• Corpus ID: 245877561

Efficient Modular Graph Transformation Rule Application

@inproceedings{Andersen2022EfficientMG,
  title={Efficient Modular Graph Transformation Rule Application},
  author={Jakob L. Andersen and Rolf Fagerberg and Juraj Kolvc'ak and Christophe V.F.P. Laurent and Daniel Merkle and Nikolai N{\o}jgaard},
  year={2022}
}
. Graph transformation formalisms have proven to be suitable tools for the modeling of chemical reactions. They are well established in theoretical studies [15] and increasingly also in practical applications in chemistry [11, 28]. The latter is made feasible via the development of programming frameworks which make the formalisms executable [5, 19, 12]. The application of such frameworks to large networks of chemical reactions poses unique computational challenges due to the nature of the… 

References

SHOWING 1-10 OF 32 REFERENCES

Rule composition in graph transformation models of chemical reactions

The formal foundations of composition of transformation rules for complete chemical pathways are explored using ideas from concurrency theory, and several special cases that each have an intuitive chemical interpretation are considered.

A Software Package for Chemically Inspired Graph Transformation

A general software package for this type of graph rewriting system, which can be used for modelling chemical systems, and has extensive procedures for automatically visualising not only graphs and rewrite rules, but also Double Pushout diagrams and graph languages in form of directed hypergraphs.

Generic Strategies for Chemical Space Exploration

A framework for the specification of exploration strategies in graph-rewriting systems is presented and the feasibility of this high-level strategy framework is demonstrated.

Graph transformation for enzymatic mechanisms

Using graph transformation, this work derives about 1000 rules for amino acid side chain chemistry from the M-CSA database, a curated repository of enzymatic mechanisms, and proposes hundreds of hypothetical catalytic mechanisms for a large number of unrelated reactions in the Rhea database.

Chemical Transformation Motifs—Modelling Pathways as Integer Hyperflows

We present an elaborate framework for formally modelling pathways in chemical reaction networks on a mechanistic level. Networks are modelled mathematically as directed multi-hypergraphs, with

A Graph-Based Toy Model of Chemistry

A Toy Model is presented that provides a consistent framework in which generic properties of extensive chemical reaction networks can be explored in detail and that at the same time preserves the "look-and-feel" of chemistry.

Algebraic Approaches to Graph Transformation - Part I: Basic Concepts and Double Pushout Approach

This chapter starts with an overwiev of the basic notions common to the two algebraic approaches, the "double-pushout (DPO) approach) and the "single-push out (SPO) approaches"; next it is presented the classical theory and some recent development of the double- pushout approach.

Double-pushout graph transformation revisited

It is shown that injective matching provides additional expressiveness in two respects: for generating graph languages by grammars without non-terminals and for computing graph functions by convergent graph transformation systems.

A (sub)graph isomorphism algorithm for matching large graphs

The algorithm is improved here to reduce its spatial complexity and to achieve a better performance on large graphs; its features are analyzed in detail with special reference to time and memory requirements.

An intermediate level of abstraction for computational systems chemistry

An extension of the basic formalism into the realm of integer hyperflows allows for the identification of complex reaction patterns, such as autocatalysis, in large reaction networks using optimization techniques.