Jakob L. Andersen

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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)
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)
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)
Graph rewriting has been applied quite successfully to model chemical and biological systems at different levels of abstraction. A particularly powerful feature of rule-based models that are rigorously grounded in category theory, is, that they admit a well-defined notion of rule composition, hence, provide their users with an intrinsic mechanism for(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)
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 acids, and lipids to " molecular food sources " that have likely been abundant on Early Earth. In a recent contribution, Albert Eschenmoser emphasised the importance of catalytic and(More)
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