Related papers: Studying self-organisation across the biosphere wi…
Mutualisms are key for structuring ecological communities, but they are sensitive to environmental change and fluctuations in population size. Consequently, how mutualisms achieve stability remains an open question in ecological theory.…
We propose a generic model of eco-systems, with a {\it hierarchical} food web structure. In our computer simulations we let the eco-system evolve continuously for so long that that we can monitor extinctions as well as speciations over…
Collective behaviors exhibited by animal groups, such as fish schools, bird flocks, or insect swarms are fascinating examples of self-organization in biology. Concepts and methods from statistical physics have been used to argue…
Biological systems and processes are networks of complex nonlinear regulatory interactions between nucleic acids, proteins, and metabolites. A natural way in which to represent these interaction networks is through the use of a graph. In…
Development combines three basic processes asymmetric --- cell division, signaling and gene regulation --- in a multitude of ways to create an overwhelming diversity of multicellular life-forms. Here, we attempt to chart this diversity…
Although it has been notoriously difficult to pin down precisely what it is that makes life so distinctive and remarkable, there is general agreement that its informational aspect is one key property, perhaps the key property. The unique…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
Self-organization offers a promising approach for designing adaptive systems. Given the inherent complexity of most cyber-physical systems, adaptivity is desired, as predictability is limited. Here I summarize different concepts and…
Self-organized criticality is a well-established phenomenon, where a system dynamically tunes its structure to operate on the verge of a phase transition. Here, we show that the dynamics inside the self-organized critical state are…
We argue that the analysis of agent/environment interactions should be extended to include the conventions and invariants maintained by agents throughout their activity. We refer to this thicker notion of environment as a lifeworld and…
Within a mathematical model, the metabolic process of glycolysis is studied. The general scheme of glycolysis is considered as a natural result of the biochemical evolution. By using the theory of dissipative structures, the conditions of…
This paper is concerned with mathematical modeling of intelligent systems, such as human crowds and animal groups. In particular, the focus is on the emergence of different self-organized patterns from non-locality and anisotropy of the…
Graphs are commonly used to characterise interactions between objects of interest. Because they are based on a straightforward formalism, they are used in many scientific fields from computer science to historical sciences. In this paper,…
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…
The behavior of complex systems is determined not only by the topological organization of their interconnections but also by the dynamical processes taking place among their constituents. A faithful modeling of the dynamics is essential…
Many living and physical systems such as cell aggregates, tissues or bacterial colonies behave as unconventional systems of particles that are strongly constrained by volume exclusion and shape interactions. Understanding how these…
The origin of diversification and coexistence of genes and species have been traditionally studied in isolated biological levels. Ecological and evolutionary views have focused on the mechanisms that enable or constrain species coexistence,…
Biological evolution is a complex blend of ever changing structural stability, variability and emergence of new phenotypes, niches, ecosystems. We wish to argue that the evolution of life marks the end of a physics world view of law…
Standard techniques for studying biological systems largely focus on their dynamical, or, more recently, their informational properties, usually taking either a reductionist or holistic perspective. Yet, studying only individual system…
To comprehend the multipartite organization of large-scale biological and social systems, we introduce a new information theoretic approach that reveals community structure in weighted and directed networks. The method decomposes a network…