相关论文: Sign patterns for chemical reaction networks
We investigate a broad family of chemical reaction networks (CRNs) assigned with mass action kinetics, called complex-balanced-produced-CRNs (CBP-CRNs), which are generated by any given complex balanced mass action system (MAS) and whose…
We consider linear elimination of variables in steady state equations of a chemical reaction network. Particular subsets of variables corresponding to sets of so-called reactant-noninteracting species, are introduced. The steady state…
We present three examples of chemical reaction networks whose ordinary differential equation scaling limit are almost identical and in all cases stable. Nevertheless, the Markov jump processes associated to these reaction networks display…
Reaction Systems (RSs) are a successful computational framework inspired by biological systems. A RS pairs a set of entities with a set of reactions over them. Entities can be used to enable or inhibit each reaction, and are produced by…
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…
In an equilibrium chemical reaction mixture, the number of molecules present obeys a Poisson distribution. We ask when the same is true of the steady state of a nonequilibrium reaction network and obtain an essentially complete answer. In…
A stochastic model for a chemical reaction network is embedded in a one-parameter family of models with species numbers and rate constants scaled by powers of the parameter. A systematic approach is developed for determining appropriate…
Reaction networks are a general framework widely used in modeling diverse phenomena in different science disciplines. The dynamical process of a reaction network endowed with mass-action kinetics is a mass-action system as an ODE defined by…
Chemical Reaction Neural Networks (CRNNs) have emerged as an interpretable machine learning framework for discovering reaction kinetics directly from data, while strictly adhering to the Arrhenius and mass action laws. However, standard…
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…
This article presents and discusses in detail the results of extensive exact calculations of the most basic ingredients of spin networks, the Racah coefficients (or Wigner 6j symbols), exhibiting their salient features when considered as a…
Chemical reaction network theory is a field of applied mathematics concerned with modeling chemical systems, and can be used in other contexts such as in systems biology to study cellular signaling pathways or epidemiology to study the…
In chemical reaction networks (CRNs) with stochastic semantics based on continuous-time Markov chains (CTMCs), the typically large populations of species cause combinatorially large state spaces. This makes the analysis very difficult in…
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…
A decomposition of a chemical reaction network (CRN) is produced by partitioning its set of reactions. The partition induces networks, called subnetworks, that are "smaller" than the given CRN which, at this point, can be called parent…
We present a uniform method for translating an arbitrary nondeterministic finite automaton (NFA) into a deterministic mass action input/output chemical reaction network (I/O CRN) that simulates it. The I/O CRN receives its input as a…
We present a differentiable formulation of abstract chemical reaction networks (CRNs) that can be trained to solve a variety of computational tasks. Chemical reaction networks are one of the most fundamental computational substrates used by…
We consider reaction networks that admit a singular perturbation reduction in a certain parameter range. The focus of this paper is on deriving "small parameters" (briefly for small perturbation parameters), to gauge the accuracy of the…
Chemical reaction networks (CRNs) are prototypical complex systems because reactions are nonlinear and connected in intricate ways, and they are also essential to understand living systems. Here, I discuss how recent developments in…
Many dynamical systems arising in biology and other areas exhibit multistationarity (two or more positive steady states with the same conserved quantities). Although deciding multistationarity for a polynomial dynamical system is an…