Related papers: Creation of fixed points in block-parallel Boolean…
The two most fundamental processes describing change in biology, development and evolu-tion, occur over drastically different timescales, difficult to reconcile within a unified framework. Development involves temporal sequences of cell…
Dynamical Systems is a field that studies the collective behavior of objects that update their states according to some rules. Discrete-time Boolean Finite Dynamical System (DT-BFDS) is a subfield where the systems have some finite number…
Consider a distributed task where the communication network is fixed but the local inputs given to the nodes of the distributed system may change over time. In this work, we explore the following question: if some of the local inputs…
Various strategies are available to construct iteratively a common fixed point of nonexpansive operators by activating only a block of operators at each iteration. In the more challenging class of composite fixed point problems involving…
Interacting biological systems at all organizational levels display emergent behavior. Modeling these systems is made challenging by the number and variety of biological components and interactions (from molecules in gene regulatory…
The structure of the graph defined by the interactions in a Boolean network can determine properties of the asymptotic dynamics. For instance, considering the asynchronous dynamics, the absence of positive cycles guarantees the existence of…
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…
We present a rigorous mathematical framework for analyzing dynamics of a broad class of Boolean network models. We use this framework to provide the first formal proof of many of the standard critical transition results in Boolean network…
Boolean automata networks (BANs) are a generalisation of Boolean cellular automata. In such, any theorem describing the way BANs compute information is a strong tool that can be applied to a wide range of models of computation. In this…
In this work we show that given a nonlinear programming problem, it is possible to construct a family of dynamical systems defined on the feasible set of the given problem, so that: (a) the equilibrium points are the unknown critical points…
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…
Dynamical systems theory and complexity science provide powerful tools for analysing artificial agents and robots. Furthermore, they have been recently proposed also as a source of design principles and guidelines. Boolean networks are a…
A complete classification of the computational complexity of the fixed-point existence problem for boolean dynamical systems, i.e., finite discrete dynamical systems over the domain {0, 1}, is presented. For function classes F and graph…
The co-evolution of network topology and dynamics is studied in an evolutionary Boolean network model that is a simple model of gene regulatory network. We find that a critical state emerges spontaneously resulting from interplay between…
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…
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.…
We demonstrate theoretically and experimentally that excitable systems can be built with autonomous Boolean networks. Their experimental implementation is realized with asynchronous logic gates on a reconfigurabe chip. When these excitable…
We investigate the renormalization group flows and fixed point structure of many coupled minimal models. The models are coupled two by two by energy-energy couplings. We take the general approach where the bare couplings are all taken to be…
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…
We investigate how classifiers for Boolean networks (BNs) can be constructed and modified under constraints. A typical constraint is to observe only states in attractors or even more specifically steady states of BNs. Steady states of BNs…