Body fitted link-cell algorithm for particulate flow simulation in curved pipeline domain

The link-cell (LC) algorithm is widely used in discrete element method (DEM) simulation, in order to increase computational efficiency. The common way is to divide the entire computational domain into a series of square sub-cells. A huge index matrix, Ω$\Omega$, is required to store the information of particles located in each of these sub-cells. However, most of these sub-cells are always empty for some anomalistic computational domain, such as particulate flow in a pipeline. These empty sub-cells also consume the limited memory bandwidth and lower the computational power. In order to reduce the size of the index matrix, a body fitted link-cell (BFLC) algorithm is established to identify the neighbors quickly. Furthermore, a simplified algorithm for simulation of two dimensional particulate flow in curved pipelines is presented. Lastly, an example is presented to validate the BFLC algorithm.     

Synthesis, structure and catalytic activity of a bimacrocylic NHC palladium allyl complex

The preparation of a bimacrocyclic NHC palladium allyl complex 4 is described. The complex was obtained by transmetalation with allyl palladium chloride dimer from the NHC silver complex 2 in 85% yield. Complex 4 was fully characterized by spectroscopic methods and by single-crystal X-ray analysis. In a preliminary catalytic study, complex 4 showed high activity in the Suzuki-Miyaura cross-coupling of unactivated aryl chlorides and bromides with 1-naphthalene-boronic acid at low catalyst loading. Good results were also obtained in the Mizoroki-Heck reaction of aryl bromides with styrene, but a decrease in yield was observed when aryl chlorides were used.     

Towards liquid chromatography time-scale peptide sequencing and characterization of post-translational modifications in the negative-ion mode using electron detachment dissociation tandem mass spectrometry

Electron detachment dissociation (EDD) of peptide poly-anions is gentle towards post-translational modifications (PTMs) and produces predictable and interpretable fragment ion types (a., x ions). However, EDD is considered an inefficient fragmentation technique and has not yet been implemented in large-scale peptide characterization strategies. We successfully increased the EDD fragmentation efficiency (up to 9%), and demonstrate for the first time the utility of EDD-MS/MS in liquid chromatography time-scale experiments. Peptides and phosphopeptides were analyzed in both positive- and negative-ion mode using electron capture/transfer dissociation (ECD/ETD) and EDD in comparison. Using approximately 1 pmol of a BSA tryptic digest, LC-EDD-MS/MS sequenced 14 peptides (27% aa sequence coverage) and LC-ECD-MS/MS sequenced 19 peptides (39% aa sequence coverage). Seven peptides (18% aa sequence coverage) were sequenced by both EDD and ECD. The relative small overlap of identified BSA peptides demonstrates the complementarity of the two dissociation modes. Phosphopeptide mixtures from three trypsin-digested phosphoproteins were subjected to LC-EDD-MS/MS resulting in the identification of five phospho-peptides. Of those, one was not found in a previous study using a similar sample and LC-ETD-MS/MS in the positive-ion mode. In this study, the ECD fragmentation efficiency (15.7% av.) was superior to the EDD fragmentation efficiency (3.6% av.). However, given the increase in amino acid sequence coverage and extended PTM characterization the new regime of EDD in combination with other ion-electron fragmentation techniques in the positive-ion mode is a step towards a more comprehensive strategy of analysis in proteome research.     

Structure-based dissection of the natural product cyclopentapeptide chitinase inhibitor argifin

Chitinase inhibitors have chemotherapeutic potential as fungicides, pesticides, and antiasthmatics. Argifin, a natural product cyclopentapeptide, competitively inhibits family 18 chitinases in the nanomolar to micromolar range and shows extensive substrate mimicry. In an attempt to map the active fragments of this large natural product, the cyclopentapeptide was progressively dissected down to four linear peptides and dimethylguanylurea, synthesized using a combination of solution and solid phase peptide synthesis. The peptide fragments inhibit chitinase B1 from Aspergillus fumigatus (AfChiB1), the human chitotriosidase, and chitinase activity in lung homogenates from a murine model of chronic asthma, with potencies ranging from high nanomolar to high micromolar inhibition. X-ray crystallographic analysis of the chitinase-inhibitor complexes revealed that the conformations of the linear peptides were remarkably similar to that of the natural product. Strikingly, the dimethylguanylurea fragment, representing only a quarter of the natural product mass, was found to harbor all significant interactions with the protein and binds with unusually high efficiency. The data provide useful information that could lead to the generation of drug-like, natural product-based chitinase inhibitors.     

Amine functionalised metal organic frameworks (MOFs) as adsorbents for carbon dioxide

Three different porous metal organic framework (MOF) materials have been prepared with and without uncoordinated amine functionalities inside the pores. The materials have been characterized and tested as adsorbents for carbon dioxide. At 298 K the materials adsorb significant amount of carbon dioxide, the amine functionalised adsorbents having the highest CO₂ adsorption capacities, the best adsorbing around 14 wt% CO₂ at 1.0 atm CO₂ pressure. At 25 atm CO₂ pressure, up to 60 wt% CO₂ can be adsorbed. At high pressures the CO₂ uptake is mostly dependent on the available surface area and pore volume of the material in question. For one of the iso-structural MOF pairs the introduction of amine functionality increases the differential adsorption enthalpy (from isosteric method) from 30 to around 50 kJ/mole at low CO₂ pressures, while the adsorption enthalpies reach the same level at increase pressures. The high pressure experimental results indicate that MOF based solid adsorbents can have a potential for use in pressure swing adsorption of carbon dioxide at elevated pressures.     

Yoctomole analysis of ganglioside metabolism in PC12 cellular homogenates

We report an ultrasensitive method for the analysis of glycosphingolipid catabolism. The substrate G(M1) and the set of seven metabolites into which it can be degraded (G(A1), G(M2), G(A2), G(M3), LacCer, GlcCer, and Cer) were labeled with the highly fluorescent dye tetramethylrhodamine. CE with LIF detection was used to assay these compounds with 150 +/- 80 yoctomole mass (1 ymol = 10(-24) mol = 0.6 copies) detection limits and 5 +/- 3 pM concentration detection limits. An alignment algorithm based on migration of two components was employed to correct for drift in the separation. The within-day and between-day precision in peak height was 20%, in peak width 15%, and in adjusted migration time 0.03%. After normalization to total sample injected, the RSD in peak height reduced to 2-6%, which approaches the limit set by molecular shot noise in the number of molecules taken for analysis. PC12 cells were incubated with the labeled G(M1). Fluorescent microscopy demonstrated uptake by the cells. CE was used to separate a cellular homogenate prepared from these cells. A set of peaks was observed, which were tentatively identified based on comigration with the standards. Roughly 120 pL of homogenate was injected, which contained a total of 150 zmol of labeled substrate and products. Metabolite that preserves the fluorescent label can be detected at the yoctomole level, which should allow characterization of this metabolic pathway in single cells.     

Suppressing one‐bond homonuclear 13C,13C scalar couplings in the J‐HMBC NMR experiment: application to 13C site‐specifically labeled oligosaccharides

Site‐specific ¹³C isotope labeling is a useful approach that allows for the measurement of homonuclear ¹³C,¹³C coupling constants. For three site‐specifically labeled oligosaccharides, it is demonstrated that using the J‐HMBC experiment for measuring heteronuclear long‐range coupling constants is problematical for the carbons adjacent to the spin label. By incorporating either a selective inversion pulse or a constant‐time element in the pulse sequence, the interference from one‐bond ¹³C,¹³C scalar couplings is suppressed, allowing the coupling constants of interest to be measured without complications. Experimental spectra are compared with spectra of a nonlabeled compound as well as with simulated spectra. The work extends the use of the J‐HMBC experiments to site‐specifically labeled molecules, thereby increasing the number of coupling constants that can be obtained from a single preparation of a molecule. Copyright © 2014 John Wiley & Sons, Ltd.     

A new approach to asymmetric feedback in a segmented broad area diode laser

We present the demonstration of a non-critical setup for asymmetric feedback in a segmented broad area diode laser. We compare the dependence of the beam quality on the position of the dispersive element for standard spectral beam combining and our new non-critical setup. We find that our new approach is significantly less critical to the position of the dispersive element. It is shown that we can displace the dispersive element by at least 50% of the focal length of the collimating lens away from the Fourier plane without compromising performance. Furthermore, our approach provides the same high beam quality as is possible using off-axis spectral beam combining. This provides the possibility of achieving a high beam quality in a more compact setup than previously possible.