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Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, since precise information on the molecular composition, the dominant reaction chemistry, and the conditions for that…
The most fundamental abstraction underlying all modern computers is the Turing Machine, that is if any modern computer can simulate a Turing Machine, an equivalence which is called Turing completeness, it is theoretically possible to…
The concept of input-independent computational time for chemistry-based analog computers was introduced in Anderson-Joshi (2025), where it was shown that arithmetic operations can be computed in a fixed time independent of the input values.…
Reaction networks (RNs) comprise a set $X$ of species and a set $\mathscr{R}$ of reactions $Y\to Y'$, each converting a multiset of educts $Y\subseteq X$ into a multiset $Y'\subseteq X$ of products. RNs are equivalent to directed…
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…
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,…
Some results are presented on how oscillation is inherited by chemical reaction networks (CRNs) when they are built in natural ways from smaller oscillatory networks. The main results describe four important ways in which a CRN can be…
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 use of mathematical models has helped to shed light on countless phenomena in chemistry and biology. Often, though, one finds that systems of interest in these fields are dauntingly complex. In this paper, we attempt to synthesize and…
Step Chemical Reaction Networks (step CRNs) are an augmentation of the Chemical Reaction Network (CRN) model where additional species may be introduced to the system in a sequence of ``steps.'' We study step CRN systems using a weak subset…
The ability to reason beyond established knowledge allows Organic Chemists to solve synthetic problems and to invent novel transformations. Here, we propose a model which mimics chemical reasoning and formalises reaction prediction as…
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…
The nonlinearities found in molecular networks usually prevent mathematical analysis of network behaviour, which has largely been studied by numerical simulation. This can lead to difficult problems of parameter determination. However,…
Autocatalysis is an important feature of metabolic networks, contributing crucially to the self-maintenance of organisms. Autocatalytic subsystems of chemical reaction networks (CRNs) are characterized in terms of algebraic conditions on…
In a reaction network, the concentration of a species with the property of dynamic absolute concentration robustness (dynamic ACR) converges to the same value independent of the overall initial values. This property endows a biochemical…
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…
We establish a generalized work theorem for stochastic chemical reaction networks (CRNs). By using a compensated Poisson jump process, we identify a martingale structure in a generalized entropy defined relative to an auxiliary backward…
Modern computational chemistry has reached a stage at which massive exploration into chemical reaction space with unprecedented resolution with respect to the number of potentially relevant molecular structures has become possible. Various…
A novel approach is presented for the solution of instantaneous chemical equilibrium problems. The chemical equilibrium can be considered, due to its intrinsically local character, as a mapping of the three-dimensional parameter space…
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…