相关论文: Boolean network model predicts cell cycle sequence…
Asynchronous Boolean networks are a type of discrete dynamical system in which each variable can take one of two states, and a single variable state is updated in each time step according to pre-selected rules. Boolean networks are popular…
Applying the mathematical circulation theory of Markov chains, we investigate the synchronized stochastic dynamics of a discrete network model of yeast cell-cycle regulation where stochasticity has been kept rather than being averaged out.…
Gene regulatory networks exhibit remarkable stability, maintaining functional phenotypes despite genetic and environmental perturbations. Discrete dynamical models, such as Boolean networks, provide systems biologists with a tractable…
This paper investigates the stabilization of probabilistic Boolean networks (PBNs) via a novel pinning control strategy based on network structure. In a PBN, the evolution equation of each gene switches among a collection of candidate…
We study time continuous branching processes with exponentially distributed lifetimes, with two types of cells that proliferate according to binary fission. A range of possible system dynamics are considered, each of which is characterized…
Because the attractors of biological networks reflect stable behaviors (e.g., cell phenotypes), identifying control interventions that can drive a system towards its attractors (attractor control) is of particular relevance when controlling…
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…
Many discrete models of biological networks rely exclusively on Boolean variables and many tools and theorems are available for analysis of strictly Boolean models. However, multilevel variables are often required to account for threshold…
Regulatory networks (RNs) are a well-accepted modelling formalism in computational systems biology. The control of RNs is currently receiving a lot of attention because it provides a computational basis for cell reprogramming -- an…
Complex dynamical systems are often modeled as networks, with nodes representing dynamical units which interact through the network's links. Gene regulatory networks, responsible for the production of proteins inside a cell, are an example…
A new kind of cellular automaton (CA) for the study of the dynamics of urban systems is proposed. The state of a cell is not described using a finite set, but by means of continuum variables. A population sector is included, taking into…
To explain the differentiation of stem cells in terms of dynamical systems theory, models of interacting cells with intracellular protein expression dynamics are analyzed and simulated. Simulations were carried out for all possible protein…
The true slime mold \textit{Physarum polycephalum} has the remarkable capability to perform self-organized activities such as network formation among food sources. Despite well reproducing the emergence of slime networks, existing models…
Tumorigenic transformation of human epithelial cells in vitro has been described experimentally as the potential result of a process known as spontaneous immortalization. In this process a generic series of cell state transitions occur in…
Living cells exhibit a complex organization comprising numerous compartments, among which are RNA- and protein-rich membraneless, liquid-like organelles known as biomolecular condensates. Energy-consuming processes regulate their formation…
Biological networks such as gene regulatory networks possess desirable properties. They are more robust and controllable than random networks. This motivates the search for structural and dynamical features that evolution has incorporated…
Boolean networks, first developed in the late 1960s as a tool for studying complex disordered dynamical systems, consist of nodes governed by Boolean functions whose evolution is entirely deterministic in that the state of the network at a…
The determination and classification of fixed points of large Boolean networks is addressed in terms of constraint satisfaction problem. We develop a general simplification scheme that, removing all those variables and functions belonging…
In this paper, we consider a flocculation model in a chemostat where one species is present in two forms: planktonic and aggregated bacteria with the presence of a single resource. The removal rates of isolated and attached bacteria are…
Active fluid transport is a hallmark of many biological transport networks. While animal circulatory systems generally rely on a single heart to drive flows, other organisms employ decentralized local pumps to distribute fluids and…