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One of the most interesting scientific challenges nowadays deals with the analysis and the understanding of complex networks' dynamics. A major issue is the definition of new frameworks for the exploration of the dynamics at play in real…
Modern biological tools have made it possible to unequivocally demonstrate the deep relationship among species in terms of genes and basic molecular mechanisms. In addition, results from genetic, physical and physiological approaches…
We compare and contrast the long-time dynamical properties of two individual-based models of biological coevolution. Selection occurs via multispecies, stochastic population dynamics with reproduction probabilities that depend nonlinearly…
The dominant paradigm in origin of life research is that of an RNA world. However, despite experimental progress towards the spontaneous formation of RNA, the RNA world hypothesis still has its problems. Here, we introduce a novel…
How multicellular life forms evolved out from unicellular ones constitutes a major problem in our understanding of the evolution of our biosphere. A recent set of experiments involving yeast cell populations has shown that selection for…
There has been a long debate on how new levels of organization have evolved. It might seem unlikely, as cooperation must prevail over competition. One well-studied example is the emergence of autocatalytic sets, which seem to be a…
To unveil the logic of cell from a level of chemical reaction dynamics, we need to clarify how ensemble of chemicals can autonomously produce the set of chemical, without assuming a specific external control echanism. A cell consists of a…
The interaction networks of biological systems are known to take on several non-random structural properties, some of which are believed to positively influence system robustness. Researchers are only starting to understand how these…
Evolutionary game theory has been successfully used to investigate the dynamics of systems, in which many entities have competitive interactions. From a physics point of view, it is interesting to study conditions under which a coordination…
A hallmark in natural systems, self-organization often stems from very simple interaction rules between individual agents. While single-species self-propelled particle (SPP) systems are well understood, the behavior of binary mixtures with…
Artificial swarm systems have been extensively studied and used in computer science, robotics, engineering and other technological fields, primarily as a platform for implementing robust distributed systems to achieve pre-defined…
Developing a mathematical understanding of autocatalysis in reaction networks has both theoretical and practical implications. We review definitions of autocatalytic networks and prove some properties for minimal autocatalytic subnetworks…
The continuity of life and its evolution, we proposed, emerge from an interactive group process manifested in networks of interaction. We term this process \textit{survival-of-the-fitted}. Here, we reason that survival of the fitted results…
We propose a mathematical framework for natural selection in finite populations. Traditionally, many of the selection-based processes used to describe cultural and genetic evolution (such as imitation and birth-death models) have been…
Collective behaviors such as swarming, chemical signaling, and clustering are fundamental to biological microorganisms, enabling hierarchical colony formation, coordinated motion, and enhanced nutrient accessibility crucial for their…
We study an autocatalytic system consisting of several interacting chemical species. We observe a strong dependence of the concentrations of the chemicals on the size of the system. This dependence is caused by the discrete nature of the…
Polymer models are a widely used tool to study the prebiotic formation of metabolism at the origins of life. Counts of the number of reactions in these models are often crucial in probabilistic arguments concerning the emergence of…
A novel approach to analyzing time series generated by complex systems, such as markets, is presented. The basic idea of the approach is the {\it Law of Self-Similar Evolution}, according to which any complex system develops self-similarly.…
Can reproduction alone in the context of survival produce intelligence in our machines? In this work, self-replication is explored as a mechanism for the emergence of intelligent behavior in modern learning environments. By focusing purely…
The synchronization of self-propelled particles (SPPs) is a fascinating instance of emergent behavior in living and man-made systems, such as colonies of bacteria, flocks of birds, robot ensembles, and many others. The recent discovery of…