Related papers: Interplay between degree and Boolean rules in the …
The recently measured yeast transcriptional network is analyzed in terms of simplified Boolean network models, with the aim of determining feasible rule structures, given the requirement of stable solutions of the generated Boolean…
In this paper, we consider the state controllability of networked systems, where the network topology is directed and weighted and the nodes are higher-dimensional linear time-invariant (LTI) dynamical systems. We investigate how the…
Boolean networks, first developed in the late 1960s as a tool for studying complex disordered dynamical systems, consist of nodes governed by Boolean functions whose evolution is entirely deterministic in that the state of the network at a…
The controllability of a network is a theoretical problem of relevance in a variety of contexts ranging from financial markets to the brain. Until now, network controllability has been characterized only on isolated networks, while the vast…
We investigate the dynamical behavior of simple modules composed of two genes with two or three regulating connections. Continuous dynamics for mRNA and protein concentrations is compared to a Boolean model for gene activity. Using a…
Gene regulatory networks play a crucial role in controlling an organism's biological processes, which is why there is significant interest in developing computational methods that are able to extract their structure from high-throughput…
The significant role of epigenetic mechanisms within natural systems has become increasingly clear. This paper uses a recently presented abstract, tunable Boolean genetic regulatory network model to explore aspects of epigenetics. It is…
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…
Boolean automata networks (aka Boolean networks) are space-time discrete dynamical systems, studied as a model of computation and as a representative model of natural phenomena. A collection of simple entities (the automata) update their…
Boolean networks (BNs) are discrete-time systems where nodes are inter-connected (here we call such connection rule among nodes as network structure), and the dynamics of each gene node is determined by logical functions. In this paper, we…
Identifying an optimal set of driver nodes to achieve synchronization via pinning control is a fundamental challenge in complex network science, limited by computational intractability and the lack of general theory. Here, leveraging a…
Turing instability in complex networks have been shown in the literature to be dominated by the distribution of the nodal degrees. The conditions for Turing instability have been derived with an explicit dependence on the eigenvalues of the…
We study the synchronizability and the synchronization dynamics of networks of nonlinear oscillators. We investigate how the synchronization of the network is influenced by some of its topological features such as variations of the power…
We present exact analysis of the physical properties of bimodal networks specified by the two peak degree distribution fully incorporating the degree-degree correlation between node connection. The structure of the correlated bimodal…
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…
The cooperative behavior of neurons and neuronal areas associated with the synchronization behavior proves to be a fundamental neural mechanism. In addition, abnormal levels of synchronization have been related to unhealthy neural…
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…
Many discrete models of biological networks rely exclusively on Boolean variables and many tools and theorems are available for analysis of strictly Boolean models. However, multilevel variables are often required to account for threshold…
Random boolean cellular automata are investigated, where each gate has two randomly chosen inputs and is randomly assigned a boolean function of its inputs. The effect of non-uniform distributions on the choice of the boolean functions is…
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…