Related papers: Compensatory interactions to stabilize multiple st…
Many biological systems, such as metabolic pathways, exhibit bistability behavior: these biological systems exhibit two distinct stable states with switching between the two stable states controlled by certain conditions. Since…
We consider multiple diseases spreading in a static Configuration Model network. We make standard assumptions that infection transmits from neighbor to neighbor at a disease-specific rate and infected individuals recover at a…
We analyse the equilibrium behaviour and non-equilibrium dynamics of sparse Boolean networks with self-interactions that evolve according to synchronous Glauber dynamics. Equilibrium analysis is achieved via a novel application of the…
Complex network theory provides a unifying framework for the study of structured dynamic systems. The current literature emphasizes a widely reported phenomenon of intermittent interaction among network vertices. In this paper, we introduce…
Simple nonlinear dynamical systems with multiple stable stationary states are often taken as models for switchlike biological systems. This paper considers the interaction of multiple such simple multistable systems when they are embedded…
We present a new experimental-computational technology of inferring network models that predict the response of cells to perturbations and that may be useful in the design of combinatorial therapy against cancer. The experiments are…
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…
Recently we have used a cellular automata model which describes the dynamics of a multi-connected network to reproduce the refractory behavior and aging effects obtained in immunization experiments performed with mice when subjected to…
This paper presents an algorithm for approximating certain types of dynamical systems given by a system of ordinary delay differential equations by a Boolean network model. Often Boolean models are much simpler to understand than complex…
Boolean networks have been the object of much attention, especially since S. Kauffman proposed them in the 1960's as models for gene regulatory networks. These systems are characterized by being defined on a Boolean state space and by…
Methods of modeling cellular regulatory networks as diverse as differential equations and Boolean networks co-exist, however, without any closer correspondence to each other. With the example system of the fission yeast cell cycle control…
Discrete dynamical systems in which model components take on categorical values have been successfully applied to biological networks to study their global dynamic behavior. Boolean models in particular have been used extensively. However,…
We present a systematic mathematical analysis of the qualitative steady-state response to rate perturbations in large classes of reaction networks. This includes multimolecular reactions and allows for catalysis, enzymatic reactions,…
The stability of Boolean networks has attracted much attention due to its wide applications in describing the dynamics of biological systems. During the past decades, much effort has been invested in unveiling how network structure and…
The paper examines the discrete-time dynamics of neuron models (of excitatory and inhibitory types) with piecewise linear activation functions, which are connected in a network. The properties of a pair of neurons (one excitatory and the…
In this paper we study the dynamical behavior of Boolean networks with firing memory, namely Boolean networks whose vertices are updated synchronously depending on their proper Boolean local transition functions so that each vertex remains…
Complex systems are characterized by many interacting units that give rise to emergent behavior. A particularly advantageous way to study these systems is through the analysis of the networks that encode the interactions among the system's…
Cellular mechanism-of-action is of fundamental concern in many biological studies. It is of particular interest for identifying the cause of disease and learning the way in which treatments act against disease. However, pinpointing such…
In many complex systems, states and interaction structure coevolve towards a dynamic equilibrium. For the adaptive contact process, we obtain approximate expressions for the degree distributions that characterize the interaction network in…
The control of biological systems presents interesting applications such as cell reprogramming or drug target identification. A common type of control strategy consists in a set of interventions that, by fixing the values of some variables,…