Bounds for the Perron root, singularity/nonsingularity conditions, and eigenvalue inclusion sets

Using a unified approach based on the monotonicity property of the Perron root and its circuit extension, a series of exact two-sided bounds for the Perron root of a nonnegative matrix in terms of paths in the associated directed graph is obtained. A method for deriving the so-called mixed upper bounds is suggested. Based on the upper bounds for the Perron root, new diagonal dominance type conditions for matrices are introduced. The singularity/nonsingularity problem for matrices satisfying such conditions is analyzed, and the associated eigenvalue inclusion sets are presented. In particular, a bridge connecting Gerschgorin disks with Brualdi eigenvalue inclusion sets is found. Extensions to matrices partitioned into blocks are proposed.     

Michael reaction. IV. NaNH2 catalyzed one stage reaction between phenylacetic acid dialkylamides and cinnamic acid methyl ester or dialkylamides. Influence of reaction conditions on the stereochemistry

The NaNH₂ catalyzed one stage reaction between phenylacetic acid dialkylamides and cinnamic acid methyl ester or dialkylamides was studied under various conditions. Conditions were found for easy preparation of each of the both possible diastereomeric derivatives of 2,3-diphenylglutaric acid. It was proved that catalytic amounts of NaNH₂ take part in the reaction. It is assumed that the observederythro/threo equilibrium ratios are determined by an isomerization via two different carbanions (at C₂ and C₄) of the reaction products.Part III:J. Stefanovsky andL. Viteva, Comun. Dept. Chem. Bulg. Acad. Sci.4, 159 (1971).     

Free Ca<Superscript>2+</Superscript> as an early intracellular biomarker of exposure of cyanobacteria to environmental pollution

Calcium functions as a versatile messenger in a wide variety of eukaryotic and prokaryotic cells. Cyanobacteria are photoautotrophs which have a great ecological impact as primary producers. Our research group has presented solid evidence of a role of calcium in the perception of environmental changes by cyanobacteria and their acclimation to these changes. We constructed a recombinant strain of the freshwater cyanobacterium Anabaena sp. PCC 7120 that constitutively expresses the calcium-binding photoprotein apoaequorin, enabling in-vivo monitoring of any fluctuation in the intracellular free calcium concentration of the cyanobacterium in response to any environmental stimulus. The “Ca²⁺ signature” is the combination of changes in all Ca²⁺ signal properties (magnitude, duration, frequency, source of the signal) produced by a specific stimulus. We recorded and analyzed the Ca²⁺ signatures generated by exposure of the cyanobacterium to different groups of environmental pollutants, for example cations, anions, organic solvents, naphthalene, and pharmaceuticals. We found that, in general, each group of tested chemicals triggered a specific calcium signature in a reproducible and dose-dependent manner. We hypothesize that these Ca²⁺ signals may be related to the cellular mechanisms of pollutant perception and ultimately to their toxic mode of action. We recorded Ca²⁺ signals triggered by binary mixtures of pollutants and a signal induced by a real wastewater sample which could be mimicked by mixing its main constituents. Because Ca²⁺ signatures were induced before toxicity was evident, we propose that intracellular free Ca²⁺ may serve as an early biomarker of exposure to environmental pollution.     

Accurate distance determination of nucleic acids via Förster resonance energy transfer: implications of dye linker length and rigidity

In Fo?rster resonance energy transfer (FRET) experiments, the donor (D) and acceptor (A) fluorophores are usually attached to the macromolecule of interest via long flexible linkers of up to 15 ? in length. This causes significant uncertainties in quantitative distance measurements and prevents experiments with short distances between the attachment points of the dyes due to possible dye-dye interactions. We present two approaches to overcome the above problems as demonstrated by FRET measurements for a series of dsDNA and dsRNA internally labeled with Alexa488 and Cy5 as D and A dye, respectively. First, we characterize the influence of linker length and flexibility on FRET for different dye linker types (long, intermediate, short) by analyzing fluorescence lifetime and anisotropy decays. For long linkers, we describe a straightforward procedure that allows for very high accuracy of FRET-based structure determination through proper consideration of the position distribution of the dye and of linker dynamics. The position distribution can be quickly calculated with geometric accessible volume (AV) simulations, provided that the local structure of RNA or DNA in the proximity of the dye is known and that the dye diffuses freely in the sterically allowed space. The AV approach provides results similar to molecular dynamics simulations (MD) and is fully consistent with experimental FRET data. In a benchmark study for ds A-RNA, an rmsd value of 1.3 ? is achieved. Considering the case of undefined dye environments or very short DA distances, we introduce short linkers with a propargyl or alkenyl unit for internal labeling of nucleic acids to minimize position uncertainties. Studies by ensemble time correlated single photon counting and single-molecule detection show that the nature of the linker strongly affects the radius of the dye's accessible volume (6-16 ?). For short propargyl linkers, heterogeneous dye environments are observed on the millisecond time scale. A detailed analysis of possible orientation effects (κ(2) problem) indicates that, for short linkers and unknown local environments, additional κ(2)-related uncertainties are clearly outweighed by better defined dye positions.     

Synthesis and photochemistry of a new class of photocleavable protein cross-linking reagents

A new series of photocleavable protein cross-linking reagents based on bis(maleimide) derivatives of diaryl disulfides have been synthesised. They have been functionalised with cysteine and transient absorption spectra for the photolysis reaction have been recorded by using the pump-probe technique with a time resolution of 100 femtoseconds. Photolysis of the disulfide bond yields the corresponding thiyl radicals in less than a picosecond. There is a significant amount of geminate recombination, but some of the radicals escape the solvent cage and the quantum yield for photocleavage is 30 % in water.     

Purification and structure elucidation of three naturally bioactive molecules from the new terrestrial Streptomyces sp. TN17 strain

Thirty litres of fermentation broth was extracted from the newly isolated Streptomyces sp. strain TN17 and various separation and purification steps led to the isolation of three pure bioactive compounds (1-3). Compound 1: cyclo (L-Leu-L-Arg), a diketopiperazine 'DKP' derivative; 2: di-(2-ethylhexyl) phthalate, a phthalate derivative; and 3: cyclo 1-[2-(cyclopentanecarbonyl-3-phenyl-propionyl]-pyrrolidine-2-carboxylic acid (1-carbamoyl-propyl)-amide, a cyclic tetrapeptide derivative. The chemical structure of these three active compounds was established on the basis of spectroscopic studies (MS and NMR) and by comparison with data from the literature. According to our biological studies, the pure compounds (1-3) possess antibacterial and antifungal activities.     

Two ZnII mononuclear coordination compounds with pyridinedicarboxylate and auxiliary N‐(pyridin‐4‐ylmethylidene)hydroxylamine ligands

Two new mononuclear coordination compounds, bis{4‐[(hydroxyimino)methyl]pyridinium} diaquabis(pyridine‐2,5‐dicarboxylato‐κ²N,O²)zincate(II), (C₆H₇N₂O)₂[Zn(C₇H₃NO₄)₂(H₂O)₂], (1), and (pyridine‐2,6‐dicarboxylato‐κ³O²,N,O⁶)bis[N‐(pyridin‐4‐ylmethylidene‐κN)hydroxylamine]zinc(II), [Zn(C₇H₃NO₄)(C₆H₆N₂O)₂], (2), have been synthesized and characterized by single‐crystal X‐ray diffractometry. The centrosymmetric Zn^II cation in (1) is octahedrally coordinated by two chelating pyridine‐2,5‐dicarboxylate ligands and by two water molecules in a distorted octahedral geometry. In (2), the Zn^II cation is coordinated by a tridentate pyridine‐2,6‐dicarboxylate dianion and by two N‐(pyridin‐4‐ylmethylidene)hydroxylamine molecules in a distorted C₂‐symmetric trigonal bipyramidal coordination geometry.     

The solvent effect in obtaining of acid–base multicomponent systems: thermal,structural and luminescence study

Journal of Thermal Analysis and Calorimetry - Acid–base multicomponent systems based on active pharmaceutical ingredients 2-chloro-5-nitrobenzoic acid (2Cl5NBH) and monoethanolamine were...     

Discontinuous Galerkin methods on graphics processing units for nonlinear hyperbolic conservation laws

We present a novel implementation of the modal DG method for hyperbolic conservation laws in two dimensions on graphics processing units (GPUs) using NVIDIA's Compute Unified Device Architecture. Both flexible and highly accurate, DG methods accommodate parallel architectures well as their discontinuous nature produces element‐local approximations. High‐performance scientific computing suits GPUs well, as these powerful, massively parallel, cost‐effective devices have recently included support for double‐precision floating‐point numbers. Computed examples for Euler equations over unstructured triangle meshes demonstrate the effectiveness of our implementation on an NVIDIA GTX 580 device. Profiling of our method reveals performance comparable with an existing nodal DG‐GPU implementation for linear problems. Copyright © 2014 John Wiley & Sons, Ltd.