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Large sets of genotypes give rise to the same phenotype because phenotypic expression is highly redundant. Accordingly, a population can accept mutations without altering its phenotype, as long as thegenotype mutates into another one on the…
Modularity structures are common in various social and biological networks. However, its dynamical origin remains an open question. In this work, we set up a dynamical model describing the evolution of a social network. Based on the…
Complex network theory provides a unifying framework for the study of structured dynamic systems. The current literature emphasizes a widely reported phenomenon of intermittent interaction among network vertices. In this paper, we introduce…
We realize autonomous Boolean networks by using logic gates in their autonomous mode-of-operation on a field-programmable gate array. This allows us to implement time-continuous systems with complex dynamical behaviors that can be…
This paper studies the mathematical properties of collectively canalizing Boolean functions, a class of functions that has arisen from applications in systems biology. Boolean networks are an increasingly popular modeling framework for…
Interactions between genes and gene products give rise to complex circuits that enable cells to process information and respond to external signals. Theoretical studies often describe these interactions using continuous, stochastic, or…
Network science provides an indispensable theoretical framework for studying the structure and function of real complex systems. Different network models are often used for finding the rules that govern their evolution, whereby the correct…
There is growing recognition that the network structures arising from interactions between different entities in physical, social and biological systems fundamentally alter the evolutionary outcomes. Previous paradigm exploring evolutionary…
With the emerging of new networks, such as wireless sensor networks, vehicle networks, P2P networks, cloud computing, mobile Internet, or social networks, the network dynamics and complexity expands from system design, hardware, software,…
Ecology and evolution are inseparable. Motivated by some recent experiments, we have developed models of evolutionary ecology from the perspective of dynamic networks. In these models, in addition to the intra-node dynamics, which…
Networks exhibiting "accelerating" growth have total link numbers growing faster than linearly with network size and can exhibit transitions from stationary to nonstationary statistics and from random to scale-free to regular statistics at…
We investigate the evolutionary dynamics of an idealised model for the robust self-assembly of two-dimensional structures called polyominoes. The model includes rules that encode interactions between sets of square tiles that drive the…
Genetic Regulatory Networks (GRNs) plays a vital role in the understanding of complex biological processes. Modeling GRNs is significantly important in order to reveal fundamental cellular processes, examine gene functions and understanding…
Genetic regulatory networks are defined by their topology and by a multitude of continuously adjustable parameters. Here we present a class of simple models within which the relative importance of topology vs. interaction strengths becomes…
Results and tools on discrete interaction networks are often concerned with Boolean variables, whereas considering more than two levels is sometimes useful. Multivalued networks can be converted to partial Boolean maps, in a way that…
Cells use genetic switches to shift between alternate stable gene expression states, e.g., to adapt to new environments or to follow a developmental pathway. Conceptually, these stable phenotypes can be considered as attractive states on an…
We present a general model for the growth of weighted networks in which the structural growth is coupled with the edges' weight dynamical evolution. The model is based on a simple weight-driven dynamics and a weights' reinforcement…
Three coarse-grained models of the double-stranded DNA are proposed and compared in the context of mechanical manipulation such as twisting and various schemes of stretching. The models differ in the number of effective beads (between two…
Networks with a prescribed power-law scaling in the spectrum of the graph Laplacian can be generated by evolutionary optimization. The Laplacian spectrum encodes the dynamical behavior of many important processes. Here, the networks are…
Biological networks of interacting agents exhibit similar topological properties for a wide range of scales, from cellular to ecological levels, suggesting the existence of a common evolutionary origin. A general evolutionary mechanism…