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In some contexts, well-formed natural language cannot be expected as input to information or communication systems. In these contexts, the use of grammar-independent input (sequences of uninflected semantic units like e.g.…

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…

Local interactions among biomolecules, and the role played by their environment, have gained increasing attention in modelling biochemical reactions. By defining the automaton of molecular perceptions, we explore an agent-based…

Living cells use readout molecules to record the state of receptor proteins, similar to measurements or copies in typical computational devices. But is this analogy rigorous? Can cells be optimally efficient, and if not, why? We show that,…

Chemical systems are interpreted through the species they contain and the reactions they may undergo, i.e., their chemical reaction network (CRN). In spite of their central importance to chemistry, the structure of CRNs continues to be…

Robustness to a wide variety of negative factors and the ability to self-repair is an inherent and natural characteristic of all life forms on earth. As opposed to nature, man-made systems are in most cases not inherently robust and a…

Living cells encode and transmit information in the temporal dynamics of biochemical components. Gaining a detailed understanding of the input-output relationship in biological systems therefore requires quantitative measures that capture…

Probabilistic inference provides a language for describing how organisms may learn from and adapt to their environment. The computations needed to implement probabilistic inference often require specific representations, akin to having the…

In current molecular communication (MC) systems, performing computational operations at the nanoscale remains challenging, restricting their applicability in complex scenarios such as adaptive biochemical control and advanced nanoscale…

While automated chemical tools excel at specific tasks, they have struggled to capture the strategic thinking that characterizes expert chemical reasoning. Here we demonstrate that large language models (LLMs) can serve as powerful tools…

This paper addresses the decomposition of biochemical networks into functional modules that preserve their dynamic properties upon interconnection with other modules, which permits the inference of network behavior from the properties of…

Molecular data systems have the potential to store information at dramatically higher density than existing electronic media. Some of the first experimental demonstrations of this idea have used DNA, but nature also uses a wide diversity of…

This work presents a new multi-chemical experimental platform for molecular communication where the transmitter can release different chemicals. This platform is designed to be inexpensive and accessible, and it can be expanded to simulate…

Interaction languages such as MSC are often associated with formal semantics by means of translations into distinct behavioral formalisms such as automatas or Petri nets. In contrast to translational approaches we propose an operational…

Background: Stochastic biochemical reaction networks are commonly modelled by the chemical master equation, and can be simulated as first order linear differential equations through a finite state projection. Due to the very high state…

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…

Embedding computation in biochemical environments incompatible with traditional electronics is expected to have wide-ranging impact in synthetic biology, medicine, nanofabrication and other fields. Natural biochemical systems are typically…

The use of mathematical methods for the analysis of chemical reaction systems has a very long history, and involves many types of models: deterministic versus stochastic, continuous versus discrete, and homogeneous versus spatially…

We present a systematic mathematical analysis of the qualitative steady-state response to rate perturbations in large classes of reaction networks. This includes multimolecular reactions and allows for catalysis, enzymatic reactions,…

A review of the mechanisms of speciation is performed. The mechanisms of the evolution of species, taking into account the feedback of the state of the environment and mechanisms of the emergence of complexity, are considered. It is shown…