Related papers: Regulatory networks and connected components of th…
We consider a model of large regulatory gene expression networks where the thresholds activating the sigmoidal interactions between genes and the signs of these interactions are shuffled randomly. Such an approach allows for a qualitative…
Control of the living cell functions with remarkable reliability despite the stochastic nature of the underlying molecular networks -- a property presumably optimized by biological evolution. We here ask to what extent the property of a…
We construct and investigate Boolean networks that follow a given reliable trajectory in state space, which is insensitive to fluctuations in the updating schedule, and which is also robust against noise. Robustness is quantified as the…
A common trait of complex systems is that they can be represented by means of a network of interacting parts. It is, in fact, the network organisation (more than the parts) what largely conditions most higher-level properties, which are not…
Bistable biological regulatory systems need to cope with stochastic noise to fine-tune their function close to bifurcation points. Here, we study stability properties of this regime in generic systems to demonstrate that cooperative…
Identity, response to external stimuli, and spatial architecture of a living system are central topics of molecular biology. Presently, they are largely seen as a result of the interplay between a gene repertoire and the regulatory…
Constraints placed upon the phenotypes of organisms result from their interactions with the environment. Over evolutionary timescales, these constraints feed back onto smaller molecular subnetworks comprising the organism. The evolution of…
Systems of dynamical interactions between competing species can be used to model many complex systems, and can be mathematically described by {\em random} networks. Understanding how patterns of activity arise in such systems is important…
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…
We have uncovered that the non-equilibrium network dynamics and global properties are determined by two essential features: the potential landscape and the flux landscape. We have found that the funneled potential landscape is crucial for…
We propose a dynamical neural network model with a hierarchical and modular structure. The network architecture can be derived by minimizing an energy function that is originally designed based on two kinds of neurons with quite different…
Effective control of biological systems can often be achieved through the control of a surprisingly small number of distinct variables. We bring clarity to such results using the formalism of Boolean dynamical networks, analyzing the…
Boolean networks model finite discrete dynamical systems with complex behaviours. The state of each component is determined by a Boolean function of the state of (a subset of) the components of the network. This paper addresses the…
The dynamics of systems of interacting agents is determined by the structure of their coupling network. The knowledge of the latter is, therefore, highly desirable, for instance, to develop efficient control schemes, to accurately predict…
We analyse the stability of linear dynamical systems defined on sparse, random graphs with predator-prey, competitive, and mutualistic interactions. These systems are aimed at modelling the stability of fixed points in large systems defined…
Various functions of a network of excitable units can be enhanced if the network is in the `critical regime', where excitations are, on average, neither damped nor amplified. An important question is how can such networks self-organize to…
Despite their topological complexity almost all functional properties of metabolic networks can be derived from steady-state dynamics. Indeed, many theoretical investigations (like flux-balance analysis) rely on extracting function from…
This paper presents a real-time simulation involving ''protozoan-like'' cells that evolve by natural selection in a physical 2D ecosystem. Selection pressure is exerted via the requirements to collect mass and energy from the surroundings…
The rigidity of elastic networks depends sensitively on their internal connectivity and the nature of the interactions between constituents. Particles interacting via central forces undergo a zero-temperature rigidity-percolation transition…
Transcription factor binding sites vary in their specificity, both within and between species. Binding specificity has a strong impact on the evolution of gene expression, because it determines how easily regulatory interactions are gained…