Related papers: A Compositional Framework for Reaction Networks
For the investigation of chemical reaction networks, the efficient and accurate determination of all relevant intermediates and elementary reactions is mandatory. The complexity of such a network may grow rapidly, in particular if reactive…
Autocatalytic Sets are reaction networks theorised as networks at the basis of life. Their main feature is the ability of spontaneously emerging and self-reproducing. The Reflexively and Food-generated theory provides a formal definition of…
Causal nets (CNs) are Petri nets where causal dependencies are modelled via inhibitor arcs. They play the role of occurrence nets when representing the behaviour of a concurrent and distributed system, even when reversibility is considered.…
Maintaining stability in an uncertain environment is essential for proper functioning of living systems. Robust perfect adaptation (RPA) is a property of a system that generates an output at a fixed level even after fluctuations in input…
Network science provides a universal framework for modeling complex systems, contrasting the reductionist approach generally adopted in physics. In a prototypical study, we utilize network models created from spectroscopic data of atoms to…
The execution of an event in a complex and distributed system where the dependencies vary during the evolution of the system can be represented in many ways, and one of them is to use Context-Dependent Event structures. Event structures are…
Interaction nets are a graphical formalism inspired by Linear Logic proof-nets often used for studying higher order rewriting e.g. \Beta-reduction. Traditional presentations of interaction nets are based on graph theory and rely on…
Passive linear networks are used in a wide variety of engineering applications, but the best studied are electrical circuits made of resistors, inductors and capacitors. We describe a category where a morphism is a circuit of this sort with…
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…
This work addresses multistationarity of fully open reaction networks equipped with mass action kinetics. We improve upon the existing results relating existence of positive feedback loops in a reaction network and multistationarity; and we…
Kahn process networks are a model of computation based on a collection of sequential, deterministic processes that communicate by sending messages through unbounded channels. They are well suited for modelling stream-based computations, but…
We develop a technique to formulate quantum field theory on arbitrary network, based on different, randomly disposed sets of scattering's. We define R-matrix of the whole network as a product of R-matrices attached to each of scattering…
Petri nets are a well-known model of concurrency and provide an ideal setting for the study of fundamental aspects in concurrent systems. Despite their simplicity, they still lack a satisfactory causally reversible semantics. We develop…
The mathematical formalisms used to model biological systems induce both latent and ambiguous assumptions that can limit or distort their representational capabilities. Developing formalisms that can represent systems more precisely is…
A detailed understanding of biochemical networks at the molecular level is essential for studying complex cellular processes. In this paper, we provide a comprehensive description of biochemical networks by considering individual atoms and…
Dialectical frameworks are a unifying model of formal argumentation, where argumentative relations between arguments are represented by assigning acceptance conditions to atomic arguments. Their generality allow them to cover a number of…
We give a definition of $\mathsf{Q}$-net, a generalization of Petri nets based on a Lawvere theory $\mathsf{Q}$, for which many existing variants of Petri nets are a special case. This definition is functorial with respect to change in…
In the study of reaction networks and the polynomial dynamical systems that they generate, special classes of networks with important properties have been identified. These include reversible, weakly reversible}, and, more recently,…
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…
In most natural sciences there is currently the insight that it is necessary to bridge gaps between different processes which can be observed on different scales. This is especially true in the field of chemical reactions where the…