26 citations · 47 across the 18 of their papers we have counts for
8 papers · 1 filter
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…
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…
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…
An Intermediate Level of Abstraction for Computational Systems Chemistry
Jakob L. Andersen, Christoph Flamm, Daniel Merkle +1
Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, since precise information on the molecular composition, t…
Support for Eschenmoser's Glyoxylate Scenario
Jakob L. Andersen, Christoph Flamm, Daniel Merkle +1
A core topic of research in prebiotic chemistry is the search for plausible synthetic routes that connect the building blocks of modern life such as sugars, nucleotides, amino acid…
Maximizing Output and Recognizing Autocatalysis in Chemical Reaction Networks is NP-Complete
Jakob L. Andersen, Christoph Flamm, Daniel Merkle +1
Background: A classical problem in metabolic design is to maximize the production of desired compound in a given chemical reaction network by appropriately directing the mass flow…