3 citations · 7 across the 16 of their papers we have counts for
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Saturation-Based Atom Provenance Tracing in Chemical Reaction Networks
Marcel Friedrichs, Daniel Merkle
Atom tracing is essential for understanding the fate of labeled atoms in biochemical reaction networks, yet existing computational methods either simplify label correlations or suf…
Continuous Petri Nets for Fast Yield Computation: Polynomial-Time and MILP Approaches
Addie Jordon, Juri Kolčák, Daniel Merkle
Petri nets provide accurate analogues to chemical reaction networks, with places representing individual molecules (the resources of the system) and transitions representing chemic…
A Sensitivity Analysis Methodology for Rule-Based Stochastic Chemical Systems
Erika M. Herrera Machado, Jakob L. Andersen, Rolf Fagerberg +1
In this study, we introduce a sensitivity analysis methodology for stochastic systems in chemistry, where dynamics are often governed by random processes. Our approach is based on…
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…
ChemReservoir -- An Open-Source Framework for Chemically-Inspired Reservoir Computing
Mehmet Aziz Yirik, Jakob Lykke Andersen, Rolf Fagerberg +1
Reservoir computing is a type of a recurrent neural network, mapping the inputs into higher dimensional space using fixed and nonlinear dynamical systems, called reservoirs. In the…
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…
Finding Pathways in Reaction Networks guided by Energy Barriers using Integer Linear Programming
Adittya Pal, Rolf Fagerberg, Jakob Lykke Andersen +2
Analyzing synthesis pathways for target molecules in a chemical reaction network annotated with information on the kinetics of individual reactions is an area of active study. This…