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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…
The Chemical Reaction Network (CRN) is a well-studied model that describes the interaction of molecules in well-mixed solutions. In 2014, Qian and Winfree [22] proposed the abstract surface chemical reaction network model (sCRN), which…
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,…
We show that some natural output conventions for error-free computation in chemical reaction networks (CRN) lead to a common level of computational expressivity. Our main results are that the standard consensus-based output convention have…
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…
The Turing completeness of continuous chemical reaction networks (CRNs) states that any computable real function can be computed by a continuous CRN on a finite set of molecular species, possibly restricted to elementary reactions, i.e.…
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…
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…
The interaction of phase-separating systems with chemical reactions is of great interest in various contexts, from biology to material science. In biology, phase separation is thought to be the driving force behind the formation of…
Chemical Reaction Networks (CRNs) are a well-established model of distributed computing characterized by quantities of molecular species that can transform or change through applications of reactions. A fundamental problem in CRNs is the…
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…
We present a data-driven verification approach that determines whether or not a given chemical reaction network (CRN) satisfies a given property, expressed as a formula in a modal logic. Our approach consists of three phases, integrating…
The concept of the limiting step is extended to the asymptotology of multiscale reaction networks. Complete theory for linear networks with well separated reaction rate constants is developed. We present algorithms for explicit…
Power law dynamics is used to describe the stability behavior in metabolic networks such as chemical reaction networks (CRN's). These systems allow multiple steady states within a single stoichiometric class. On the other side thermodynamic…
Chemically reacting flows are common in engineering, such as hypersonic flow, combustion, explosions, manufacturing processes and environmental assessments. For combustion, the number of reactions can be significant (over 100) and due to…
Chemical reactor networks (CRNs) enable simulations of combustion reactors with detailed chemical kinetics and strongly simplified flow structure. In this paper, the implementation of a reactor component with less idealized flow structure,…
The study of the dynamics of chemical reactions, and in particular phenomena such as oscillating reactions, has led to the recognition that many dynamical properties of a chemical reaction can be predicted from graph theoretical properties…
Chemical reaction datasets such as USPTO suffer from substantial incompleteness, frequently missing byproducts, co-reactants, and stoichiometric coefficients. This limits their applicability and reliability in downstream applications. Here,…
We present two quantitative behavioral equivalences over species of a chemical reaction network (CRN) with semantics based on ordinary differential equations. Forward CRN bisimulation identifies a partition where each equivalence class…
Many important phenomena in biochemistry and biology exploit dynamical features such as multi-stability, oscillations, and chaos. Construction of novel chemical systems with such rich dynamics is a challenging problem central to the fields…