Related papers: Self-Organization in Computation & Chemistry: Retu…

Complex systems often exhibit highly structured network topologies that reflect functional constraints. In this work, we investigate how, under varying combinations of system-wide selection rules and special agents, different classes of…

The network of biochemical reactions inside living organisms is characterized by an overwhelming complexity which stems from the sheer number of reactions and from the complicated topology of biochemical cycles. However the high speed of…

The growth of world population, limitation of resources, economic problems and environmental issues force engineers to develop increasingly efficient solutions for logistic systems. Pure optimization for efficiency, however, has often led…

While showing impressive performance on various kinds of learning tasks, it is yet unclear whether deep learning models have the ability to robustly tackle reasoning tasks. than by learning the underlying reasoning process that is actually…

While large language models (LLMs) with Chain-of-Thought (CoT) reasoning excel in mathematics and coding, their potential for systematic reasoning in chemistry, a domain demanding rigorous structural analysis for real-world tasks like drug…

The functioning of many biochemical networks is often robust -- remarkably stable under changes in external conditions and internal reaction parameters. Much recent work on robustness and evolvability has focused on the structure of neutral…

Metabolic networks perform some of the most fundamental functions in living cells, including energy transduction and building block biosynthesis. While these are the best characterized networks in living systems, understanding their…

Biological systems exhibit large-scale self-organized dynamics and structures which enable organisms to perform the functions of life. The field of active matter strives to develop and understand microscopically-driven nonequilibrium…

Living organisms have some common structures, chemical reactions and molecular structures. The organisms consist of cells with cell division, they have homochirality of protein and carbohydrate units, and metabolism, and genetics, and they…

Tailoring the performance of next-generation high entropy materials requires a deep understanding of the competition between entropy-driven random solid solution and enthalpy-driven chemical ordering. Investigating such order and disorder…

We propose an artificial life framework aimed at facilitating the emergence of intelligent organisms. In this framework there is no explicit notion of an agent: instead there is an environment made of atomic elements. These elements contain…

We study two mechanisms for the formation of protein patterns near membranes of living cells by mathematical modelling. Self-assembly of protein domains by electrostatic lipid-protein interactions is contrasted with self-organization due to…

Measures of complexity and entropy have not converged to a single quantitative description of levels of organization of complex systems. The need for such a measure is increasingly necessary in all disciplines studying complex systems. To…

In a cell or microorganism the processes that generate mass, energy, information transfer, and cell fate specification are seamlessly integrated through a complex network of various cellular constituents and reactions. However, despite the…

The conceptual background for a detailed study of the urban form of the city of Bologna is discussed with a view to modern methodological insight as it is being presented by recent results of complexity theory and the theory of…

Applications of machine learning in chemistry are often limited by the scarcity and expense of labeled data, restricting traditional supervised methods. In this work, we introduce a framework for molecular reasoning using general-purpose…

Flocks of birds and schools of fish are familiar examples of spatial patterns formed by living organisms. In contrast to the patterns on the skins of, say, zebra and giraffe, the patterns of our interest are {\it transient} although…

We show that fluid organizations display higher levels of cooperation than attainable by groups with either a fixed social structure or lacking one altogether. By moving within the organization, individuals cause restructurings that…

The true slime mold \textit{Physarum polycephalum} has the remarkable capability to perform self-organized activities such as network formation among food sources. Despite well reproducing the emergence of slime networks, existing models…

Compositionality is a key feature of process algebras which is often cited as one of their advantages as a modelling technique. It is certainly true that in biochemical systems, as in many other systems, model construction is made easier in…