Related papers: Information content and optimization of self-organ…
Self-organized systems, from synthetic nanostructures to developing organisms, are composed of fluctuating units capable of forming robust functional structures despite noise. Here, we ask: are there fundamental bounds on the robustness of…
The proper functioning of multicellular organisms requires the robust establishment of precise proportions between distinct cell-types. This developmental differentiation process typically involves intracellular regulatory and stochastic…
Over the last decade, significant progress has been made in understanding complex biological systems, however there have been few attempts at incorporating this knowledge into nature inspired optimization algorithms. In this paper, we…
Cells in a developing embryo have no direct way of "measuring" their physical position. Through a variety of processes, however, the expression levels of multiple genes come to be correlated with position, and these expression levels thus…
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…
During development, spatio-temporal patterns ranging from checkerboard to engulfing occur with precise proportions of the respective cell fates. Key developmental regulators are intracellular transcriptional interactions and intercellular…
A punctuated equilibrium model of biological evolution with relative fitness between different species being the fundamental driving force of evolution is introduced. Mutation is modeled as a fitness updating cellular automaton process…
We consider biological individuality in terms of information theoretic and graphical principles. Our purpose is to extract through an algorithmic decomposition system-environment boundaries supporting individuality. We infer or detect…
We propose a theoretical model for species that is focused on intrinsic organization and processes. Specifically, we regard species to be networks of organisms integrated by reproductive mechanisms (e.g., conjugation, meiosis, syngamy)…
Self-organization is the autonomous assembly of a network of interacting components into a stable, organized pattern. This article shows that the process of self-assembly can be encoded in terms of evolutionary entropy, a statistical…
It is not obvious what fraction of all the potential information residing in the molecules and structures of living systems is significant or meaningful to the system. Sets of random sequences or identically repeated sequences, for example,…
Changes in a cell's external or internal conditions are usually reflected in the concentrations of the relevant transcription factors. These proteins in turn modulate the expression levels of the genes under their control and sometimes need…
We suggest that ensembles of self-replicating entities such as biological systems naturally evolve into a self-organized critical state in which fluctuations, as well as waiting-times between phase transitions are distributed according to a…
Information theory and the framework of information dynamics have been used to provide tools to characterise complex systems. In particular, we are interested in quantifying information storage, information modification and information…
Many biological systems approach physical limits to their performance, motivating the idea that their behavior and underlying mechanisms could be determined by such optimality. Nevertheless, optimization as a predictive principle has only…
In a developing embryo, information about the position of cells is encoded in the concentrations of "morphogen" molecules. In the fruit fly, the local concentrations of just a handful of proteins encoded by the gap genes are sufficient to…
The subject of this paper is the evolution of the concept of information processing in regular structures based on multi-level processing in nested cellular automata. The essence of the proposed model is a discrete space-time containing…
A self-organized model with social percolation process is proposed to describe the propagations of information for different trading ways across a social system and the automatic formation of various groups within market traders. Based on…
Development in multi-cellular organisms is marked by a high degree of spatial organization of the cells attaining distinct fates in the embryo. We show that receptor-ligand interaction between cells in close physical proximity adaptively…
Our knowledge of how individual cells self-organize to form complex multicellular systems is being revolutionized by a data outburst, coming from high-throughput experimental breakthroughs such as single-cell RNA sequencing and spatially…