相关论文: Linear Conjugacy of Chemical Reaction Networks
Most complex systems are nonlinear, relying on emergent behavior from interacting subsystems, often characterized by oscillatory dynamics. Collective oscillatory behavior is essential for the proper functioning of many real world systems.…
The control of complex networks is of paramount importance in areas as diverse as ecosystem management, emergency response, and cell reprogramming. A fundamental property of networks is that perturbations to one node can affect other nodes,…
The concept of limiting step gives the limit simplification: the whole network behaves as a single step. However, in its simplest form this idea is applicable only to the simplest linear cycles in steady states. For such the simplest cycles…
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…
Controllability of chemical reactions is an important problem in chemical engineering science. In control theory, analysis of the controllability of linear systems is well-founded, however the dynamics of chemical reactions is usually…
We study a family of networks of autocatalytic reactions, which we call hyperchains, that are a generalization of hypercycles. Hyperchains, and the associated dynamical system called replicator equations, are a possible mechanism for…
We consider some mathematical issues raised by the modelling of gene networks. The expression of genes is governed by a complex set of regulations, which is often described symbolically by interaction graphs. Once such a graph has been…
A dynamical system obtains a wide variety of kinetic realizations, which is advantageous for the analysis of biochemical systems. A reaction network, derived from a dynamical system, may or may not possess some properties needed for a…
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…
Mass-action chemical reaction systems are frequently used in Computational Biology. The corresponding polynomial dynamical systems are often large (consisting of tens or even hundreds of ordinary differential equations) and poorly…
We study stationary distributions in the context of stochastic reaction networks. In particular, we are interested in complex balanced reaction networks and reduction of such networks by assuming a set of species (called non-interacting…
Living organisms must respond to environmental changes. Generally, accurate and rapid responses are provided by simple, unidirectional networks that connect inputs with outputs. Besides accuracy and speed, biological responses should also…
Information thermodynamics relates the rate of change of mutual information between two interacting subsystems to their thermodynamics when the joined system is described by a bipartite stochastic dynamics satisfying local detailed balance.…
Under the assumption of mass-action kinetics, a dynamical system may be induced by several different reaction networks and/or parameters. It is therefore possible for a mass-action system to exhibit complex-balancing dynamics without being…
The emergence of self-sustaining autocatalytic networks in chemical reaction systems has been studied as a possible mechanism for modelling how living systems first arose. It has been known for several decades that such networks will form…
We show that if a chemical reaction network (CRN) admits nondegenerate (resp., linearly stable) oscillation, and we add new reversible reactions involving new species to this CRN, then the new CRN so created also admits nondegenerate…
We formulate a reduction theory that describes the response of an oscillator network as a whole to external forcing applied nonuniformly to its constituent oscillators. The phase description of multiple oscillator networks coupled weakly is…
We present an experimental system of networks of coupled non-linear chemical reactors, which we theoretically model within a reaction-diffusion framework. The networks consist of patterned arrays of diffusively coupled nanoliter-scale…
For continuous-time Markov chains and open unimolecular chemical reaction networks, we prove that any two stationary currents are linearly related upon perturbations of a single edge's transition rates, arbitrarily far from equilibrium. We…
It is becoming widely accepted that very early in the origin of life, even before the emergence of genetic encoding, reaction networks of diverse small chemicals might have manifested key properties of life, namely self-propagation and…