Related papers: Boolean Models of Bistable Biological Systems
The bittide mechanism enables logically synchronous computation across distributed systems by leveraging the continuous frame transmission inherent to wired networks such as Ethernet. Instead of relying on a global clock, bittide uses a…
A probabilistic Boolean network (PBN) is a discrete-time system composed of a collection of Boolean networks between which the PBN switches in a stochastic manner. This paper focuses on the study of quotients of PBNs. Given a PBN and an…
The tryptophan (trp) operon in E. coli codes for the proteins responsible for the synthesis of the amino acid tryptophan from chorismic acid, and has been one of the most well-studied gene networks since its discovery in the 1960s. The…
The characterization of the "most connected" nodes in static or slowly evolving complex networks has helped in understanding and predicting the behavior of social, biological, and technological networked systems, including their robustness…
Habituation - a phenomenon in which a dynamical system exhibits a diminishing response to repeated stimulations that eventually recovers when the stimulus is withheld - is universally observed in living systems from animals to unicellular…
Boolean networks are extensively applied as models of complex dynamical systems, aiming at capturing essential features related to causality and synchronicity of the state changes of components along time. Dynamics of Boolean networks…
System identification of complex and nonlinear systems is a central problem for model predictive control and model-based reinforcement learning. Despite their complexity, such systems can often be approximated well by a set of linear…
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…
Additive noise is known to produce counter-intuitive behaviors in nonlinear dynamical systems. Previously, it was shown that systems with a deterministic limit cycle can display bistable switching between metastable states in the presence…
This article presents an algorithm that allows modeling of biological networks in a qualitative framework with continuous time. Mathematical modeling is used as a systems biology tool to answer biological questions, and more precisely, to…
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…
Piecewise smooth hybrid systems, involving continuous and discrete variables, are suitable models for describing the multiscale regulatory machinery of the biological cells. In hybrid models, the discrete variables can switch on and off…
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…
Many biological systems are governed by difference equations and exhibit discrete-time dynamics. Examples include the size of a population when generations are non-overlapping, and the incidence of a disease when infections are recorded at…
Stochastic processes govern the time evolution of a huge variety of realistic systems throughout the sciences. A minimal description of noisy many-particle systems within a Markovian picture and with a notion of spatial dimension is given…
Dialectical frameworks are a unifying model of formal argumentation, where argumentative relations between arguments are represented by assigning acceptance conditions to atomic arguments. Their generality allow them to cover a number of…
Switching dynamical systems provide a powerful, interpretable modeling framework for inference in time-series data in, e.g., the natural sciences or engineering applications. Since many areas, such as biology or discrete-event systems, are…
A stochastic system where bistability is caused by noise has been recently investigated by Biancalani et al. (PRL 112:038101, 2014). They have computed the mean switching time for such a system using a continuous Fokker-Planck equation…
Living systems have time-evolving interactions that, until recently, could not be identified accurately from recorded time series in the presence of noise. Stankovski et al. (Phys. Rev. Lett. 109 024101, 2012) introduced a method based on…
Delay differential equations are used as a model when the effect of past states has to be taken into account. In this work we consider delay models of chemical reaction networks with mass action kinetics. We obtain a sufficient condition…