相关论文: Positive and negative cycles in Boolean networks

Oscillation has an important role in bio-dynamical systems such as circadian rhythms and eukaryotic cell cycle. John Tyson et. al. in Nature Review Mol Cell Biol 2008 examined a limited number of network topologies consisting of three nodes…

By incorporating feedback loops, that engender amplification and damping so that output is not proportional to input, the biological neural networks become highly nonlinear and thus very likely chaotic in nature. Research in control theory…

The molecular network in an organism consists of transcription/translation regulation, protein-protein interactions/modifications and a metabolic network, together forming a system that allows the cell to respond sensibly to the multiple…

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…

Temporal networks have been increasingly used to model a diversity of systems that evolve in time; for example human contact structures over which dynamic processes such as epidemics take place. A fundamental aspect of real-life networks is…

Boolean networks serve as discrete models of regulation and signaling in biological cells. Identifying the key controllers of such processes is important for understanding the dynamical systems and planning further analysis. Here we…

Boolean networks have been the object of much attention, especially since S. Kauffman proposed them in the 1960's as models for gene regulatory networks. These systems are characterized by being defined on a Boolean state space and by…

The presence of noise in non linear dynamical systems can play a constructive role, increasing the degree of order and coherence or evoking improvements in the performance of the system. An example of this positive influence in a biological…

Boolean networks is a well-established formalism for modelling biological systems. A vital challenge for analysing a Boolean network is to identify all the attractors. This becomes more challenging for large asynchronous Boolean networks,…

Feedback loops are major components of biochemical systems. Many systems show multiple such (positive or negative) feedback loops. Nevertheless, very few quantitative analyses address the question how such multiple feedback loops evolved.…

We investigate how elimination of variables can affect the asymptotic dynamics and phenotype control of Boolean networks. In particular, we look at the impact on minimal trap spaces, and identify a structural condition that guarantees their…

We study the target control of asynchronous Boolean networks, to identify efficacious interventions that can drive the dynamics of a given Boolean network from any initial state to the desired target attractor. Based on the application…

Recent progress in experimental techniques has enabled us to quantitatively study stochastic and flexible behavior of biological systems. For example, gene regulatory networks perform stochastic information processing and their…

We demonstrate the effects of embedding subgraphs using a Boolean network, which is one of the discrete dynamical models for transcriptional regulatory networks. After comparing the dynamical properties of network embedded seven different…

We study the target control problem of asynchronous Boolean networks, to identify a set of nodes, the perturbation of which can drive the dynamics of the network from any initial state to the desired steady state (or attractor). We are…

The theory of mixed-feedback systems provides an effective framework for the design of robust and tunable oscillations in nonlinear systems characterized by interleaved fast positive and slow negative feedback loops. The goal of this paper…

Empirical evidence has revealed that biological regulatory systems are controlled by high-level coordination between topology and Boolean rules. In this study, we study the joint effects of degree and Boolean functions on the stability of…

There are three main aims of this paper. 1- I explain reasons why I await life to lie significantly deeper in chaos than Kauffman approach does, however still in boundary area near `the edge of chaos and order'. The role of negative…

Chaos control in Random Boolean networks is implemented by freezing part of the network to drive it from chaotic to ordered phase. However, controlled nodes are only viewed as passive blocks to prevent perturbation spread. This paper…

In this paper, we consider the relationship between phase-type distributions and positive systems through practical examples. Phase-type distributions, commonly used in modelling dynamic systems, represent the temporal evolution of a set of…