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 ).     

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.     

Synthesis and Biochemical Evaluation of Warhead-Decorated Psoralens as (Immuno)Proteasome Inhibitors

The immunoproteasome is a multicatalytic protease that is predominantly expressed in cells of hematopoietic origin. Its elevated expression has been associated with autoimmune diseases, various types of cancer, and inflammatory diseases. Selective inhibition of its catalytic activities is therefore a viable approach for the treatment of these diseases. However, the development of immunoproteasome-selective inhibitors with non-peptidic scaffolds remains a challenging task. We previously reported 7H-furo[3,2-g]chromen-7-one (psoralen)-based compounds with an oxathiazolone warhead as selective inhibitors of the chymotrypsin-like (β5i) subunit of immunoproteasome. Here, we describe the influence of the electrophilic warhead variations at position 3 of the psoralen core on the inhibitory potencies. Despite mapping the chemical space with different warheads, all compounds showed decreased inhibition of the β5i subunit of immunoproteasome in comparison to the parent oxathiazolone-based compound. Although suboptimal, these results provide crucial information about structure–activity relationships that will serve as guidance for the further design of (immuno)proteasome inhibitors.     

Combining [Arene–Ru] with Azocarboxamide to Generate a Complex with Cytotoxic Properties

Azocarboxamide (azcH) has been combined for the first time with [Ru–Cym] to generate metal complexes with N,N‐ and N,O‐coordination mode, [(Cym)Ru(azc)Cl] and [(Cym)Ru(azcH)Cl]⁺[PF₆]^?. Geometric and electronic structures of the complexes are reported along with their in vitro activities against different tumour cell lines and preliminary results on solution chemistry. Compound [(Cym)Ru(azc)Cl] exhibited remarkable cytotoxic properties. It was cell‐type specific and had comparable IC₅₀ values towards both cancer cells and their drug‐resistant subline. A tenfold increase in the sensitivity towards [(Cym)Ru(azc)Cl] was noted for the tumour cells with depleted intracellular glutathione (GSH) level, suggesting the essential role of GSH in cell response to this compound.     

Anisotropic Electrical,Magnetic, and Thermal Properties of In3Ni2 Intermetallic Catalyst

We present the anisotropic electrical and thermal transport coefficients (electrical resistivity, magnetoresistance, thermoelectric power, thermal conductivity), the magnetic properties, the specific heat and the electronic density of states of a monocrystalline In₃Ni₂ intermetallic compound, representing a precious-metal-free (and noble-metal-free) intermetallic catalyst for the selective hydrogenation of α,β-unsaturated aldehydes. The investigated physical parameters were determined along three orthogonal crystal-symmetry directions of the trigonal structure, the twofold axis, the 3 axis and within the mirror plane. All the investigated tensorial and vectorial quantities show the same anisotropy, with the quantities being isotropic for the twofold direction and in the mirror plane, whereas there is small, though still significant anisotropy to the 3 direction. The In₃Ni₂ crystal conducts the electricity and heat somewhat less efficiently along the 3 direction than along the twofold direction and in the mirror plane, but the differences are not large, of about 20 %. In₃Ni₂ is a diamagnetic intermetallic compound, with a presumably simple Fermi surface and electrons as the majority charge carriers.     

Approach to nonadiabatic transitions by density matrix evolution and molecular dynamics simulations

Many biological processes are characterized by an essentially quantum dynamical event, such as electron or proton transfer, in a complex classical environment. To treat such processes properly by computer simulation, allowing nonadiabatic transitions involving excited states, we recently developed a density matrix evolution (DME ) method [H. J. C. Berendsen and J. Mavri, J. Phys. Chem, 97 , 13464 (1993)] which simulates the dynamics of quantum systems embedded in a classical environment. The formalism of the method is presented and an overview of the applications ranging from collisions of a quantum harmonic oscillator with noble gas atoms to proton tunneling in a double-well hydrogen bond is given. The methodology for treatment of proton-transfer processes with inclusion of excited states is presented. Future application of the method on biologically interesting processes, such as proton transfer in enzymatic reactions, is discussed. © 1996 John Wiley & Sons, Inc.