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Background: A classical problem in metabolic design is to maximize the production of a desired compound in a given chemical reaction network by appropriately directing the mass flow through the network. Computationally, this problem is addressed as a linear optimization problem over the flux cone. The prior construction of the flux cone is computationally… (More)

- Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
- I. J. Computational Biology and Drug Design
- 2014

The chemical universe of molecules reachable from a set of start compounds by iterative application of a finite number of reactions is usually so vast, that sophisticated and efficient exploration strategies are required to cope with the combinatorial complexity. A stringent analysis of (bio)chemical reaction networks, as approximations of these complex… (More)

Modeling molecules as undirected graphs and chemical reactions as graph rewriting operations is a natural and convenient approach to modeling chemistry. Graph grammar rules are most naturally employed to model elementary reactions like merging, splitting, and isomerisation of molecules. It is often convenient, in particular in the analysis of larger… (More)

Polymers of hydrogen cyanide and their hydrolysis products constitute a plausible, but still poorly understood proposal for early prebiotic chemistry on Earth. HCN polymers are generated by the interplay of more than a dozen distinctive reaction mechanisms and form a highly complex mixture. Here we use a computational model based on graph grammars as a… (More)

Chemical reaction networks can be automatically generated from graph grammar descriptions, where rewrite rules model reaction patterns. Because a molecule graph is connected and reactions in general involve multiple molecules, the rewriting must be performed on multisets of graphs. We present a general software package for this type of graph rewriting… (More)

1 Department of Mathematics and Computer Science University of Southern Denmark, Denmark 2 Institute for Theoretical Chemistry University of Vienna, Austria 3 Department of Computer Science University of Leipzig, Germany 4 Max Planck Institute for Mathematics in the Sciences Leipzig, Germany 5 Fraunhofer Institute for Cell Therapy and Immunology Leipzig,… (More)

Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, since precise information on the molecular composition, the dominant reaction chemistry, ∗Email: daniel@imada.sdu.dk 1 ar X iv :1 70 1. 09 09 7v 1 [ qbi o. M N ] 3 1 Ja n 20 17 and the conditions for that era are scarce. The exploration… (More)

We model chemical reaction networks as directed hypergraphs that are generated in rule-based manner, using graph grammars as models of given sets of reaction mechanisms. Graphs serve as abstractions of molecules. This provide a level of chemical realism sufficient to ensure conservation of mass, atom type, and charge. Atom maps, for instance, are thus… (More)