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Both natural and synthetic chemical systems not only exhibit a range of non-trivial dynamics, but also transition between qualitatively different dynamical behaviours as environmental parameters change. Such transitions are called…
The chemical reaction network (CRN) is a widely used formalism to describe macroscopic behavior of chemical systems. Available tools for CRN modelling and simulation require local access, installation, and often involve local file storage,…
Molecular computation in chemical reaction networks (CRNs) now constitutes a foundational framework for designing programmable biological systems. However, prevailing design methodologies primarily treat parallelism of chemical reactions as…
Stochastic evolution of Chemical Reactions Networks (CRNs) over time is usually analysed through solving the Chemical Master Equation (CME) or performing extensive simulations. Analysing stochasticity is often needed, particularly when some…
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…
An algorithm is given in this paper for the computation of dynamically equivalent weakly reversible realizations with the maximal number of reactions, for chemical reaction networks (CRNs) with mass action kinetics. The original problem…
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…
Graph transformation systems have the potential to be realistic models of chemistry, provided a comprehensive collection of reaction rules can be extracted from the body of chemical knowledge. A first key step for rule learning is the…
Metal energy carriers recently gained growing interest in research as a promising storage and transport material for renewable electricity. Within the development of a metal-fueled circular energy economy, research involves a model…
We mathematically prove that chemical reaction networks without hidden layers can solve tasks for which spiking neural networks require hidden layers. Our proof uses the deterministic mass-action kinetics formulation of chemical reaction…
The thermodynamic and dynamical conditions necessary to observe indefinite growth in homogeneous open chemical reaction networks (CRNs) satisfying mass action kinetics were presented in Srinivas et al. (2023): Unimolecular CRNs can only…
We extend the traditional framework of steady state energy transduction -- typically characterized by a single input and output -- to multi-resource transduction in open chemical reaction networks (CRNs). Transduction occurs when…
An algorithm is given in this paper for the computation of dynamically equivalent weakly reversible realizations with the maximal number of reactions, for chemical reaction networks (CRNs) with mass action kinetics.
Similarly to gear systems in vehicles, most chemical reaction networks (CRNs) involved in energy transduction have at their disposal multiple transduction pathways, each characterized by distinct efficiencies. We conceptualize these…
In this paper we study a class of stochastic chemical reaction networks (CRNs) for which chemical species are created by a sequence of chain reactions. We prove that under some convenient conditions on the initial state, some of these…
We identify the thermodynamic conditions necessary to observe indefinite growth in homogeneous open chemical reaction networks (CRNs) satisfying mass action kinetics. We also characterize the thermodynamic efficiency of growth by…
The behavior of some stochastic chemical reaction networks is largely unaffected by slight inaccuracies in reaction rates. We formalize the robustness of state probabilities to reaction rate deviations, and describe a formal connection…
Continuous time Markov chains are commonly used as models for the stochastic behavior of chemical reaction networks. More precisely, these Stochastic Chemical Reaction Networks (SCRNs) are frequently used to gain a mechanistic understanding…
Well-mixed chemical reaction networks (CRNs) contain many distinct chemical species with copy numbers that fluctuate in correlated ways. While those correlations are typically monitored via Monte Carlo sampling of stochastic trajectories,…
In this paper, a new fractional step method is proposed for simulating stiff and nonstiff chemically reacting flows. In stiff cases, a well-known spurious numerical phenomenon, i.e. the incorrect propagation speed of discontinuities, may be…