10 citations · 14 across the 6 of their papers we have counts for
11 papers
Cayley Graphs of Semigroups Applied to Atom Tracking in Chemistry
Nikolai Nøjgaard, Walter Fontana, Marc Hellmuth +1
While atom tracking with isotope-labeled compounds is an essential and sophisticated wet-lab tool in order to, e.g., illuminate reaction mechanisms, there exists only a limited amo…
Defining Autocatalysis in Chemical Reaction Networks
Jakob L. Andersen, Christoph Flamm, Daniel Merkle +1
Autocatalysis is a deceptively simple concept, referring to the situation that a chemical species catalyzes its own formation. From the perspective of chemical kinetics, autoca…
Graph Transformation for Enzymatic Mechanisms
Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm +5
Motivation: The design of enzymes is as challenging as it is consequential for making chemical synthesis in medical and industrial applications more efficient, cost-effective and e…
A Graph-Based Tool to Embed the π-Calculus into a Computational DPO Framework
Jakob Lykke Andersen, Marc Hellmuth, Daniel Merkle +2
Graph transformation approaches have been successfully used to analyse and design chemical and biological systems. Here we build on top of a DPO framework, in which molecules are m…
Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows
Jakob L. Andersen, Christoph Flamm, Daniel Merkle +1
We present an elaborate framework for formally modelling pathways in chemical reaction networks on a mechanistic level. Networks are modelled mathematically as directed multi-hyper…
A Generic Framework for Engineering Graph Canonization Algorithms
Jakob L. Andersen, Daniel Merkle
The state-of-the-art tools for practical graph canonization are all based on the individualization-refinement paradigm, and their difference is primarily in the choice of heuristic…