Pathway Realisability in Chemical Networks
Fuente:
arXiv
Salvato in:
| Autori principali: | , , , , , |
|---|---|
| Natura: | Preprint |
| Pubblicazione: |
2023
|
| Soggetti: | |
| Accesso online: | |
| Tags: |
Aggiungi Tag
Nessun Tag, puoi essere il primo ad aggiungerne!!
|
| _version_ | 1866910754518597632 |
|---|---|
| author | Andersen, Jakob L. Banke, Sissel Fagerberg, Rolf Flamm, Christoph Merkle, Daniel Stadler, Peter F. |
| author_facet | Andersen, Jakob L. Banke, Sissel Fagerberg, Rolf Flamm, Christoph Merkle, Daniel Stadler, Peter F. |
| contents | The exploration of pathways and alternative pathways that have a specific function is of interest in numerous chemical contexts. A framework for specifying and searching for pathways has previously been developed, but a focus on which of the many pathway solutions are realisable, or can be made realisable, is missing. Realisable here means that there actually exists some sequencing of the reactions of the pathway that will execute the pathway. We present a method for analysing the realisability of pathways based on the reachability question in Petri nets. For realisable pathways, our method also provides a certificate encoding an order of the reactions which realises the pathway. We present two extended notions of realisability of pathways, one of which is related to the concept of network catalysts. We exemplify our findings on the pentose phosphate pathway. Furthermore, we discuss the relevance of our concepts for elucidating the choices often implicitly made when depicting pathways. Lastly, we lay the foundation for the mathematical theory of realisability. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2309_10629 |
| institution | arXiv |
| publishDate | 2023 |
| record_format | arxiv |
| spellingShingle | Pathway Realisability in Chemical Networks Andersen, Jakob L. Banke, Sissel Fagerberg, Rolf Flamm, Christoph Merkle, Daniel Stadler, Peter F. Molecular Networks Discrete Mathematics The exploration of pathways and alternative pathways that have a specific function is of interest in numerous chemical contexts. A framework for specifying and searching for pathways has previously been developed, but a focus on which of the many pathway solutions are realisable, or can be made realisable, is missing. Realisable here means that there actually exists some sequencing of the reactions of the pathway that will execute the pathway. We present a method for analysing the realisability of pathways based on the reachability question in Petri nets. For realisable pathways, our method also provides a certificate encoding an order of the reactions which realises the pathway. We present two extended notions of realisability of pathways, one of which is related to the concept of network catalysts. We exemplify our findings on the pentose phosphate pathway. Furthermore, we discuss the relevance of our concepts for elucidating the choices often implicitly made when depicting pathways. Lastly, we lay the foundation for the mathematical theory of realisability. |
| title | Pathway Realisability in Chemical Networks |
| topic | Molecular Networks Discrete Mathematics |
| url | https://arxiv.org/abs/2309.10629 |