14 citations · 15 across the 7 of their papers we have counts for
7 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…
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…
Every atom-atom map can be explained by electron pushing diagrams
Christoph Flamm, Stefan Müller, Peter F. Stadler
Chemical reactions can be understood as transformations of multigraphs (molecules) that preserve vertex labels (atoms) and degrees (sums of bonding and non-bonding electrons), ther…
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…
Funnels in Energy Landscapes
Konstantin Klemm, Christoph Flamm, Peter F. Stadler
Local minima and the saddle points separating them in the energy landscape are known to dominate the dynamics of biopolymer folding. Here we introduce a notion of a "folding funnel…