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MC networks are envisioned to enable synthetic information exchange between nanoscale biological entities. For many algorithm proposals in the MC research field, the question of implementation at nanoscales and in biological environments…
Chemical reaction networks (CRNs) provide a convenient language for modelling a broad variety of biological systems. These models are commonly studied with respect to the time series they generate in deterministic or stochastic simulations.…
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 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…
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,…
Analysis of large continuous-time stochastic systems is a computationally intensive task. In this work we focus on population models arising from chemical reaction networks (CRNs), which play a fundamental role in analysis and design of…
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 reaction networks (CRNs) are fundamental computational models used to study the behavior of chemical reactions in well-mixed solutions. They have been used extensively to model a broad range of biological systems, and are primarily…
Molecular computation based on chemical reaction networks (CRNs) has emerged as a promising paradigm for designing programmable biochemical systems. However, the implementation of complex computations still requires excessively large and…
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…
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,…
We present a differentiable formulation of abstract chemical reaction networks (CRNs) that can be trained to solve a variety of computational tasks. Chemical reaction networks are one of the most fundamental computational substrates used by…
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,…
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.…
Chemical reactions are a prominent feature of molecular communication (MC) systems, with no direct parallels in wireless communications. While chemical reactions may be used inside the transmitter nodes, receiver nodes or the communication…
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,…
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…
Motivation: A Chemical Reaction Network (CRN) is a set of chemical reactions, which can be very complex and difficult to analyze. Indeed, dynamical properties of CRNs can be described by a set of non-linear differential equations that…
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,…
Chemical Reaction Networks (CRNs) provide a useful abstraction of molecular interaction networks in which molecular structures as well as mass conservation principles are abstracted away to focus on the main dynamical properties of the…