Related papers: A Compositional Framework for Reaction Networks
A class of systems is considered, where immobile species associated to distinct patches, the nodes of a network, interact both locally and at a long-range, as specified by an (interaction) adjacency matrix. Non local interactions are…
Networks are fundamental for our understanding of complex systems. Interactions between individual nodes in networks generate network motifs - small recurrent patterns that can be considered the network's building-block components,…
Automated synthesis from behavioural specifications is an attractive and powerful way of constructing concurrent systems. Here we focus on the problem of synthesising a membrane system from a behavioural specification given in the form of a…
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,…
Open chemical reaction systems involve matter-exchange with the surroundings. As a result, species can accumulate inside a system during the course of the reaction. We study the role of network topology in governing the concentration…
Reaction systems are discrete dynamical systems that model biochemical processes in living cells using finite sets of reactants, inhibitors, and products. We investigate the computational complexity of a comprehensive set of problems…
Violent nuclear collisions are open systems which require a non-equilibrium description when the process should be followed from the first instants. The heated system produced in the collision, can no more be treated within an…
Biomolecular networks underpin emerging technologies in synthetic biology-from robust biomanufacturing and metabolic engineering to smart therapeutics and cell-based diagnostics-and also provide a mechanistic language for understanding…
This thesis (defended 10/07/2019) develops a theory of networks of hybrid open systems and morphisms. It builds upon a framework of networks of continuous-time open systems as product and interconnection. We work out categorical notions for…
Human communication is often executed in the form of a narrative, an account of connected events composed of characters, actions, and settings. A coherent narrative structure is therefore a requisite for a well-formulated narrative -- be it…
The GENERIC theory provides a framework for the description of non-equilibrium phenomena in isolated systems beyond local thermal equilibrium and beyond linear non-equilibrium (i.e., linear relations between thermodynamic forces and…
We study the structure of Fermionic networks, i.e., a model of networks based on the behavior of fermionic gases, and we analyze dynamical processes over them. In this model, particle dynamics have been mapped to the domain of networks,…
Motivation: Cell-biological processes are regulated through a complex network of interactions between genes and their products. The processes, their activating conditions, and the associated transcriptional responses are often unknown.…
Very often, models in biology, chemistry, physics, and engineering are systems of polynomial or power-law ordinary differential equations, arising from a reaction network. Such dynamical systems can be generated by many different reaction…
Temporal networks model how the interaction between elements in a complex system evolve over time. Just like complex systems display collective dynamics, here we interpret temporal networks as trajectories performing a collective motion in…
Interacting systems are increasingly common. Many examples pervade our everyday lives: automobiles, aircraft, defense systems, telephone switching systems, financial systems, national governments, and so on. Closer to computer science,…
Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, since precise information on the molecular composition, the dominant reaction chemistry, and the conditions for that…
We introduce a new formalism for dealing with networks of queues. The formalism is based on the Doi-Peliti second quantization method for reaction diffusion systems. As a demonstration of the method's utility we compute perturbatively the…
Petri nets have found widespread use among many application domains, not least due to their human-friendly graphical syntax for the composition of interacting distributed and asynchronous processes and services, based in partial-order…
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.…