Formalized rules for protein-protein interactions have recently been introduced to represent
the binding and enzymatic activities of proteins in cellular signaling. Rules encode an …

An introduction to the fundamental concepts of the emerging field of Artificial Chemistries,
covering both theory and practical applications. The field of Artificial Life (ALife) is now firmly …

We introduce a graph-theoretic formalism suitable for modeling biochemical networks
marked by combinatorial complexity, such as signal-transduction systems, in which protein …

Background Modeling molecules as undirected graphs and chemical reactions as graph
rewriting operations is a natural and convenient approach to modeling chemistry. Graph …

In distributed and mobile systems with volatile bandwidth and fragile connectivity, non-
functional aspects like performance and reliability become more and more important. To …

Conflict and dependency analysis (CDA) is a static analysis for the detection of conflicting
and dependent rule applications in a graph transformation system. The state-of-the-art CDA …

Double Pushout graph transformation naturally facilitates the modelling of chemical
reactions: labelled undirected graphs model molecules and direct derivations model …

A novel holistic approach is proposed for process retrofitting. Unlike conventional
approaches, the proposed approach totally resynthesizes the entire process by …

A computer-aided methodology for process synthesis is introduced here by utilizing the P-
graph (process graph) framework. A process system or network endeavors to create certain …

A graph formalism and grammar suitable for multi-scale modelling is introduced in this
paper. Existing rule-based rewriting mechanisms related to L-systems do not take scales …