Related papers: A Compositional Framework for Reaction Networks
Petri nets provide accurate analogues to chemical reaction networks, with places representing individual molecules (the resources of the system) and transitions representing chemical reactions which convert educt molecules into product…
A crisp survey is given of chemical reaction networks from the perspective of general nonlinear network dynamics, in particular of consensus dynamics. It is shown how by starting from the complex-balanced assumption the reaction dynamics…
The spatially distributed reaction networks are indispensable for the understanding of many important phenomena concerning the development of organisms, coordinated cell behavior, and pattern formation. The purpose of this brief discussion…
We derive the nonequilibrium conductance matrix for open stationary Chemical Reaction Networks (CRNs) described by a deterministic mass action kinetic equation. As an illustration, we determine the nonequilibrium conductance matrix of a CRN…
Petri nets are an established graphical formalism for modeling and analyzing the behavior of systems. An important consideration of the value of Petri nets is their use in describing both the syntax and semantics of modeling formalisms.…
Experiments with networks of discrete reactive bistable electrochemical elements organized in regular and nonregular tree networks are presented to confirm an alternative to the Turing mechanism for the formation of self-organized…
We identify and demonstrate a weakness of Petri Nets (PN) in specifying composite behavior of reactive systems. Specifically, we show how, when specifying multiple requirements in one PN model, modelers are obliged to specify mechanisms for…
The human organism is an integrated network where complex physiologic systems, each with its own regulatory mechanisms, continuously interact, and where failure of one system can trigger a breakdown of the entire network. Identifying and…
The formalism of the models with Petri networks provides a sound theoretical base, supported by powerful mathematical methods able to extract information necessary for the formalism and simulation of the real system that provides features…
Reaction networks are systems in which the populations of a finite number of species evolve through predefined interactions. Such networks are found as modeling tools in many biological disciplines such as biochemistry, ecology,…
Nucleosynthesis is a complex process in astro-nuclear evolution. In this work, we construct a directed multi-layer nuclear reaction network using the substrate-product method from a thermonuclear reaction database, JINA REACLIB. The network…
Event structures have emerged as a foundational model for concurrent computation, explaining computational processes by outlining the events and the relationships that dictate their execution. They play a pivotal role in the study of key…
We establish a new relationship between monotonicity and contractivity and use this connection to describe a new general class of weakly contractive reaction networks. The new class is characterized by the stoichiometry matrix of the…
Many categorical frameworks have been proposed to formalize the idea of gluing Petri nets with each other. Such frameworks model net gluings in terms of sharing of resources or synchronization of transitions. Interpretations given to these…
Over the last two decades, network science has greatly advanced our understanding of how the collective behaviors of a complex system emerge from the interactions among its basic units. Multiplex networks, i.e. networks with many layers,…
Complex networks, comprised of individual elements that interact with each other through reaction channels, are ubiquitous across many scientific and engineering disciplines. Examples include biochemical, pharmacokinetic, epidemiological,…
Barwise and Seligman stated the first principle of information flow: "Information flow results from regularities in the distributed system." They represent a distributed system in terms of a classification consisting of a set of objects or…
We define catalytic networks as chemical reaction networks with an essentially catalytic reaction pathway: one which is on in the presence of certain catalysts and off in their absence. We show that examples of catalytic networks include…
We present an experimental system of networks of coupled non-linear chemical reactors, which we theoretically model within a reaction-diffusion framework. The networks consist of patterned arrays of diffusively coupled nanoliter-scale…
Dynamical reaction-diffusion processes and meta-population models are standard modeling approaches for a wide variety of phenomena in which local quantities - such as density, potential and particles - diffuse and interact according to the…