Publications - Published papers

Please find below publications of our group. Currently, we list 564 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (access) is restricted to our local network and chosen collaborators. If you have problems accessing electronic information, please let us know:

©NOTICE: All papers are copyrighted by the authors; If you would like to use all or a portion of any paper, please contact the author.

Rule Composition in Graph Transformation Models of Chemical Reactions

Andersen, Jakob Lykke and Flamm, Christoph and Merkle, Daniel and Stadler, Peter F.


PREPRINT 18-076:
[ Publishers's page ]  paperID

Status: Published

MATCH Commun. Math. Comput. Chem. 80: 661-704


Graph transformation form a natural model for chemical reaction systems and provide a su cient level of detail to track individual atoms. Among alternative graph transformation formalisms the Double Pushout approach, which is firmly grounded in category theory, is particularly well-suited as a model of chemistry. We explore here the formal foundations of defining composition of transformation rules using ideas from concurrency theory. In addition of a generic construction we consider several special cases that each have an intuitive chemical interpretation. We illustrate the usefulness of these specialised operations by automatically calculating coarse-grained transformation rules for complete chemical pathways, that preserve the traces of atoms through the pathways. This type of computation has direct practical relevance for the analysis and design of isotope labelling experiments.