Related papers: On Natural Genetic Engineering: Structural Dynamis…

In this paper we present a network model to study the impact of spatial distribution of constituents, coupling between them and diffusive processes in the context of biological situations. The model is in terms of network of mobile elements…

Complex evolving systems such as the biosphere, ecosystems and societies exhibit sudden collapses, for reasons that are only partially understood. Here we study this phenomenon using a mathematical model of a system that evolves under…

Stochastic simulation has been a powerful tool for studying the dynamics of gene regulatory networks, particularly in terms of understanding how cell-phenotype stability and fate-transitions are impacted by noisy gene expression. However,…

This article is set in the field of regulation networks modeled by discrete dynamical systems. It focuses on Boolean automata networks. In such networks, there are many ways to update the states of every element. When this is done…

Cellular phenotypes are determined by the dynamical activity of networks of co-regulated genes. Elucidating such networks is crucial for the understanding of normal cell physiology as well as for the dissection of complex pathologic…

Translating metabolic networks into dynamic models is difficult if kinetic constants are unknown. Structural Kinetic Modelling (SKM) replaces reaction elasticities by independent random numbers. Here I propose a variant that accounts for…

Boolean networks are special types of finite state time-discrete dynamical systems. A Boolean network can be described by a function from an n-dimensional vector space over the field of two elements to itself. A fundamental problem in…

We consider a dynamic social network model in which agents play repeated games in pairings determined by a stochastically evolving social network. Individual agents begin to interact at random, with the interactions modeled as games. The…

Despite the large quantity of information available, thorough researches in various biological databases are still needed in order to reconstruct and understand the steps that lead to known or new phenomena. By using protein-protein…

Phenotypical variability in the absence of genetic variation often reflects complex energetic landscapes associated with underlying gene regulatory networks (GRNs). In this view, different phenotypes are associated with alternative states…

Recent technological advances and long-term data studies provide interaction data that can be modelled through dynamic networks, i.e a sequence of different snapshots of an evolving ecological network. Most often time is the parameter along…

The study of adaptive dynamics, involving many degrees of freedom on two separated timescales, one for fast changes of state variables and another for the slow adaptation of parameters controlling the former's dynamics is crucial for…

This is the second paper of a series of two about the structural properties that influence the asymptotic dynamics of Random Boolean Networks. Here we study the functionally independent clusters in which the relevant elements, introduced…

In both natural and artificial studies, evolution is often seen as synonymous to natural selection. Individuals evolve under pressures set by environments that are either reset or do not carry over significant changes from previous…

We analyse a collection of empirical networks in a wide spectrum of disciplines and show that strong non-normality is ubiquitous in network science. Dynamical processes evolving on non-normal networks exhibit a peculiar behaviour, as…

We give a overview of stochastic models of evolution that have found applications in genetics, ecology and linguistics for an audience of nonspecialists, especially statistical physicists. In particular, we focus mostly on neutral models in…

The regulation of metabolic activity by tuning enzyme expression levels is crucial to sustain cellular growth in changing environments. Metabolic networks are often studied at steady state using constraint-based models and optimization…

The parallel mutation-selection evolutionary dynamics, in which mutation and replication are independent events, is solved exactly in the case that the Malthusian fitnesses associated to the genomes are described by the Random Energy Model…

Here we propose a new approach to modeling gene expression based on the theory of random dynamical systems (RDS) that provides a general coupling prescription between the nodes of any given regulatory network given the dynamics of each node…

The whole complex process to obtain a protein encoded by a gene is difficult to include in a mathematical model. There are many models for describing different aspects of a genetic network. Finding a better model is one of the most…