Related papers: Boolean network model predicts cell cycle sequence…
One of the characteristic features of genetic networks is their inherent robustness, that is, their ability to retain functionality in spite of the introduction of random errors. In this paper, we seek to better understand how robustness is…
Gene regulatory networks can be successfully modeled as Boolean networks. A much discussed hypothesis says that such model networks reproduce empirical findings the best if they are tuned to operate at criticality, i.e. at the borderline…
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…
Study of network dynamics is very active area in biological and social sciences. However, the relationship between the network structure and the attractors of the dynamics has not been fully understood yet. In this study, we numerically…
The gene networks that comprise the circadian clock modulate biological function across a range of scales, from gene expression to performance and adaptive behaviour. The clock functions by generating endogenous rhythms that can be…
We calculate the network fluid regime and phase diagrams of binary mixtures of patchy colloids, using Wertheim's first order perturbation theory and a generalization of Flory-Stockmayer's theory of polymerization. The colloids are modelled…
Boolean networks constitute relevant mathematical models to study the behaviours of genetic and signalling networks. These networks define regulatory influences between molecular nodes, each being associated to a Boolean variable and a…
We demonstrate the advantages of feedforward loops using a Boolean network, which is one of the discrete dynamical models for transcriptional regulatory networks. After comparing the dynamical behaviors of network embedded feedback and…
Bistability is considered wide-spread among bacteria and eukaryotic cells, useful e.g. for enzyme induction, bet hedging, and epigenetic switching. However, this phenomenon has mostly been described with deterministic dynamic or well-mixed…
The dynamic stability of the Boolean networks representing a model for the gene transcriptional regulation (Kauffman model) is studied by calculating analytically and numerically the Hamming distance between two evolving configurations.…
Cellular transformations which involve a significant phenotypical change of the cell's state use bistable biochemical switches as underlying decision systems. In this work, we aim at linking cellular decisions taking place on a time scale…
Boolean networks have been proposed as potentially useful models for genetic control. An important aspect of these networks is the stability of their dynamics in response to small perturbations. Previous approaches to stability have assumed…
We study molecular dynamics within populations of diffusively coupled cells under the assumption of fast diffusive exchange. As a technical tool, we propose conditions on boundedness and ultimate boundedness for systems with a singular…
Probabilistic Boolean Networks have been proposed for estimating the behaviour of dynamical systems as they combine rule-based modelling with uncertainty principles. Inferring PBNs directly from gene data is challenging however, especially…
Biofilament-motor protein complexes are ubiquitous in biology and drive the transport of cargo vital for many fundamental cellular processes. As they move, motor proteins exert compressive forces on the filaments to which they are attached,…
An evolving yeast colony is simulated by means of a cellular automaton that takes care of many important features of the system under study. A complete survey of the properties of the colony is done and a set of scaling relations is found,…
Boolean networks are one of the most studied discrete models in the context of the study of gene expression. In order to define the dynamics associated to a Boolean network, there are several \emph{update schemes} that range from parallel…
Discrete dynamical systems in which model components take on categorical values have been successfully applied to biological networks to study their global dynamic behavior. Boolean models in particular have been used extensively. However,…
Boolean Networks and their dynamics are of great interest as abstract modeling schemes in various disciplines, ranging from biology to computer science. Whereas parallel update schemes have been studied extensively in past years, the level…
Gene regulatory network of lambda phage is one the best studied model systems in molecular biology. More 50 years of experimental study has provided a tremendous amount of data at all levels: physics, chemistry, DNA, protein, and function.…