相关论文: Hierarchy and Feedback in the Evolution of the E. …

We show that the protein-protein interaction networks can be surprisingly well described by a very simple evolution model of duplication and divergence. The model exhibits a remarkably rich behavior depending on a single parameter, the…

A common theme among the proposed models for network epidemics is the assumption that the propagating object, i.e., a virus or a piece of information, is transferred across the nodes without going through any modification or evolution.…

Co-evolutionary adaptive mechanisms are not only ubiquitous in nature, but also beneficial for the functioning of a variety of systems. We here consider an adaptive network of oscillators with a stochastic, fitness-based, rule of…

Oscillatory behavior is ubiquitous in many natural and engineered systems, often emerging through self-regulating mechanisms. In this paper, we address the challenge of stabilizing a desired oscillatory pattern in a networked system where…

Hierarchy is one of the most conspicuous features of numerous natural, technological and social systems. The underlying structures are typically complex and their most relevant organizational principle is the ordering of the ties among the…

Life systems are complex and hierarchical, with diverse components at different scales, yet they sustain themselves, grow, and evolve over time. How can a theory of such complex biological states be developed? Here we note that for a…

We study the evolution of the network properties of a populated network embedded in a genotype space characterised by either a low or a high number of potential links, with particular emphasis on the connectivity and clustering. Evolution…

In prokaryotic genomes the number of transcriptional regulators is known to quadratically scale with the total number of protein-coding genes. Toolbox model was recently proposed to explain this scaling for metabolic enzymes and their…

The possibility that evolutionary forces -- together with a few fundamental factors such as thermodynamic constraints, specific computational features enabling information processing, and ecological processes -- might constrain the logic of…

Aspects of cell metabolism are modeled by ordinary differential equations describing the change of intracellular chemical concentrations. There is a correspondence between this dynamical system and a complex network. As in the classic…

Biological diversity has evolved despite the essentially infinite complexity of protein sequence space. We present a hierarchical approach to the efficient searching of this space and quantify the evolutionary potential of our approach with…

Human communication systems, such as language, evolve culturally; their components undergo reproduction and variation. However, a role for selection in cultural evolutionary dynamics is less clear. Often neutral evolution (also known as…

Although a number of models have been developed to investigate the emergence of culture and evolutionary phases in social systems, one important aspect has not yet been sufficiently emphasized. This is the structure of the underlaying…

Eukaryotic DNA replication follows a specific temporal program, with some genomic regions consistently replicating earlier than others, yet what determines this program is largely unknown. Highly transcribed regions have been observed to…

A model of an evolving network of interacting molecular species is shown to exhibit repeated rounds of crashes in which several species get rapidly depopulated, followed by recoveries. The network inevitably self-organizes into an…

microRNAs (miRNAs) regulate gene expression at post-transcriptional level by repressing target RNA molecules. Competition to bind miRNAs tends in turn to correlate their targets, establishing effective RNA-RNA interactions that can…

We study the effects of conformity, the tendency of humans to imitate locally common behaviors, in the evolution of cooperation when individuals occupy the vertices of a graph and engage in the one-shot Prisoner's Dilemma or the Snowdrift…

Recently, plenty research has been done on discovering the role of energy dissipation in biological networks, most of which focus on the relationship of dissipation and functionality. However, the development of networks science urged us to…

A recurring motif in gene regulatory networks is transcription factors (TFs) that regulate each other, and then bind to overlapping sites on DNA, where they interact and synergistically control transcription of a target gene. Here, we…

We build a simple model for feedback systems involving small RNA (sRNA) molecules based on the iron metabolism system in the bacterium E. coli, and compare it with the corresponding system in H. pylori which uses purely transcriptional…