Beskrivelse
We have developed a graph grammar based formalism to model chemical transformations. Within our formalism molecules are treated as vertex and edge labeled graphs and reactions (between molecules) are handled as graph rewrite. This approach nicely captures the algebraic properties of real chemistry, where novel molecules can be produced during chemical reactions. Graph grammars, i.e. a set of reaction rules and starting molecules, are very compact representations of entire chemical space. These spaces can contain interesting chemical transformation patterns such as auto-catalytic sub-networks, or alternative routes to molecules of interest. Such sub-networks are usually hard to find due to the vastness of chemical spaces. The situation is especially bad in the origin of life realm, where several putative prebiotic chemistries, all combinatorial complex in nature, have been suggested. Efficient computational methods for constructing and exploring chemical spaces are therefore essential to explore alternative scenarios, or to shade light on potential chemical processes which could have resulted in the emergence of life. The tutorial will offer a mix between short background presentations and accompanying practical examples. To ensure that attendees have the right libraries and programs available, we will provide a working environment. The attendees will learn (i) how to translate chemical reactions to graph rewrite rules, (ii) various methods to explicitly construct chemical spaces (iii) query the chemical space for interesting sub-networks.| Periode | 3. sep. 2013 |
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| Begivenhedstitel | European Conference on Artificial Life |
| Begivenhedstype | Konference |
| Konferencenummer | 2013 |
| Placering | Taormina, ItalienVis på kort |