Optimal Self-Organization

We present computational and analytical results indicating that systems of driven entities with repulsive interactions tend to reach an optimal state associated with minimal interaction and minimal dissipation. Using concepts from non-equilibrium thermodynamics and game theoretical ideas, we generalize this finding to an even wider class of self-organizing systems which have the ability to reach a state of maximal overall ``success''. This principle is expected to be relevant for driven systems in physics like sheared granular media, but it is also applicable to biological, social, and economic systems, for which only a limited number of quantitative principles are available yet.Comment: This is the detailled revised version of a preprint on ``Self-Organised Optimality'' (cond-mat/9903319). For related work see http://www.theo2.physik.uni-stuttgart.de/helbing.html and http://angel.elte.hu/~vicsek

Self-organization of collaboration networks

We study collaboration networks in terms of evolving, self-organizing bipartite graph models. We propose a model of a growing network, which combines preferential edge attachment with the bipartite structure, generic for collaboration networks. The model depends exclusively on basic properties of the network, such as the total number of collaborators and acts of collaboration, the mean size of collaborations, etc. The simplest model defined within this framework already allows us to describe many of the main topological characteristics (degree distribution, clustering coefficient, etc.) of one-mode projections of several real collaboration networks, without parameter fitting. We explain the observed dependence of the local clustering on degree and the degree--degree correlations in terms of the ``aging'' of collaborators and their physical impossibility to participate in an unlimited number of collaborations.Comment: 10 pages, 8 figure

The self-organization of genomes

Menzerath-Altmann law is a general law of human language stating, for instance, that the longer a word, the shorter its syllables. With the metaphor that genomes are words and chromosomes are syllables, we examine if genomes also obey the law. We find that longer genomes tend to be made of smaller chromosomes in organisms from three different kingdoms: fungi, plants, and animals. Our findings suggest that genomes self-organize under principles similar to those of human language.Peer ReviewedPostprint (author's final draft

Self-organization of signal transduction

We propose a model of parameter learning for signal transduction, where the objective function is defined by signal transmission efficiency. We apply this to learn kinetic rates as a form of evolutionary learning, and look for parameters which satisfy the objective. This is a novel approach compared to the usual technique of adjusting parameters only on the basis of experimental data. The resulting model is self-organizing, i.e. perturbations in protein concentrations or changes in extracellular signaling will automatically lead to adaptation. We systematically perturb protein concentrations and observe the response of the system. We find compensatory or co-regulation of protein expression levels. In a novel experiment, we alter the distribution of extracellular signaling, and observe adaptation based on optimizing signal transmission. We also discuss the relationship between signaling with and without transients. Signaling by transients may involve maximization of signal transmission efficiency for the peak response, but a minimization in steady-state responses. With an appropriate objective function, this can also be achieved by concentration adjustment. Self-organizing systems may be predictive of unwanted drug interference effects, since they aim to mimic complex cellular adaptation in a unified way.Comment: updated version, 13 pages, 4 figures, 3 Tables, supplemental tabl

Self-organization on surfaces: foreword

After decades of work, the growth of continuous thin films, i.e., two-dimensional structures, is progressively becoming a technological issue more than a field of fundamental research. Incidentally self-organization of nanostructures on surfaces is now an important field of research, i.e., structures of dimensionality one or zero, with a steep rise of attention in the past five years. Whereas self-organization was initially motivated by potential applications, it has up to now essentially contributed to the advancement of fundamental science in low dimensions, as model systems could be produced that could not have been fabricated by lithography. This Special Issue aims at giving a cross-community timely overview of the field. The Issue gathers a broad panel of articles covering various self-organization mechanisms, specific structural characterization, physical properties, and current trends in extending the versatility of growth. The materials mostly covered here are semiconductors and magnetic materials.Comment: Foreword of the Editor to Special Issue on Self-organization on surface