Semi-algebraic methods for symbolic analysis of complex reaction networks

The identification of chemical mechanism that can exhibit oscillatory phenomena in reaction networks are currently of intense interest. In particular, the parametric question of the existence of Hopf bifurcations has gained increasing popularity due to its relation to the oscillatory behavior around the fixed points. However, the detection of oscillations in high-dimensional systems and systems with constraints by the available symbolic methods has proven to be difficult. The development of new efficient methods are therefore required to tackle the complexity caused by the high-dimensionality and non-linearity of these systems. In this thesis, we mainly present efficient algorithmic methods to detect Hopf bifurcation fixed points in (bio)-chemical reaction networks with symbolic rate constants, thereby yielding information about their oscillatory behavior of the networks. The methods use the representations of the systems on convex coordinates that arise from stoichiometric network analysis. One of the methods called HoCoQ reduces the problem of determining the existence of Hopf bifurcation fixed points to a first-order formula over the ordered field of the reals that can then be solved using computational-logic packages. The second method called HoCaT uses ideas from tropical geometry to formulate a more efficient method that is incomplete in theory but worked very well for the attempted high-dimensional models involving more than 20 chemical species. The instability of reaction networks may lead to the oscillatory behaviour. Therefore, we investigate some criterions for their stability using convex coordinates and quantifier elimination techniques. We also study Muldowney's extension of the classical Bendixson-Dulac criterion for excluding periodic orbits to higher dimensions for polynomial vector fields and we discuss the use of simple conservation constraints and the use of parametric constraints for describing simple convex polytopes on which periodic orbits can be excluded by Muldowney's criteria. All developed algorithms have been integrated into a common software framework called PoCaB (platform to explore bio- chemical reaction networks by algebraic methods) allowing for automated computation workflows from the problem descriptions. PoCaB also contains a database for the algebraic entities computed from the models of chemical reaction networks.

The continuation of the periodic table up to Z = 172.

The chemical elements up to Z = 172 are calculated with a relativistic Hartree-Fock-Slater program taking into account the effect of the extended nucleus. Predictions of the binding energies, the X-ray spectra and the number of electrons inside the nuclei are given for the inner electron shells. The predicted chemical behaviour will be discussed for a11 elements between Z = 104-120 and compared with previous known extrapolations. For the elements Z = 121-172 predictions of their chemistry and a proposal for the continuation of the Periodic Table are given. The eighth chemical period ends with Z = 164 located below Mercury. The ninth period starts with an alkaline and alkaline earth metal and ends immediately similarly to the second and third period with a noble gas at Z = 172. Mit einem relativistischen Hartree-Fock-Slater Rechenprogramm werden die chemischen Elemente bis zur Ordnungszahl 172 berechnet, wobei der Einfluß des ausgedehnten Kernes berücksichtigt wurde. Für die innersten Elektronenschalen werden Voraussagen über deren Bindungsenergie, das Röntgenspektrum und die Zahl der Elektronen im Kern gemacht. Die voraussichtliche Chemie der Elemente zwischen Z = 104 und 120 wird diskutiert und mit bereits vorhandenen Extrapolationen verglichen. Für die Elemente Z = 121-172 wird eine Voraussage über das chemische Verhalten gegeben, sowie ein Vorschlag für die Fortsetzung des Periodensystems gemacht. Die achte chemische Periode endet mit dem Element 164 im Periodensystem unter Quecksilber gelegen. Die neunte Periode beginnt mit einem Alkali- und Erdalkalimetall und endet sofort wieder wie in der zweiten und dritten Periode mit einem Edelgas bei Z = 172.