Related papers: Studying self-organisation across the biosphere wi…
The concept of multilayer networks has become recently integrated into complex systems modeling since it encapsulates a very general concept of complex relationships. Biological pathways are an example of complex real-world networks, where…
A central and long-standing issue in evolutionary theory is the origin of the biological variation upon which natural selection acts1. Some hypotheses suggest that evolutionary change represents an adaptation to the surrounding environment…
In this essay I aim to investigate and discuss the process through which bundles of things "self-organize" into other things. In particular, I engage in such investigation by trying to apply a framework of analysis of structural stability…
In this paper, we develop a natural (empirical) relational theory for describing and modeling complex biological phenomena. We have as stepping stone the assertion: function implies structure. The theory is built upon a graph's theory…
Spatial self-organization emerges in distributed systems exhibiting local interactions when nonlinearities and the appropriate propagation of signals are at work. These kinds of phenomena can be modeled with different frameworks, typically…
We present a method for logical specification of the behavior of a system based on the specification of its components and for representing and specifying the effect of a class of communication "signaling pathways" among them. Variations in…
Following extensive numerical experiments, it has been suggested that the evolution of competing computer programs in artificial life simulations shows signs of being a self-organized critical process. The primary evidence for this claim…
A simple periodically driven system displaying rich behavior is introduced and studied. The system self-organizes into a mosaic of static ordered regions with three possible patterns, which are threaded by one-dimensional paths on which a…
In this paper, we demonstrate that considering experiments in a graph-theoretic manner allows us to exploit automorphisms of the graph to reduce the number of evaluations of candidate designs for those experiments, and thus find optimal…
Predicting the fate of ecologies is a daunting, albeit extremely important, task. As part of this task one needs to develop an understanding of the organization, hierarchies, and correlations among the species forming the ecology. Focusing…
Biological systems, unlike physical or chemical systems, are characterized by the very inhomogeneous distribution of their components. The immune system, in particular, is notable for self-organizing its structure. Classically, the dynamics…
All aspects of our society, including the life sciences, need a mechanism for people working within them to represent the concepts they employ to carry out their research. For the information systems being designed and developed to support…
Multiparticle systems on complicated metric graphs might have many applications in physics, biology and social life. But the corresponding science still does not exist. Here we start it with simplest examples where there is quadratic…
Natural physical, chemical, and biological dynamical systems are often complex, with heterogeneous components interacting in diverse ways. We show how simple graph neural networks can be designed to jointly learn the interaction rules and…
Many organisms exhibit branching morphologies that twist around each other and become entangled. Entanglement occurs when different objects interlock, creating complex and often irreversible configurations. This physical phenomenon is…
Often fairness assumptions need to be made in order to establish liveness properties of distributed systems, but in many situations these lead to false conclusions. This document presents a research agenda aiming at laying the foundations…
We have generalized our ``unified'' model of evolutionary ecology by taking into account the possible movements of the organisms from one ``patch'' to another within the same eco-system. We model the spatial extension of the eco-system…
Time-discrete dynamical systems on a finite state space have been used with great success to model natural and engineered systems such as biological networks, social networks, and engineered control systems. They have the advantage of being…
One of the most compelling problems in science consists in understanding how living systems process information. After all, the way they process information defines their capacities to learning and adaptation. There is an increasing…
We present a stochastic approach to modeling the dynamics of coexistence of prey and predator populations. It is assumed that the space of coexistence is explicitly subdivided in a grid of cells. Each cell can be occupied by only one…