Related papers: A Software Package for Chemically Inspired Graph T…
Graph rewrite systems are powerful tools to model and study complex problems in various fields of research. Their successful application to chemical reaction modelling on a molecular level was shown but no appropriate and simple system is…
Graph transformation formalisms have proven to be suitable tools for the modelling of chemical reactions. They are well established in theoretical studies and increasingly also in practical applications in chemistry. The latter is made…
Graph transformation systems have the potential to be realistic models of chemistry, provided a comprehensive collection of reaction rules can be extracted from the body of chemical knowledge. A first key step for rule learning is the…
We address a fundamental problem in chemistry known as chemical reaction product prediction. Our main insight is that the input reactant and reagent molecules can be jointly represented as a graph, and the process of generating product…
Modeling molecules as undirected graphs and chemical reactions as graph rewriting operations is a natural and convenient approach tom odeling chemistry. Graph grammar rules are most naturally employed to model elementary reactions like…
Accurately modeling chemical reactions in molecular dynamics simulations requires detailed pre- and post-reaction templates, often created through labor-intensive manual workflows. This work introduces a Python-based algorithm that…
Computational approaches to exploring "chemical universes", i.e., very large sets, potentially infinite sets of compounds that can be constructed by a prescribed collection of reaction mechanisms, in practice suffer from a combinatorial…
Motivation: The design of enzymes is as challenging as it is consequential for making chemical synthesis in medical and industrial applications more efficient, cost-effective and environmentally friendly. While several aspects of this…
The basic principle of graph rewriting is the stepwise replacement of subgraphs inside a host graph. A challenge in such replacement steps is the treatment of the patch graph, consisting of those edges of the host graph that touch the…
The analysis of the structure of chemical reaction networks is crucial for a better understanding of chemical processes. Such networks are well described as hypergraphs. However, due to the available methods, analyses regarding network…
Given a graph rewrite system, a graph G is a quine graph if it has a non-void maximal collection of non-conflicting matches of left patterns of graphs rewrites, such that after the parallel application of the rewrites we obtain a graph…
In this study, a versatile methodology for initiating polymerization from monomers in highly cross-linked materials is investigated. As polymerization progresses, force-field parameters undergo continuous modification due to the formation…
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 vertices corresponding to molecules and…
Graphs are central to the chemical sciences, providing a natural language to describe molecules, proteins, reactions, and industrial processes. They capture interactions and structures that underpin materials, biology, and medicine. This…
We describe a tool to create, edit, visualise and compute with interaction nets - a form of graph rewriting systems. The editor, called GraphPaper, allows users to create and edit graphs and their transformation rules using an intuitive…
Chemical algorithms are statistical algorithms described and represented as chemical reaction networks. They are particularly attractive for traffic shaping and general control of network dynamics; they are analytically tractable, they…
It is fundamental for science and technology to be able to predict chemical reactions and their properties. To achieve such skills, it is important to develop good representations of chemical reactions, or good deep learning architectures…
Retrosynthesis is one of the fundamental problems in organic chemistry. The task is to identify reactants that can be used to synthesize a specified product molecule. Recently, computer-aided retrosynthesis is finding renewed interest from…
The Bond Graph approach and the Chemical Reaction Network approach to modelling biomolecular systems developed independently. This paper brings together the two approaches by providing a bond graph interpretation of the chemical reaction…
Given graphs as input, Graph Neural Networks (GNNs) support the inference of nodes, edges, attributes, or graph properties. Graph Rewriting investigates the rule-based manipulation of graphs to model complex graph transformations. We…