6 papers
On the realizability of abstract reaction networks with real molecules and reactions
Tuyet-Minh Phan, Daniel Merkle, Tieu-Long Phan +2
Abstract reaction networks appear not only as models of chemical reactions but also as models of complex systems, with applications in areas such as ecology and epidemiology, and a…
Rule-Based Gillespie Simulation of Chemical Systems
Erika M. Herrera Machado, Jakob L. Andersen, Rolf Fagerberg +3
The MØD computational framework implements rule-based generative chemistries as explicit transformations of graphs representing chemical structural formulae. Here, we expand MØD by…
Finding Thermodynamically Favorable Pathways in Chemical Reaction Networks Using Flows in Hypergraphs and Mixed-Integer Linear Programming
Adittya Pal, Rolf Fagerberg, Jakob Lykke Andersen +3
The search for pathways that optimize the formation of a particular target molecule in a reaction network is a key problem in many settings, including reactor systems. Chemical rea…
Assembly in Directed Hypergraphs
Christoph Flamm, Daniel Merkle, Peter F. Stadler
Assembly theory has received considerable attention in the recent past. Here we analyze the formal framework of this model and show that assembly pathways coincide with certain min…
Pathway Realisability in Chemical Networks
Jakob L. Andersen, Sissel Banke, Rolf Fagerberg +3
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 pathwa…
Automated Inference of Graph Transformation Rules
Jakob L. Andersen, Akbar Davoodi, Rolf Fagerberg +8
The explosion of data available in life sciences is fueling an increasing demand for expressive models and computational methods. Graph transformation is a model for dynamic system…