Related papers: Recursive Self-Composite Approach Towards Structur…
Complex networks are an important paradigm of modern complex systems sciences which allows quantitatively assessing the structural properties of systems composed of different interacting entities. During the last years, intensive efforts…
Boolean networks are discrete dynamical systems where each automaton has its own Boolean function for computing its state according to the configuration of the network. The updating mode then determines how the configuration of the network…
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…
We realize autonomous Boolean networks by using logic gates in their autonomous mode-of-operation on a field-programmable gate array. This allows us to implement time-continuous systems with complex dynamical behaviors that can be…
Due to the scarcity of quantitative details about biological phenomena, quantitative modeling in systems biology can be compromised, especially at the subcellular scale. One way to get around this is qualitative modeling because it requires…
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…
The relationship between the properties of a dynamical system and the structure of its defining equations has long been studied in many contexts. Here we study this problem for the class of conjunctive (resp. disjunctive) Boolean networks,…
The regulation of the cell state is a complex process involving several components. These complex dynamics can be modeled using Boolean networks, allowing us to explain the existence of different cell states and the transition between them.…
Boolean networks are discrete dynamical systems in which the state (zero or one) of each node is updated at each time t to a state determined by the states at time t-1 of those nodes that have links to it. When these systems are used to…
In automata networks, it is well known that the way entities update their states over time has a major impact on their dynamics. In particular, depending on the chosen update schedule, the underlying dynamical systems may exhibit more or…
It is an increasingly important problem to study conditions on the structure of a network that guarantee a given behavior for its underlying dynamical system. In this paper we report that a Boolean network may fall within the chaotic…
We study classes of dynamical systems that can be obtained by constructing recursive networks with monotone Boolean functions. Stack filters in nonlinear signal processing are special cases of such systems. We show an analytical connection…
We construct and investigate Boolean networks that follow a given reliable trajectory in state space, which is insensitive to fluctuations in the updating schedule, and which is also robust against noise. Robustness is quantified as the…
Boolean threshold networks have recently been proposed as useful tools to model the dynamics of genetic regulatory networks, and have been successfully applied to describe the cell cycles of \textit{S. cerevisiae} and \textit{S. pombe}.…
Boolean networks have been successfully used in modelling gene regulatory networks. In this paper we propose a reduction method that reduces the complexity of a Boolean network but keeps dynamical properties and topological features and…
A logical function can be used to characterizing a property of a state of Boolean network (BN), which is considered as an aggregation of states. To illustrate the dynamics of a set of logical functions, which characterize our concerned…
Despite the large quantity of information available, thorough researches in various biological databases are still needed in order to reconstruct and understand the steps that lead to known or new phenomena. By using protein-protein…
The recent discovery of universal principles underlying many complex networks occurring across a wide range of length scales in the biological world has spurred physicists in trying to understand such features using techniques from…
As a discrete approach to genetic regulatory networks, Boolean models provide an essential qualitative description of the structure of interactions among genes and proteins. Boolean models generally assume only two possible states…
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…