Related papers: Nets with Mana: A Framework for Chemical Reaction …
Chemical reaction network theory is a powerful framework to describe and analyze chemical systems. While much about the concentration profile in an equilibrium state can be determined in terms of the graph structure, the overall reaction's…
We consider approaches for causal semantics of Petri nets, explicitly representing dependencies between transition occurrences. For one-safe nets or condition/event-systems, the notion of process as defined by Carl Adam Petri provides a…
The construction of a reaction network containing all relevant intermediates and elementary reactions is necessary for the accurate description of chemical processes. In the case of a complex chemical reaction (involving, for instance, many…
We develop a thermodynamic framework for closed and open chemical networks applicable to non-elementary reactions that do not need to obey mass action kinetics. It only requires the knowledge of the kinetics and of the standard chemical…
Petri-nets are a simple formalism for modeling concurrent computation. Recently, they have emerged as a powerful tool for the modeling and analysis of biochemical reaction networks, bridging the gap between purely qualitative and…
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…
We describe modeling approaches to a "network" of connected enzyme-catalyzed reactions, with added (bio)chemical processes that introduce biochemical filtering steps into the functioning of such a biocatalytic cascade. Theoretical…
Chemical reaction networks (CRNs) model the behavior of chemical reactions in well-mixed solutions and they can be designed to perform computations. In this tutorial we give an overview of various computational models for CRNs. Moreover, we…
We build on the correspondence between Petri nets and free symmetric strict monoidal categories already investigated in the literature, and present a categorical semantics for Petri nets with guards. This comes in two flavors: Deterministic…
We consider how to generate chemical reaction networks (CRNs) from functional specifications. We propose a two-stage approach that combines synthesis by satisfiability modulo theories and Markov chain Monte Carlo based optimisation. First,…
Chemical reaction networks (CRNs) exhibit complex dynamics governed by their underlying network structure. In this paper, we propose a novel approach to study the dynamics of CRNs by representing them on species graphs (S-graphs). By…
We show how a particular variety of hierarchical nets, where the firing of a transition in the parent net must correspond to an execution in some child net, can be modelled utilizing a functorial semantics from a free category --…
RNA function crucially depends on its structure. Thermodynamic models currently used for secondary structure prediction rely on computing the partition function of folding ensembles, and can thus estimate minimum free-energy structures and…
Petri Nets (PN) are a central, theoretically sound model for concurrent or distributed systems but, at least in their classical definition, not expressive enough to represent dynamic reconfiguration capabilities. On the other side,…
We propose a framework for the specification of behaviour-preserving reconfigurations of systems modelled as Petri nets. The framework is based on open nets, a mild generalisation of ordinary Place/Transition nets suited to model open…
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,…
Based on the theory of stochastic chemical kinetics, the inherent randomness and stochasticity of biochemical reaction networks can be accurately described by discrete-state continuous-time Markov chains. The analysis of such processes is,…
Petri Nets (PN) are extensively used as a robust formalism to model concurrent and distributed systems; however, they encounter difficulties in accurately modeling adaptive systems. To address this issue, we defined rewritable PT nets…
In this paper we study Hornets extended with firing probabilities. Hornets are a Nets-within-Nets formalism, i.e., a Petri net formalism where the tokens are Petri nets again. Each of these net-tokens has its own firing rate, independent…
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.…