (80–86 ppm) in kraft pulp spectra but substantially less to the corresponding region in wood spectra.     

Recombination of simple molecular ions studied in storage ring: dissociative recombination of H2O+

Dissociative recombination of vibrationally relaxed H2O+ ions with electrons has been studied in the heavy-ion storage ring CRYRING. Absolute cross-sections have been measured for collision energies between 0 eV and 30 eV. The energy dependence of the cross-section below 0.1 eV is found to be much steeper than the E-1 behaviour associated with the dominance of the direct recombination mechanism. Resonant structures found at 4 eV and 11 eV have been attributed to the electron capture to Rydberg states converging to electronically excited ionic states. Complete branching fractions for all dissociation channels have been measured at a collision energy of 0 eV. The dissociation process is dominated by three-body H + H + O breakup that occurs with a branching ratio of 0.71.     

On the accessibility and structure of xylan in birch kraft pulp

The structure of -(14)-xylan, both in isolated form and as a component of bleached birch kraft pulp, was studied employing CP/MAS ¹³C NMR spectroscopy. Bleached birch kraft pulp was treated with xylanases or alkali in order to distinguish between accessible and inaccessible xylan. In xylan which was alkali-extracted from bleached birch kraft pulp, the relative contents of xylose and 4-O-methylglucuronic acid were 99.4 and 0.6 weight %, respectively, and the degree of polymerization was 70. The supermolecular structure of xylan is very sensitive to the surrounding environment. All extracted xylan chains were accessible to water and methanol and the solvent molecules easily exchanged. In bleached birch kraft pulp, cellulose fibrils interact with xylan chains, causing these to adopt a conformation similar to one of the configurations observed for dry xylan. In birch pulp, about 1/3 of the xylan was found to be accessible to digestion by xylanases or extraction with 5% w/w potassium hydroxide (aq). A signal at 81.7ppm in the C-4 region of the CP/MAS ¹³C NMR spectrum of bleached birch kraft pulp originated from xylan at the accessible fibril surfaces. A portion of a broad signal at 83.5ppm reflected inaccessible xylan, which is probably present as co-aggregates with cellulose fibril aggregates.     

Mass spectrometric determination of selected microbial constituents using fused silica and chiral glass capillary gas chromatography

Summary Applications of quantitative gas chromatography/mass spectrometry (selected ion monitoring) to clinical and ecological microbiology are described. The technique permits determination of selected microbial metabolites and can be used for the rapid diagnosis of, for example, tuberculosis by ion-focusing of specific branch-chain fatty acids. The technique is also used to determine diaminopimelic and muramic acids, and D- and L-amino acids separated by chiral gas chromatography, in the low picogram range. The latter method has the potential to detect and quantitate microbial populations.Presented at the 14th International Symposium on Chromatography London, September, 1982