On the use of dense matrix techniques within sparse simplex

In this paper we discuss some instances where dense matrix techniques can be utilized within a sparse simplex linear programming solver. The main emphasis is on the use of the Schur complement matrix as a part of the basis matrix representation. This approach enables to represent the basis matrix as an easily invertible sparse matrix and one or more dense Schur complement matrices. We describe our variant of this method which uses updating of the QR factorization of the Schur complement matrix. We also discuss some implementation issues of the LP software package which is based on this approach.     

Phospholipid mesophases at solid interfaces: in-situ X-ray diffraction and spin-label studies

In this work, we report on recent investigations, both on the global and on the local molecular architecture of supported phospholipid model membranes. A brief theoretical introduction explains how global structural information on supramolecular lipid ensembles can be retrieved from surface X-ray diffraction measurements as well as how spin-label electron paramagnetic resonance spectroscopy (EPR) provides complementary information on the local environment of probe molecules. The combination of especially designed X-ray cells with the technique of small- and wide-angle X-ray surface scattering makes it possible to explore various fields of lipid research and its applications. Examples for different physico-chemical conditions are presented: (i) in situ chemistry under excess of water conditions demonstrating how solid-supported lipid films sense salinity, (ii) the 3D electron density reconstruction of a vesicle-fusion intermediate under controlled humidity, and (iii) complementary temperature and pressure effects on oriented phospholipid samples. Further, special attention has been given to the influence of different film preparation techniques with respect to quality and the defect structure manifestation. To resolve the proportions and local properties of defects in a hydrated lipid-deposited surface, spin-label EPR was applied. The results from 9.6 GHz EPR as well as from 1.2 GHz EPR suggest the alignment to be in the range between 30% and 80%. In addition, slow time-dependent EPR measurements point to nano-structural rearrangements due to water flow and reduction of alignment quality.     

Synthesis of 3‐thiocyanato‐1H,3H‐quinoline‐2,4‐diones

4‐Hydroxy‐1H‐quinolin‐2‐ones ( 1 ) react with thiocyanogen in acetic acid to the corresponding 3‐thiocyanato‐1H,3H‐quinoline‐2,4‐diones ( 2 ) in good yields. In some cases, 3‐bromo‐1H,3H‐quinoline‐2,4‐diones ( 4 ) were isolated as minor reaction products. Compounds 2 are very reactive towards nucleophiles and easily hydrolyze to the corresponding 4‐hydroxy‐1H‐quinoline‐2‐ones ( 1 ).     

Exploring the local conformational space of a membrane protein by site-directed spin labeling

Molecular modeling based on a hybrid evolutionary optimization and an information condensation algorithm, called GHOST, of spin label ESR spectra was applied to study the structure and dynamics of membrane proteins. The new method is capable of providing detailed molecular information about the conformational space of the spin-labeled segment of the protein in a membrane system. The method is applied to spin-labeled bacteriophage M13 major coat protein, which is used as a model membrane protein. Single cysteine mutants of the coat protein were labeled with nitroxide spin labels and incorporated in 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) bilayers. The new computational method allows us to monitor distributions of local spatial constraints and molecular mobility, in addition to information about the location of the protein in a membrane. Furthermore, the results suggest that different local conformations may coexist in the membrane protein. The knowledge of different local conformations may help us to better understand the function-structure relationship of membrane proteins.     

Analysis of the Thermal Stability of Very Thin Surface Layers of Corrosion Inhibitors by Time-of-Flight Secondary Ion Mass Spectrometry

The powerful nature of the secondary ion mass spectrometry (SIMS) technique was explored in order to analyse very thin surface layers that were self-assembled on steel material from acidic solution. These surface layers are adsorbed corrosion inhibitors. The SIMS technique proved useful to characterise the molecular structure and homogeneity of thin surface layers in the nanometre range of specific analytes on the metallic substrate. Using SIMS, the thermal stability of these layers was further investigated and the desorption energy at a certain temperature was determined, where special attention was devoted to the method’s static limit. In order to compare, and for certain cases emphasise, the benefits gained by using SIMS in such surface analysis compared with the X-ray photoelectron spectroscopy (XPS) method, the same samples were also analysed by means of the latter. XPS is usually considered to be the most powerful analytical tool in surface analysis studies, but, as shown herein, it has certain limitations compared to SIMS. Finally, the surface topography was investigated by employing atomic force microscopy (AFM) in order to carry out a comprehensive surface analysis.

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Application of X-ray fluorescence analytical techniques in phytoremediation and plant biology studies

Phytoremediation is an emerging technology that employs the use of higher plants for the clean-up of contaminated environments. Progress in the field is however handicapped by limited knowledge of the biological processes involved in plant metal uptake, translocation, tolerance and plant–microbe–soil interactions; therefore a better understanding of the basic biological mechanisms involved in plant/microbe/soil/contaminant interactions would allow further optimization of phytoremediation technologies. In view of the needs of global environmental protection, it is important that in phytoremediation and plant biology studies the analytical procedures for elemental determination in plant tissues and soil should be fast and cheap, with simple sample preparation, and of adequate accuracy and reproducibility. The aim of this study was therefore to present the main characteristics, sample preparation protocols and applications of X-ray fluorescence-based analytical techniques (energy dispersive X-ray fluorescence spectrometry—EDXRF, total reflection X-ray fluorescence spectrometry—TXRF and micro-proton induced X-ray emission—micro-PIXE). Element concentrations in plant leaves from metal polluted and non-polluted sites, as well as standard reference materials, were analyzed by the mentioned techniques, and additionally by instrumental neutron activation analysis (INAA) and atomic absorption spectrometry (AAS). The results were compared and critically evaluated in order to assess the performance and capability of X-ray fluorescence-based techniques in phytoremediation and plant biology studies. It is the EDXRF, which is recommended as suitable to be used in the analyses of a large number of samples, because it is multi-elemental, requires only simple preparation of sample material, and it is analytically comparable to the most frequently used instrumental chemical techniques. The TXRF is compatible to FAAS in sample preparation, but relative to AAS it is fast, sensitive and multi-elemental. The micro-PIXE technique requires rather expensive instrumentation, but offers multi-elemental analysis on the tissue and cellular level.     

In situ Fourier transform infrared spectroscopy as an efficient tool for determination of reaction kinetics

The performance of new FTIR-based monitoring technology to representatively determine reaction kinetics has been demonstrated on an example of homogeneously catalyzed liquid-phase sucrose hydrolysis to fructose and glucose. The reaction kinetics were investigated by using the ReactIR 1000 reaction analysis system, which enables determination of the component concentration from its characteristic FTIR spectrum. During the sucrose inversion, the ReactIR 1000 instrument connected to a computer controlled standard glass batch reactor provided the required operating conditions and information about the component concentration in real-time. We have studied the influence of hydrogen ion concentration, temperature and initial concentration of sucrose on the sucrose disappearance rate. It was found out that the inversion of sucrose is an irreversible reaction, which is not affected by the formation of fructose and glucose in the liquid-phase. Then, the parameters of the kinetic model (i.e., reaction rate constant and activation energy) were calculated. A comparison of the model output and the measured data showed that the kinetics of the sucrose inversion could be well described by means of the pseudo first-order kinetic model. Finally, the method of determining the kinetic model by FTIR spectroscopy was verified by comparing the results obtained in the batch reactor with the results obtained in the continuously stirred tank reactor.     

endo/exo isomerism in norcarane and 2-norcaranol hydrotrioxides (ROOOH)

Ozonation of norcarane (1) yielded endo and exo norcarane hydrotrioxides (2a, 2b), as characterized by (1)H and (13)C NMR spectroscopy. Further ozonation of the primary decomposition products of these hydrotrioxides, i.e., 2-norcaranols (3), produced the corresponding isomeric 2-norcaranol hydrotrioxides (4a, 4b), and hydrogen trioxide (HOOOH).     

Synthesis of alkyl‐modified poly(sodium glutamate)s for preparation of polymer‐protein nanoparticles in combination with N,N,N‐trimethyl chitosan

The negatively charged, water‐soluble, hydrophobically modified poly(sodium glutamate)s containing different amounts of alkyl grafts were synthesized. First, poly(γ‐benzyl‐L‐glutamate) was prepared by ring‐opening polymerization of the corresponding N‐carboxyanhydride, which was in the next step aminolysed with octylamine. After removal of the remaining benzyl protective groups, the alkyl‐modified poly(sodium glutamate)s [P(Glu‐oa)] were obtained and, together with the oppositely charged N,N,N‐trimethyl chitosan (TMC), used for the preparation of nanoparticles (NPs) of a recombinant granulocyte colony‐stimulating factor (GCSF) protein by polyelectrolyte complexation method. It is observed that, beside electrostatic interaction, the hydrophobic grafts on poly(sodium glutamate)s significantly contribute to association efficiency (AE) with GCSF protein. The addition of TMC solution to the dispersion of GCSF/P(Glu‐oa) complexes results in formation of much more defined NPs with high AE and final protein loading. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2014 , 52, 2976–2985     

Studies towards the Synthesis of Alkyl N‐(4‐Nitrophenyl)‐3/2‐oxomorpholine‐2/3‐carboxylates

The syntheses of methyl 4‐(4‐nitrophenyl)‐3‐oxomorpholine‐2‐carboxylate ( 3a ) and ethyl 4‐(4‐nitrophenyl)‐2‐oxomorpholine‐3‐carboxylate ( 5b ), important building blocks for the synthesis of factor Xa inhibitor rivaroxaban analogs with potential dual antithrombotic activity, via Rh₂(OAc)₄‐catalyzed O? H and N? H carbene insertion reactions are described.