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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,…

We delve into growing open chemical reaction systems (CRSs) characterized by autocatalytic reactions within a variable volume, which changes in response to these reactions. Understanding the thermodynamics of such systems is crucial for…

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…

Convergence of solutions to a partially diffusive chemotaxis system with indirect signal production and phenotype switching is shown in a two-dimensional setting when the switching rate increases to infinity, thereby providing a rigorous…

A class of chemical reaction networks is described with the property that each positive equilibrium is locally asymptotically stable relative to its stoichiometry class, an invariant subspace on which it lies. The reaction systems treated…

Causal discovery is challenging in general dynamical systems because, without strong structural assumptions, the underlying causal graph may not be identifiable even from interventional data. However, many real-world systems exhibit…

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…

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…

The rigorous asymptotics from reaction-cross-diffusion systems for three species with known entropy to cross-diffusion systems for two variables is investigated. The equations are studied in a bounded domain with no-flux boundary…

Reaction networks taken with mass-action kinetics arise in many settings, from epidemiology to population biology to systems of chemical reactions. Bistable reaction networks are posited to underlie biochemical switches, which motivates the…

Complex chemical reaction networks, which underlie many industrial and biological processes, often exhibit non-monotonic changes in chemical species concentrations, typically described using nonlinear models. Such non-monotonic dynamics are…

Experiments with networks of discrete reactive bistable electrochemical elements organized in regular and nonregular tree networks are presented to confirm an alternative to the Turing mechanism for the formation of self-organized…

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…

Reaction and retrosynthesis prediction are fundamental tasks in computational chemistry that have recently garnered attention from both the machine learning and drug discovery communities. Various deep learning approaches have been proposed…

Universal intermittent dynamics in a random catalytic reaction network, induced by smallness in the molecule number is reported. Stochastic simulations for a random catalytic reaction network subject to a flow of chemicals show that the…

In the setting of stochastic dynamical systems that eventually go extinct, the quasi-stationary distributions are useful to understand the long-term behavior of a system before evanescence. For a broad class of applicable continuous-time…

Machine learning models that predict the feasibility of chemical reactions have become central to automated synthesis planning. Despite their predictive success, these models often lack transparency and interpretability. We introduce a…

According to contemporary views, equilibrium constant is relevant only to true thermodynamic equilibria in isolated systems with one chemical reaction. The paper presents a novel formula that ties-up equilibrium constant and chemical system…

Chemical reactions occur in energy, environmental, biological, and many other natural systems, and the inference of the reaction networks is essential to understand and design the chemical processes in engineering and life sciences. Yet,…

Enzyme catalysis in reactors for industrial applications usually require an external intervention of the species involved in the chemical reactions. We analyze the most elementary open enzyme catalysis with competitive inhibition where a…