Reaction graphs and a construction of reaction networks

Summary A general definition of reaction graphs is presented. For a pair of isomeric molecular graphs and , related by a chemical transformation , the reaction graph is determined using a maximal common subgraph defined for vertex mapping . A binary operation defined for graphs constructed over the same vertex set enables us to decompose the reaction graph into the sum of prototype reaction graphs. A decomposition of an overall reaction graph can be advantageously used for the construction of a reaction network. An oriented path in this network beginning at and ending at corresponds to a breakdown of the transformation into a sequence of intermediates.     

The search for a new model structure of β-Factor XIIa

We present the search for a new model of -factor XIIa, a blood coagulation enzyme, with an unknown experimental 3D-structure. We decided to build not one but three different models using different homologous proteins as well as different techniques and different modellers. Additional studies, including extensive molecular dynamics simulations on the solvated state, allowed us to draw several conclusions concerning homology modelling, in general, and -factor XIIa, in particular.     

Theoretical study of the mechanisms of substrate recognition by catalase

A variety of theoretical methods including classical molecular interaction potentials, classical molecular dynamics, and activated molecular dynamics have been used to analyze the substrate recognition mechanisms of peroxisomal catalase from Saccharomyces cerevisiae. Special attention is paid to the existence of channels connecting the heme group with the exterior of the protein. On the basis of these calculations a rationale is given for the unique catalytic properties of this enzyme, as well as for the change in enzyme efficiency related to key mutations. According to our calculations the water is expected to be a competitive inhibitor of the enzyme, blocking the access of hydrogen peroxide to the active site. The main channel is the preferred route for substrate access to the enzyme and shows a cooperative binding to hydrogen peroxide. However, the overall affinity of the main channel for H(2)O(2) is only slightly larger than that for H(2)O. Alternative channels connecting the heme group with the monomer interface and the NADP(H) binding site are detected. These secondary channels might be important for product release.     

Introducing a Cell-Free Approach for the Identification of Brewing Yeast (<Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis>) Strains Using MALDI-TOF MS

Matrix-assisted laser desorption ionization (MALDI) time-of-flight mass spectrometry (TOF MS) is now accepted as a quick, easy-to-use, cost-effective, and accurate technique for the identification of microorganisms. However, the successful identification of microorganisms is dependent upon careful attention to factors such as growth conditions, extraction methods, mass spectral data collection, and data analysis procedures. Currently, most microorganism identification has been limited to the species level, and only a limited number of publications have been successful in achieving strain-level identification. In this work, a “cell-free” approach is introduced where peptide analytes secreted by several Saccharomyces cerevisiae strains during their growth period are analyzed. The analysis of the cell supernatant generates mass spectral patterns that are specific to each strain. The patterns generated in combination with a robust data analysis workflow using the open-source programs MALDIquant and Mass-Up allows for strain-level identification of S. cerevisiae. The cell-free approach using the yeast supernatant to accurately identify yeast strains is presented here as a proof of concept.

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Graphical Abstract

     

Combination of flow injection analysis and voltammetry

The flow injection analyzer for students, teaching and research (FIAstar) is used in conjunction with a new micropool mercury flow-through electrode, to explore the possibilities offered by using d.c. polarography, rapid scan and amperometric titrations on a dispersed sample zone in motion. The work outlines the principles of the use of a scanning detector for investigation of the concentration gradients and chemical reactions taking place during the dispersion of sample solution within a carrier stream. The data, which are collected in real time, are displayed in three-dimensional diagrams.     

Strukturelle Charakterisierung der Dicyanamid-Komplexe von Kupfer(II), Nickel(II) bzw. Kobalt(II) mit Aminopyridinen

Summary New dicyanamide complexes of the typeM[N(CN)₂]₂ L ₂ (M=Cu or Ni;L=2-, 3-, 4-aminopyridine, 2-amino-5-nitropyridine) and Co[N(CN)₂]₂ (2-amino-5-nitropyridine)₂ were prepared and studied by spectroscopic methods as well as by room-temperature magnetic moments. The results show that the Cu(II) complexes have elongated pseudooctahedral structures while the Ni(II) and Co(II) complexes are octahedral. In most cases the N(CN)₂ groups are in bridging function and through their cyanide nitrogens, or-more rarely-amide and cyanide nitrogens connect the basic structure units into polymeric conglomerates. In the Cu(II) systems exchange coupling is seen from the _eff value or ESR spectrum.

Professor Viktor Gutmann zum 70. Geburtstag gewidmet     

Sampling Eulerian orientations of triangular lattice graphs

We consider the problem of sampling from the uniform distribution on the set of Eulerian orientations of subgraphs of the triangular lattice. Although Mihail and Winkler (1989) showed that this can be achieved in polynomial time for any graph, the algorithm studied here is more natural in the context of planar Eulerian graphs. We analyse the mixing time of a Markov chain on the Eulerian orientations of a planar graph which moves between orientations by reversing the edges of directed faces. Using path coupling and the comparison method we obtain a polynomial upper bound on the mixing time of this chain for any solid subgraph of the triangular lattice. By considering the conductance of the chain we show that there exist non-solid subgraphs (subgraphs with holes) for which the chain will always take an exponential amount of time to converge. Finally, we show that the problem of counting Eulerian orientations remains #P-complete when restricted to planar graphs (Mihail and Winkler had already established this for general graphs).     

A comment on the jäger-kačur linearization scheme for strongly nonlinear parabolic equations

The aim of this paper is to demonstrate how the variational equations from [11] can be formulated and solved in some abstract Banach spaces without any a priori construction of special linearization schemes. This should be useful e.g. in the analysis of heat conduction problems and modelling of flows in porous media.