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Much of the theory on chemical-reaction networks (CRNs) has been developed in the ideal-solution limit, where interactions between the solutes are negligible. However, there is a large variety of phenomena in biological cells and…
While the field of first-principles explorations into chemical reaction space has been continuously growing, the development of strategies for analyzing resulting chemical reaction networks (CRNs) is lagging behind. A CRN consists of…
It is useful to have complete lists of nonisomorphic chemical reaction networks (CRNs) of a given size, with or without various restrictions. One may, for example, be interested in exploring how often certain dynamical behaviours occur in…
Motivated by recent progress on the interplay between graph theory, dynamics, and systems theory, we revisit the analysis of chemical reaction networks described by mass action kinetics. For reaction networks possessing a thermodynamic…
Chemical systems are interpreted through the species they contain and the reactions they may undergo, i.e., their chemical reaction network (CRN). In spite of their central importance to chemistry, the structure of CRNs continues to be…
We examine reaction networks (CRNs) through their associated continuous-time Markov processes. Studying the dynamics of such networks is in general hard, both analytically and by simulation. In particular, stationary distributions of…
Recurrent stochastic configuration networks (RSCNs) have shown promise in modelling nonlinear dynamic systems with order uncertainty due to their advantages of easy implementation, less human intervention, and strong approximation…
Recent research into analog computing has introduced new notions of computing real numbers. Huang, Klinge, Lathrop, Li, and Lutz defined a notion of computing real numbers in real-time with chemical reaction networks (CRNs), introducing the…
The popularity of molecular computation has given rise to several models of abstraction, one of the more recent ones being Chemical Reaction Networks (CRNs). These are equivalent to other popular computational models, such as Vector…
We classify the functions $f:\mathbb{N}^2 \rightarrow \mathbb{N}$ which are stably computable by output-oblivious Stochastic Chemical Reaction Networks (CRNs), i.e., systems of reactions in which output species are never reactants. While it…
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…
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…
Magombedze and Mulder (2013) studied the gene regulatory system of \textit{Mycobacterium Tuberculosis} (\textit{Mtb}) by partitioning this into three subsystems based on putative gene function and role in dormancy/latency development. Each…
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,…
The quasi-steady-state approximation (QSSA) is a standard technique for reducing the complexity of chemical reaction networks (CRNs). The validity of any QSSA-based model is restricted to specific parameter regimes. Selecting the…
The catalytic reaction system (CRS) formalism by Hordijk and Steel is a versatile method to model autocatalytic biochemical reaction networks. It is particularly suited, and has been widely used, to study self-sustainment and…
We propose a direct optimization framework for learning reduced and sparse chemical reaction networks (CRNs) from time-series trajectory data. In contrast to widely used indirect methods-such as those based on sparse identification of…
Structures and properties of many inorganic compounds have been collected historically. However, it only covers a very small portion of possible inorganic crystals, which implies the presence of numerous currently unknown compounds. A…
Compositional disorder is common in crystal compounds. In these compounds, some atoms are randomly distributed at some crystallographic sites. For such compounds, randomness forms many non-identical independent structures. Thus, calculating…
Mass-action kinetics is frequently used in systems biology to model the behaviour of interacting chemical species. Many important dynamical properties are known to hold for such systems if they are weakly reversible and have a low…