Related papers: Molecular Network Control Through Boolean Canaliza…
The control of complex systems is an ongoing challenge of complexity research. Recent advances using concepts of structural control deduce a wide range of control related properties from the network representation of complex systems. Here,…
Cancer forms a robust system and progresses as stages over time typically with increasing aggressiveness and worsening prognosis. Characterizing these stages and identifying the genes driving transitions between them is critical to…
Random Boolean networks (RBNs) are models of genetic regulatory networks. It is useful to describe RBNs as self-organizing systems to study how changes in the nodes and connections affect the global network dynamics. This article reviews…
Standard Random Boolean Networks display an order-disorder phase transition. We add to the standard Random Boolean Networks a disconnection rule which couples the control and order parameters. By this way, the system is driven to the…
Molecular networks guide the biochemistry of a living cell on multiple levels: its metabolic and signalling pathways are shaped by the network of interacting proteins, whose production, in turn, is controlled by the genetic regulatory…
We study experimentally the synchronization patterns in time-delayed directed Boolean networks of excitable systems. We observe a transition in the network dynamics when the refractory time of the individual systems is adjusted. When the…
Boolean networks are a valuable class of discrete dynamical systems models, but they remain fundamentally limited by their inability to capture multi-way interactions in their components. To remedy this limitation, we propose a model of…
In recent years, data-driven approaches have become increasingly pervasive across all areas of control engineering. However, the applications of data-based techniques to Boolean control networks (BCNs) are still very limited. In this paper…
Boolean networks can be viewed as functions on the set of binary strings of a given length, described via logical rules. They were introduced as dynamic models into biology, in particular as logical models of intracellular regulatory…
Molecular communication (MC) enables cooperation of spatially dispersed molecular robots through the feedback control mediated by diffusing signal molecules. However, conventional analysis frameworks for the MC channels mostly consider the…
Molecular communication is a novel approach for data transmission between miniaturized devices, especially in contexts where electrical signals are to be avoided. The communication is based on sending molecules (or other particles) at nano…
Random Boolean networks have been used widely to explore aspects of gene regulatory networks. A modified form of the model through which to systematically explore the effects of increasing the number of gene states has previously been…
Changes in an animal's behavioral state, such as arousal and movements, induce {complex modulations of the baseline input currents to sensory areas, eliciting sensory modality-specific effects. A simple computational principle explaining…
This short paper presents an abstract, tunable model of genomic structural change within the cell lifecycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include…
The dynamics of Boolean networks (the N-K model) with scale-free topology are studied here. The existence of a phase transition governed by the value of the scale-free exponent of the network is shown analytically by analyzing the overlap…
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…
In this paper we study the phase transitions of different types of Random Boolean networks. These differ in their updating scheme: synchronous, semi-synchronous, or asynchronous, and deterministic or non-deterministic. It has been shown…
The Unfolded Protein Response is the cell mechanism for maintaining the balance of properly folded proteins in the endoplasmic reticulum , the specialized cellular compartment. Although it is largely studied from a biological point of view,…
To model biological systems using networks, it is desirable to allow more than two levels of expression for the nodes and to allow the introduction of parameters. Various modeling and simulation methods addressing these needs using Boolean…
We obtain the phase diagram of random Boolean networks with nested canalizing functions. Using the annealed approximation, we obtain the evolution of the number $b_t$ of nodes with value one, and the network sensitivity $\lambda$, and we…