Related papers: Nets with Mana: A Framework for Chemical Reaction …
In this talk we are concerned with the intrinsic similarities and differences between Petri nets on the one hand, and membrane systems and reaction systems on the other hand.
We present a data-driven verification approach that determines whether or not a given chemical reaction network (CRN) satisfies a given property, expressed as a formula in a modal logic. Our approach consists of three phases, integrating…
Modelling, specifying and reasoning about complex systems requires to process in an integrated fashion declarative and procedural aspects of the target domain. The paper reports on an experiment conducted with a propositional version of…
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…
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…
Reversible computation is an emerging computing paradigm that allows any sequence of operations to be executed in reverse order at any point during computation. Its appeal lies in its potential for lowpower computation and its relevance to…
In a recent paper it was shown that, for chemical reaction networks possessing a subtle structural property called concordance, dynamical behavior of a very circumscribed (and largely stable) kind is enforced, so long as the kinetics lies…
We formally characterize a set of causality-based properties of metabolic networks. This set of properties aims at making precise several notions on the production of metabolites, which are familiar in the biologists' terminology. From a…
Motivated by recent progress on the interplay between graph theory, dynamics, and systems theory, we revisit the analysis of chemical reaction networks described by mass action kinetics. For reaction networks possessing a thermodynamic…
New checkable criteria for persistence of chemical reaction networks are proposed, which extend and complement those obtained by the authors in previous work. The new results allow the consideration of reaction rates which are time-varying,…
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.…
Thermodynamic constraints on reactions directions are inherent in the structure of a given biochemical network. However, concrete procedures for determining feasible reaction directions for large-scale metabolic networks are not well…
The automated inference of physically interpretable (bio)chemical reaction network models from measured experimental data is a challenging problem whose solution has significant commercial and academic ramifications. It is demonstrated,…
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.…
Chemical systems are traditionally described by lists of species, reactions, and externally imposed kinetic laws, a framework that lacks an intrinsic algebraic structure governing how transformations compose. We propose an axiomatic…
Can we objectively distinguish chemical systems that are able to process meaningful information from those that are not suitable for information processing? Here, we present a formal method to assess the semantic capacity of a chemical…
Petri nets are a popular formalism for modeling and analyzing distributed systems. Tokens in Petri net models can represent the control flow state or resources produced/consumed by transition firings. We define a resource as a part (a…
Let $X$ be a chemical reaction process, modeled as a multi-dimensional continuous-time jump process. Assume that at given times $0< t_1 < \cdots <t_n$, linear combinations $v_i = L_i X(t_i),\, i=1,\dots ,n$ are observed for given matrices…
Finite 1-safe Petri nets, also called \emph{net systems}, are natural models of asynchronous concurrency. The event structure of a net system describes all its possible executions and their concurrent nature: two events may be causally…
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…