相关论文: Positive and negative cycles in Boolean networks

Biological networks such as gene regulatory networks possess desirable properties. They are more robust and controllable than random networks. This motivates the search for structural and dynamical features that evolution has incorporated…

Random Boolean networks, originally invented as models of genetic regulatory networks, are simple models for a broad class of complex systems that show rich dynamical structures. From a biological perspective, the most interesting networks…

Boolean networks, widely used to model gene regulation, exhibit a phase transition between regimes in which small perturbations either die out or grow exponentially. We show and numerically verify that this phase transition in the dynamics…

A dynamic logic method was developed to analyze molecular networks of cells by combining Kauffman and Thomas's logic operations with molecular interaction parameters. The logic operations characterize the discrete interactions between…

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…

Links in many real-world networks activate and deactivate in correspondence to the sporadic interactions between the elements of the system. The activation patterns may be irregular or bursty and play an important role on the dynamics of…

Boolean networks (BNs) are widely used to model the qualitative dynamics of biological systems. Besides the logical rules determining the evolution of each component with respect to the state of its regulators, the scheduling of component…

Biological cells encode information about their environment through biochemical signaling networks that control their internal state and response. This information is often encoded in the dynamical patterns of the signaling molecules,…

We study asymptotic dynamical patterns that emerge among a set of nodes that interact in a dynamically evolving signed random network. Node interactions take place at random on a sequence of deterministic signed graphs. Each node receives…

The last decade has witnessed a surge of theoretical and computational models to describe the dynamics of complex gene regulatory networks, and how these interactions can give rise to multistable and heterogeneous cell populations. As the…

In many natural synchronization phenomena, communication between individual elements occurs not directly, but rather through the environment. One of these instances is bacterial quorum sensing, where bacteria release signaling molecules in…

Networks of globally coupled, noise activated, bistable elements with connection time delays are considered. The dynamics of these systems is studied numerically using a Langevin description and analytically using (1) a Gaussian…

Gene regulatory networks (GRNs) play a central role in cellular decision-making. Understanding their structure and how it impacts their dynamics constitutes thus a fundamental biological question. GRNs are frequently modeled as Boolean…

We prove that the fully asynchronous dynamics of a Boolean network $f:\{0,1\}^n\to\{0,1\}^n$ without negative loop can be simulated, in a very specific way, by a monotone Boolean network with $2n$ components. We then use this result to…

Traditional percolation theory assumes static microscopic rules, limiting its ability to describe real-world complex systems where macroscopic order actively regulates local interactions. Here, we introduce feedback percolation, an unified…

In this work we consider random Boolean networks that provide a general model for genetic regulatory networks. We extend the analysis of James Lynch who was able to proof Kauffman's conjecture that in the ordered phase of random networks,…

Widespread deployment of societal-scale machine learning systems necessitates a thorough understanding of the resulting long-term effects these systems have on their environment, including loss of trustworthiness, bias amplification, and…

Boolean networks with canalizing functions are used to model gene regulatory networks. In order to learn how such networks may behave under evolutionary forces, we simulate the evolution of a single Boolean network by means of an adaptive…

Mounting evidence shows that oscillatory activity is widespread in cell signaling. Here we review some of this recent evidence, focusing on both the molecular mechanisms that potentially underlie such dynamical behavior, and the potential…

A quantum theory of feedback of bosonic many-atom systems is formulated. The feedback-induced many-atom correlations are treated by use of a parameterized correlation function, for which closed equations of motion are derived. Therefrom the…