Generic Properties of Chemical Networks: Artificial Chemistry Based on Graph Rewriting

We use a Toy Model of chemistry that represents molecules in terms of usual structural formulae to generate large chemical reaction networks. An extremely simplified quantum mechanical energy calculation and a straightforward implementation of reactions as graph rewritings ensure both transparency and closeness to chemical reality, both conditions that are necessary for the analysis of generic properties of large reaction networks. We show that some chemical networks graphs, e.g., repetitive Diels-Alder reactions, have the small-world property and exhibit a scale-free degree distribution. On the other hand, the Formose reaction does not fit well to this paradigm

Multi-Phase Artificial Chemistry

Artificial chemistries can be used to explore the generic properties of chemical reaction networks. In order to simulate for instance scenarios of prebiotic evolution the model must be close enough to real chemistry to allow at least semi-quantitative comparisons. One example is a previously described Toy Model that represents molecules as graphs, thereby neglecting 3D space, and employs a highly simplified version of the Extended H¨uckel Theory (EHT) to compute molecular properties. Here we show how the Toy Model can be extended to multiple phases by connecting the EHT calculations with chemical thermodynamics

Explicit Collision Simulation of Chemical Reactions in a Graph Based Artificial Chemistry

A Toy Model of an artificial chemistry that treats molecules as graphs was implemented based on a simple Extended Hückel Theory method. Here we describe an extension of the model that models chemical reactions as the result of “collisions”. In order to avoid a possible bias arising from prescribed generic reaction mechanisms, the reactions are simulated in a way that treats the formation and breakage of individual chemical bonds as elementary operations

Graph Grammars as Models for the Evolution of Developmental Pathways

The large quantity and ready availability of developmental-genetic data, coupled with increased rigor and detail in the characterization of morphological phenotypes, has made the genotype-phenotype map of whole organisms a central challenge in evolutionary developmental biology. This in turn necessitates more general modeling strategies that can efficiently represent different types of biological knowledge and systematically applied across levels of organization, spatiotemporal scales, and taxonomic groups. Graph-based models appear useful in this context but have been remarkably underutilized in biology. Simulation of ontogenetic and evolutionary change by means of graphrewriting algorithms has been explored as a means of providing a coordinate-free approach to form transformation in time and space. A finite set of rules describing generic graph transformations is used to encode knowledge about morphogenetic steps. Their application to skeletal growth in sea urchins effectively models ontogenesis in terms of topology rather than specific geometry, suggesting a promising approach to general modeling of developmental evolution

Multi-Phase Artificial Chemistry

Artificial chemistries can be used to explore the generic properties of chemical reaction networks. In order to simulate for instance scenarios of prebiotic evolution the model must be close enough to real chemistry to allow at least semi-quantitative comparisons. One example is a previously described Toy Model that represents molecules as graphs, thereby neglecting 3D space, and employs a highly simplified version of the Extended H¨uckel Theory (EHT) to compute molecular properties. Here we show how the Toy Model can be extended to multiple phases by connecting the EHT calculations with chemical thermodynamics

Multi-Phase Artificial Chemistry

Artificial chemistries can be used to explore the generic properties of chemical reaction networks. In order to simulate for instance scenarios of prebiotic evolution the model must be close enough to real chemistry to allow at least semi-quantitative comparisons. One example is a previously described Toy Model that represents molecules as graphs, thereby neglecting 3D space, and employs a highly simplified version of the Extended H¨uckel Theory (EHT) to compute molecular properties. Here we show how the Toy Model can be extended to multiple phases by connecting the EHT calculations with chemical thermodynamics

A graph-based toy model of chemistry

Large scale chemical reaction networks are a ubiquitous phenomenon, from the metabolism of living cells to processes in planetary atmospheres and chemical technology. At least some of these networks exhibit distinctive global features such as the “small world ” behavior

Neues vollständiges Zwickauisches Gesangbuch Darinnen 1200. alte und neue geistliche Lieder enthalten sind, dem noch beygefüget ist ein Gebetbuch, Nebst einer Vorrede von Joh. Gottfried Weller

Layoutgetreues Digitalisat der Ausg.: Zwickau : Höfer, [1778]. - Standort: Universität Marburg, Bibliothek Evangelische Theologie [381] (Gesangbuchsammlung) Signatur: PTh Dp Zwi 1778 sekr. - Bemerkungen: In Fraktur. - Ebenfalls enthalten: Neu eingerichtetes Gebetbuch zur Haus- und Kirchenandacht. - Digitalisiert 201