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

To what extent do the characteristic features of a chemical reaction network reflect its purpose and function? In general, one argues that correlations between specific features and specific functions are key to understanding a complex…

Chemical reaction networks in living cells maintain precise control over thousands of metabolites despite operating far from equilibrium under constant perturbations. While mass action kinetics accurately describe the underlying dynamics,…

Analyzing qualitative behaviors of biochemical reactions using its associated network structure has proven useful in diverse branches of biology. As an extension of our previous work, we introduce a graph-based framework to calculate steady…

Chemical reaction networks (CRNs) exhibit complex dynamics governed by their underlying network structure. In this paper, we propose a novel approach to study the dynamics of CRNs by representing them on species graphs (S-graphs). By…

Many physical systems--from mechanical lattices and electrical circuits to biological tissues and architected metamaterials--can be understood as networks transmitting physical quantities. We present a unified mathematical framework for…

We provide a new decomposition of the Laplacian matrix (for labeled directed graphs with strongly connected components), involving an invertible $\textit{core matrix}$, the vector of tree constants, and the incidence matrix of an auxiliary…

In this paper, we provide a graphic formulation of non-isothermal reaction systems and show that a non-isothermal detailed balanced network system converges (locally) asymptotically to the unique equilibrium within the invariant manifold…

Within a fully microscopic setting, we derive a variational principle for the non-equilibrium steady states of chemical reaction networks, valid for time-scales over which chemical potentials can be taken to be slowly varying: at…

Very often, models in biology, chemistry, physics, and engineering are systems of polynomial or power-law ordinary differential equations, arising from a reaction network. Such dynamical systems can be generated by many different reaction…

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,…

A reaction network is a chemical system involving multiple reactions and chemical species. Stochastic models of such networks treat the system as a continuous time Markov chain on the number of molecules of each species with reactions as…

We further clarify the relation between detailed-balanced and complex-balanced equilibria of reversible chemical reaction networks. Our results hold for arbitrary kinetics and also for boundary equilibria. Detailed balance, complex balance,…

It has recently been shown that structural conditions on the reaction network, rather than a 'fine-tuning' of system parameters, often suffice to impart 'absolute concentration robustness' on a wide class of biologically relevant,…

We present a simple model of network dynamics that can be solved analytically for uniform networks. We obtain the dynamics of response of the system to perturbations. The analytical solution is an excellent approximation for random…

With an increasing amount of observations on the dynamics of many complex systems, it is required to reveal the underlying mechanisms behind these complex dynamics, which is fundamentally important in many scientific fields such as climate,…

The graph-related symmetries of a reaction network give rise to certain special equilibria (such as complex balanced equilibria) in deterministic models of dynamics of the reaction network. Correspondingly, in the stochastic setting, when…

It has been recently observed that the dynamical properties of mass action systems arising from many models of biochemical reaction networks can be derived by considering the corresponding properties of a related generalized mass action…

We propose a unified framework that allows for the full mechanistic reconstruction of chemical reaction networks (CRNs) from concentration data. The framework utilizes an integral formulation of the differential equations governing the…

This paper develops the concept of decomposition for chemical reaction networks, based on which a network decomposition technique is proposed to capture the stability of large-scale networks characterized by a high number of species, high…

The analysis of non-equilibrium steady states of biochemical reaction networks relies on finding the configurations of fluxes and chemical potentials satisfying stoichiometric (mass balance) and thermodynamic (energy balance) constraints.…