Related papers: MetaChem: An Algebraic Framework for Artificial Ch…
Artificial Chemistries (ACs) are symbolic chemical metaphors for the exploration of Artificial Life, with specific focus on the origin of life. In this work we define a P system based artificial graph chemistry to understand the principles…
Artificial Chemistries (ACs) are symbolic chemical metaphors for the exploration of Artificial Life, with specific focus on the problem of biogenesis or the origin of life. This paper presents authors thoughts towards defining a unified…
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…
Atomistic simulations are essential tools in chemistry and materials science, accelerating the discovery of novel catalysts, energy storage materials, and pharmaceuticals. However, running these simulations remains challenging due to the…
Advancing artificial intelligence for physical sciences requires representations that are both interpretable and compatible with the underlying laws of nature. We introduce METASTRINGS, a symbolic language for photonics that expresses…
Artificial chemistry simulations produce many intriguing emergent behaviors, but they are often difficult to steer or control. This paper proposes a method for steering the dynamics of a classic artificial chemistry model, known as AlChemy…
The mathematical formalisms used to model biological systems induce both latent and ambiguous assumptions that can limit or distort their representational capabilities. Developing formalisms that can represent systems more precisely is…
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…
Chemical transformations depend not only on the identities of the reacting species but also on the catalytic, environmental, and intermediate conditions under which they occur. Classical binary reaction formalisms usually treat such…
Representing molecular structures effectively in chemistry remains a challenging task. Language models and graph-based models are extensively utilized within this domain, consistently achieving state-of-the-art results across an array of…
Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, since precise information on the molecular composition, the dominant reaction chemistry, and the conditions for that…
Graph-based modeling plays a fundamental role in many areas of computer science. In this paper, we introduce systems of graph formulas with variables for specifying graph properties; this notion generalizes the graph formulas introduced in…
Swarm robotics has potential for a wide variety of applications, but real-world deployments remain rare due to the difficulty of predicting emergent behaviors arising from simple local interactions. Traditional engineering approaches design…
Analyzing qualitative behaviors of biochemical reactions using its associated network structure has proven useful in diverse branches of biology. As an extension of our previous work, we introduce a graph-based framework to calculate steady…
CHEMSMART (Chemistry Simulation and Modeling Automation Toolkit) is an open-source, Python-based framework designed to streamline quantum chemistry workflows for homogeneous catalysis and molecular modeling. By integrating job preparation,…
Molecules composed of atoms exhibit properties not inherent to their constituent atoms. Similarly, meta-molecules consisting of multiple meta-atoms possess emerging features that the meta-atoms themselves do not possess. Metasurfaces…
Chemical systems are traditionally described by lists of species, reactions, and externally imposed kinetic laws, a framework that lacks an intrinsic algebraic structure governing how transformations compose. We propose an axiomatic…
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…
We recently presented the so-called allagmatic method, which includes a system metamodel providing a framework for describing, modelling, simulating, and interpreting complex systems. Its development and programming was guided by…
Chemists now routinely use software as part of their work. For example, virtual chemistry allows chemical reactions to be simulated. In particular, a selection of software is available for the visualisation of complex 3-dimensional…