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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…
Chemical reaction networks (CRNs) model the behavior of molecules in a well-mixed system. The emerging field of molecular programming uses CRNs not only as a descriptive tool, but as a programming language for chemical computation.…
Across many disciplines, chemical reaction networks (CRNs) are an established population model defined as a system of coupled nonlinear ordinary differential equations. In many applications, for example, in systems biology and epidemiology,…
Chemical reaction networks (CRNs) model systems where molecules interact according to a finite set of reactions such as $A + B \to C$, representing that if a molecule of $A$ and $B$ collide, they disappear and a molecule of $C$ is produced.…
Chemical reaction networks (CRN) comprise an important class of models to understand biological functions such as cellular information processing, the robustness and control of metabolic pathways, circadian rhythms, and many more. However,…
We analyze the computational complexity of basic reconfiguration problems for the recently introduced surface Chemical Reaction Networks (sCRNs), where ordered pairs of adjacent species nondeterministically transform into a different…
Stochastic chemical reaction networks (CRNs) are complex systems which combine the features of concurrent transformation of multiple variables in each elementary reaction event, and nonlinear relations between states and their rates of…
Random graph models have been instrumental in characterizing complex networks, but chemical reaction networks (CRNs) are better represented as hypergraphs. Traditional models of random CRNs often reduce CRNs to bipartite graphs,…
Formal methods have enabled breakthroughs in many fields, such as in hardware verification, machine learning and biological systems. The key object of interest in systems biology, synthetic biology, and molecular programming is chemical…
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…
Coupled chemical interactions in a well-mixed solution are commonly formalized as chemical reaction networks (CRNs). However, despite the widespread use of CRNs in the natural sciences, the range of computational behaviors exhibited by CRNs…
Biological regulatory networks depend upon chemical interactions to process information. Engineering such molecular computing systems is a major challenge for synthetic biology and related fields. The chemical reaction network (CRN) model…
In a previous paper we introduced immediate observation Petri nets, a subclass of Petri nets with application domains in distributed protocols (population protocols) and theoretical chemistry (chemical reaction networks). IO nets enjoy many…
Chemical reaction networks (CRNs) are directed graphs with reactant or product complexes as vertices, and reactions as arcs. A CRN is weakly reversible if each of its connected components is strongly connected. Weakly reversible networks…
Reaction networks are commonly used to model the evolution of populations of species subject to transformations following an imposed stoichiometry. This paper focuses on the efficient characterisation of dynamical properties of Discrete…
A chemical reaction network (CRN) is composed of reactions that can be seen as interactions among entities called species, which exist within the system. Endowed with kinetics, CRN has a corresponding set of ordinary differential equations…
Chemical reaction networks (CRNs) formally model chemistry in a well-mixed solution. CRNs are widely used to describe information processing occurring in natural cellular regulatory networks, and with upcoming advances in synthetic biology,…
In order to fully exploit the potential of molecular communication (MC) for intra-body communication, practically implementable cellular receivers are an important long-term goal. A variety of receiver architectures based on chemical…
Inspired by Anderson et al. [J. R. Soc. Interface, 2014] we study the long-term behavior of discrete chemical reaction networks (CRNs). In particular, using techniques from both Petri net theory and CRN theory, we provide a powerful…
Chemical reaction networks (CRNs) are a standard formalism used in chemistry and biology to reason about the dynamics of molecular interaction networks. In their interpretation by ordinary differential equations, CRNs provide a…