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We define and study a few properties of a class of random automata networks. While regular finite one-dimensional cellular automata are defined on periodic lattices, these automata networks, called randomized cellular automata, are defined…
Automata learning is a technique that has successfully been applied in verification, with the automaton type varying depending on the application domain. Adaptations of automata learning algorithms for increasingly complex types of automata…
We study the ability to maintain information in a population of reacting polymers under the influence of decay, i.e., spontaneous breakdown of large polymers. At a certain decay rate, it becomes impossible to maintain a significant…
The analysis of complex reaction networks is of great importance in several chemical and biochemical fields (interstellar chemistry, prebiotic chemistry, reaction mechanism, etc). In this article, we propose to simultaneously refine and…
For the investigation of chemical reaction networks, the efficient and accurate determination of all relevant intermediates and elementary reactions is mandatory. The complexity of such a network may grow rapidly, in particular if reactive…
Reaction networks are a general formalism for describing collections of classical entities interacting in a random way. While reaction networks are mainly studied by chemists, they are equivalent to Petri nets, which are used for similar…
Sets with atoms serve as an alternative to ZFC foundations for mathematics, where some infinite, though highly symmetric sets, behave in a finitistic way. Therefore, one can try to carry over analysis of the classical algorithms from finite…
This paper is centered on using chemical reaction as a computational metaphor for simultaneously solving problems. An artificial chemical reactor that can simultaneously solve instances of three unrelated problems was created. The reactor…
We present a simple mathematical model that captures the evolutionary capabilities of a prebiotic compartment or protocell. In the model the protocell contains an autocatalytic set whose chemical dynamics is coupled to the growth-division…
Autonomous robotic systems are complex, hybrid, and often safety-critical; this makes their formal specification and verification uniquely challenging. Though commonly used, testing and simulation alone are insufficient to ensure the…
Self-Other Reorganization (SOR) is a theory of how interacting entities or individuals, each of which can be described as an autocatalytic network, collectively exhibit cumulative, adaptive, open-ended change, or evolution. Zachar et al.'s…
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…
Continual learning refers to the ability of a biological or artificial system to seamlessly learn from continuous streams of information while preventing catastrophic forgetting, i.e., a condition in which new incoming information strongly…
The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same…
Synthesis is the automated construction of a system from its specification. The system has to satisfy its specification in all possible environments. Modern systems often interact with other systems, or agents. Many times these agents have…
We present a novel approach to represent ecological systems using reaction networks, and show how a particular framework called Chemical Organization Theory (COT) sheds new light on the longstanding complexity-stability debate. Namely, COT…
The analytical description of charts is an exciting and important research area with many applications in academia and industry. Yet, this challenging task has received limited attention from the computational linguistics research…
A computational system is called autonomous if it is able to make its own decisions, or take its own actions, without human supervision or control. The capability and spread of such systems have reached the point where they are beginning to…
Biological cells with all of their surface structure and complex interior stripped away are essentially vesicles - membranes composed of lipid bilayers which form closed sacs. Vesicles are thought to be relevant as models of primitive…
The wavefront set provides a precise description of the singularities of a distribution. Because of its ability to control the product of distributions, the wavefront set was a key element of recent progress in renormalized quantum field…