相关论文: A network dynamics approach to chemical reaction n…

The induced kinetic differential equation of a reaction network endowed with mass action type kinetics is a system of polynomial differential equations. The problem studied here is: Given a polynomial differential equation, is it possible…

The detailed balance property is a fundamental property that must be satisfied in all the macroscopic systems with a well defined temperature at each point. On the other hand, many biochemical networks work in non-equilibrium conditions and…

Many real-world complex systems, such as epidemic spreading networks and ecosystems, can be modeled as networked dynamical systems that produce multivariate time series. Learning the intrinsic dynamics from observational data is pivotal for…

Determining the relative importance of nodes in directed networks is important in, for example, ranking websites, publications, and sports teams, and for understanding signal flows in systems biology. A prevailing centrality measure in this…

The influence of networks topology on collective properties of dynamical systems defined upon it is studied in the thermodynamic limit. A network model construction scheme is proposed where the number of links, the average eccentricity and…

Inferring network topology from dynamical observations is a fundamental problem pervading research on complex systems. Here, we present a simple, direct method to infer the structural connection topology of a network, given an observation…

The design and synthesis of complex and large mimicked biochemical networks de novo is an unsolved problem in synthetic biology. To address this limitation without resorting to ad hoc computations and experiments, a predictive mathematical…

The process of genetic recombination can be seen as a chemical reaction network with mass-action kinetics. We review the known results on existence, uniqueness, and global stability of an equilibrium in every compatibility class and for all…

Many sociological networks, as well as biological and technological ones, can be represented in terms of complex networks with a heterogeneous connectivity pattern. Dynamical processes taking place on top of them can be very much influenced…

The equilibration of enzyme and complex concentrations in deterministic Michaelis-Menten reaction networks underlies the hyperbolic dependence between the input (substrates) and output (products). This relationship was first obtained by…

The construction of a reaction network containing all relevant intermediates and elementary reactions is necessary for the accurate description of chemical processes. In the case of a complex chemical reaction (involving, for instance, many…

The formation and regulation of macromolecular complexes provides the backbone of most cellular processes, including gene regulation and signal transduction. The inherent complexity of assembling macromolecular structures makes current…

Cataloging the complex behaviors of dynamical systems can be challenging, even when they are well-described by a simple mechanistic model. If such a system is of limited analytical tractability, brute force simulation is often the only…

Here we present the entropic dynamics formalism for networks. That is, a framework for the dynamics of graphs meant to represent a network derived from the principle of maximum entropy and the rate of transition is obtained taking into…

The use of mathematical models has helped to shed light on countless phenomena in chemistry and biology. Often, though, one finds that systems of interest in these fields are dauntingly complex. In this paper, we attempt to synthesize and…

We propose to model the dynamics of metabolic networks from a systems biology point of view by four dynamical structure elements: potential function, transverse matrix, degradation matrix, and stochastic force. These four elements are…

We derive a simple sufficient condition for the local asymptotic stability of spatially discrete, continuous-time reaction-diffusion systems of networked dynamical systems at a homogeneous equilibrium point. The framework explicitly…

Mays celebrated theoretical work of the 70s contradicted the established paradigm by demonstrating that complexity leads to instability in biological systems. Here Mays random-matrix modelling approach is generalized to realistic…

We study a non-linear dynamical system on networks inspired by the pitchfork bifurcation normal form. The system has several interesting interpretations: as an interconnection of several pitchfork systems, a gradient dynamical system and…

Key insights in molecular biology, such as enzyme kinetics, protein allostery and gene regulation emerged from quantitative analysis based on time-scale separation, allowing internal complexity to be eliminated and resulting in the…