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09/19/2023
On the Realisability of Chemical Pathways
The exploration of pathways and alternative pathways that have a specifi...
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01/12/2022
Representing catalytic mechanisms with rule composition
Reaction mechanisms are often presented as sequences of elementary steps...
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01/12/2022
Efficient Modular Graph Transformation Rule Application
Graph transformation formalisms have proven to be suitable tools for the...
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07/07/2021
Defining Autocatalysis in Chemical Reaction Networks
Autocatalysis is a deceptively simple concept, referring to the situatio...
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06/04/2021
Rewriting Theory for the Life Sciences: A Unifying Theory of CTMC Semantics (Long version)
The Kappa biochemistry and the MØD organic chemistry frameworks are amon...
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02/05/2021
Graph Transformation for Enzymatic Mechanisms
Motivation: The design of enzymes is as challenging as it is consequenti...
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12/07/2017
Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows
We present an elaborate framework for formally modelling pathways in che...
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11/22/2017