Complex Systems Built by Simple Elements

There are a lot of systems, which behave complexly, around us. We cannot predict their behaviour. Unpredictability is almost a character of complexity but how can we tackle the phenomenon of it. The formal mathematical descriptions of them are more and more complex and only several times solvable. Is the making a system of non-linear equations the only way to handle and descript systems like them? Using simple elements we can build models which show complex behaviour. Simple rule-systems can be a model of a complex system. For example algorithms can be appropriate for this task. We can implement these models for the language of computers, as well, and running simulations. Can we observe or perceive emergent characters? What is the measure of emergent phenomena? These are the questions to which I am searching the answers. The algorithms can give us a better way to understand the complex world

25 Years of Self-Organized Criticality: Solar and Astrophysics

Shortly after the seminal paper {\sl "Self-Organized Criticality: An explanation of 1/f noise"} by Bak, Tang, and Wiesenfeld (1987), the idea has been applied to solar physics, in {\sl "Avalanches and the Distribution of Solar Flares"} by Lu and Hamilton (1991). In the following years, an inspiring cross-fertilization from complexity theory to solar and astrophysics took place, where the SOC concept was initially applied to solar flares, stellar flares, and magnetospheric substorms, and later extended to the radiation belt, the heliosphere, lunar craters, the asteroid belt, the Saturn ring, pulsar glitches, soft X-ray repeaters, blazars, black-hole objects, cosmic rays, and boson clouds. The application of SOC concepts has been performed by numerical cellular automaton simulations, by analytical calculations of statistical (powerlaw-like) distributions based on physical scaling laws, and by observational tests of theoretically predicted size distributions and waiting time distributions. Attempts have been undertaken to import physical models into the numerical SOC toy models, such as the discretization of magneto-hydrodynamics (MHD) processes. The novel applications stimulated also vigorous debates about the discrimination between SOC models, SOC-like, and non-SOC processes, such as phase transitions, turbulence, random-walk diffusion, percolation, branching processes, network theory, chaos theory, fractality, multi-scale, and other complexity phenomena. We review SOC studies from the last 25 years and highlight new trends, open questions, and future challenges, as discussed during two recent ISSI workshops on this theme.Comment: 139 pages, 28 figures, Review based on ISSI workshops "Self-Organized Criticality and Turbulence" (2012, 2013, Bern, Switzerland

OxyGene: an innovative platform for investigating oxidative-response genes in whole prokaryotic genomes

International audienceBACKGROUND: Oxidative stress is a common stress encountered by living organisms and is due to an imbalance between intracellular reactive oxygen and nitrogen species (ROS, RNS) and cellular antioxidant defence. To defend themselves against ROS/RNS, bacteria possess a subsystem of detoxification enzymes, which are classified with regard to their substrates. To identify such enzymes in prokaryotic genomes, different approaches based on similarity, enzyme profiles or patterns exist. Unfortunately, several problems persist in the annotation, classification and naming of these enzymes due mainly to some erroneous entries in databases, mistake propagation, absence of updating and disparity in function description. DESCRIPTION: In order to improve the current annotation of oxidative stress subsystems, an innovative platform named OxyGene has been developed. It integrates an original database called OxyDB, holding thoroughly tested anchor-based signatures associated to subfamilies of oxidative stress enzymes, and a new anchor-driven annotator, for ab initio detection of ROS/RNS response genes. All complete Bacterial and Archaeal genomes have been re-annotated, and the results stored in the OxyGene repository can be interrogated via a Graphical User Interface. CONCLUSION: OxyGene enables the exploration and comparative analysis of enzymes belonging to 37 detoxification subclasses in 664 microbial genomes. It proposes a new classification that improves both the ontology and the annotation of the detoxification subsystems in prokaryotic whole genomes, while discovering new ORFs and attributing precise function to hypothetical annotated proteins. OxyGene is freely available at: http://www.umr6026.univ-rennes1.fr/english/home/research/basic/software