Related papers: A Compositional Framework for Reaction Networks
Deep neural networks give us a powerful method to model the training dataset's relationship between input and output. We can regard that as a complex adaptive system consisting of many artificial neurons that work as an adaptive memory as a…
Mobile computing systems, service-based systems and some other systems with mobile interacting components have recently received much attention. However, because of their characteristics such as mobility and disconnection, it is difficult…
Dynamic networks are structured interconnections of dynamical systems (modules) driven by external excitation and disturbance signals. In order to identify their dynamical properties and/or their topology consistently from measured data, we…
Petri nets are a mathematical language for modeling and reasoning about distributed systems. In this paper we propose an approach to Petri nets for embedding reversibility, i.e., the ability of reversing an executed sequence of operations…
Event structures are a well-accepted model of concurrency. In a seminal paper by Nielsen, Plotkin and Winskel, they are used to establish a bridge between the theory of domains and the approach to concurrency proposed by Petri. A basic role…
Cycloids are particular Petri nets for modelling processes of actions or events. They belong to the fundaments of Petri's general systems theory and have very different interpretations, ranging from Einstein's relativity theory and…
Mechanisms of pattern formation---of which the Turing instability is an archetype---constitute an important class of dynamical processes occurring in biological, ecological and chemical systems. Recently, it has been shown that the Turing…
Taking an interaction network oriented perspective in informatics raises the challenge to describe deterministic finite systems which take part in networks of nondeterministic interactions. The traditional approach to describe processes as…
A neuron transforms its input into output spikes, and this transformation is the basic unit of computation in the nervous system. The spiking response of the neuron to a complex, time-varying input can be predicted from the detailed…
We present a computational procedure to characterize the signs of sensitivities of steady states to parameter perturbations in chemical reaction networks.
In the first part of this paper, we propose new optimization-based methods for the computation of preferred (dense, sparse, reversible, detailed and complex balanced) linearly conjugate reaction network structures with mass action dynamics.…
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…
Reaction diffusion systems describe the behaviour of dynamic, interacting, particulate systems. Quantum stochastic processes generalise Brownian motion and Poisson processes, having operator valued It\^{o} calculus machinery. Here it is…
Tensor networks and circuits are widely used data structures to represent pseudo-Boolean functions. These two formalisms have been studied primarily in separate communities, and this paper aims to establish equivalences between them. We…
The theory of patterns formation for a reaction-diffusion system defined on a multiplex is developed by means of a perturbative approach. The intra-layer diffusion constants act as small parameter in the expansion and the unperturbed state…
Living systems operate out of equilibrium, continuously consuming energy to sustain organised, functional states. Their emergent behaviour usually relies on a set of interconnected chemical reaction networks (CRNs) driven by external fluxes…
Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as…
The emergence of an autocatalytic network from an available set of elements is a fundamental step in early evolutionary processes, such as the origin of metabolism. Given a set of elements, the reactions between them (chemical or…
A detailed algorithmic explanation is required for how a network of chemical reactions can generate the sophisticated behavior displayed by living cells. Though several previous works have shown that reaction networks are computationally…
A compositional Petri net-based semantics is given to a simple language allowing pointer manipulation and parallelism. The model is then applied to give a notion of validity to the judgements made by concurrent separation logic that…