相关论文: Determining the Equivalence of Small Zero-one Reac…
We give an simple criterion for ODE equivalence in identical edge homogeneous coupled cell networks. This allows us to give a simple proof of Theorem 10.3 of Aquiar and Dias "Minimal Coupled Cell Networks", which characterizes minimal…
The metabolic network of a living cell involves several hundreds or thousands of interconnected biochemical reactions. Previous research has shown that under realistic conditions only a fraction of these reactions is concurrently active in…
In systems and synthetic biology, much research has focused on the behavior and design of single pathways, while, more recently, experimental efforts have focused on how cross-talk (coupling two or more pathways) or inhibiting molecular…
In a recent paper it was shown that, for chemical reaction networks possessing a subtle structural property called concordance, dynamical behavior of a very circumscribed (and largely stable) kind is enforced, so long as the kinetics lies…
Biochemical reaction networks are widely applied across scientific disciplines to model complex dynamic systems. We investigate the diffusion approximation of reaction networks with mass-action kinetics, focusing on the identifiability of…
We consider a chemical reaction network governed by mass action kinetics and composed of N different species which can reversibly form heterodimers. A fast iterative algorithm is introduced to compute the equilibrium concentrations of such…
Bistability plays a central role in the gene regulatory networks (GRNs) controlling many essential biological functions, including cellular differentiation and cell cycle control. However, establishing the network topologies that can…
We compare reaction-diffusion processes of the $A+A\to 0$ type on scale-free networks created with either the configuration model or the uncorrelated configuration model. We show via simulations that except for the difference in the…
This paper focuses on computing the frequency response and transfer functions for large self-similar networks under different circumstances. Modeling large scale systems is difficult due, typically, to the dimension of the problem, and…
We study the problem of computing outer bounds for the region of steady states of biochemical reaction networks modelled by ordinary differential equations, with respect to parameters that are allowed to vary within a predefined region.…
Network inference approaches are widely used to shed light on regulatory interplay between molecular players such as genes and proteins. Biochemical processes underlying networks of interest (e.g. gene regulatory or protein signalling…
We introduce the notion of corresponding a chemical reaction network to a split network translation, and use this novel process to extend the scope of existing network-based theory for characterizing the steady state set of mass-action…
Detailed balance of a chemical reaction network can be defined in several different ways. Here we investigate the relationship among four types of detailed balance conditions: deterministic, stochastic, local, and zero-order local detailed…
This work addresses whether a reaction network, taken with mass-action kinetics, is multistationary, that is, admits more than one positive steady state in some stoichiometric compatibility class. We build on previous work on the effect…
The ability to detect whether a species (or dimension) is zero in Chemical Reaction Networks (CRN), Vector Addition Systems, or Petri Nets is known to increase the power of these models -- making them capable of universal computation. While…
Chemical reaction systems are dynamical systems that arise in chemical engineering and systems biology. In this work, we consider the question of whether the minimal (in a precise sense) multistationary chemical reaction networks, which we…
Deficiency zero is an important network structure and has been the focus of many celebrated results within reaction network theory. In our previous paper \textit{Prevalence of deficiency zero reaction networks in an Erd\H os-R\'enyi…
The stability (or instability) of synchronization is important in a number of real world systems, including the power grid, the human brain and biological cells. For identical synchronization, the synchronizability of a network, which can…
Steady states are frequently used to investigate the long-term behaviors of (bio)-chemical systems. Recently, there has been a growing interest in network-based approaches due to their efficiency in deriving parametrizations of positive…
This paper analyses of a stochastic model of a chemical reaction network with three types of chemical species ${\cal R}$, ${\cal M}$ and ${\cal U}$ that interact to transform a flow of external resources, the chemical species ${\cal Q}$, to…