Related papers: Nets with Mana: A Framework for Chemical Reaction …
During the last decade, various approaches have been put forward to integrate business processes with different types of data. Each of such approaches reflects specific demands in the whole process-data integration spectrum. One particular…
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…
There are many processes in biology in which mechanical forces are generated. Force-bearing networks can transduce locally developed mechanical signals very extensively over different parts of the cell or tissues. In this article we conduct…
Switch-like motifs are among the basic building blocks of biochemical networks. A common motif that can serve as an ultrasensitive switch consists of two enzymes acting antagonistically on a substrate, one making and the other removing a…
We lay the foundation of a circuit theory for chemical reaction networks. Chemical reactions are grouped into chemical modules solely characterized by their current-concentration characteristic, as electrical devices by their…
In this paper we introduce a formalism that allows to describe the response of a part of a biochemical system in terms of renewal equations. In particular, we examine under which conditions the interactions between the different parts of a…
In order to speed up the synthesis of Petri nets from labelled transition systems, a divide and conquer strategy consists in defining decompositions of labelled transition systems, such that each component is synthesisable iff so is the…
We introduce the notion of corresponding a chemical reaction network to a split network translation, and use this novel process to extend the scope of existing network-based theory for characterizing the steady state set of mass-action…
We investigate the problem of parameter synthesis for time Petri nets with a cost variable that evolves both continuously with time, and discretely when firing transitions. More precisely, parameters are rational symbolic constants used for…
A fundamental advantage of Petri net models is the possibility to automatically compute useful system invariants from the syntax of the net. Classical techniques used for this are place invariants, P-components, siphons or traps. Recently,…
We study families of chemical reaction networks whose positive steady states are toric, and therefore can be parameterized by monomials. Families are constructed algorithmically from a core network; we show that if a family member is…
Synthesis for a type $\tau$ of Petri nets is the following search problem: For a transition system $A$, find a Petri net $N$ of type $\tau$ whose state graph is isomorphic to $A$, if there is one. To determine the computational complexity…
Step net bisimilarity \cite{Gor23} is a truly concurrent behavioral equivalence for finite Petri nets, which is defined as a smooth generalization of standard step bisimilarity \cite{NT84} on Petri nets, but with the property of relating…
Network models are used to study interconnected systems across many physical, biological, and social disciplines. Such models often assume a particular network-generating mechanism, which when fit to data produces estimates of…
This study introduces the concept of finite element network analysis (FENA) which is a physics-informed, machine-learning-based, computational framework for the simulation of complex physical systems. The framework leverages the extreme…
In this work, we analyse Petri nets where places are allowed to have a negative number of tokens. For each net we build its correspondent category of executions, which is compact closed, and prove that this procedure is functorial. We…
This paper explores the problem of determining which classes of Petri nets can be encoded into behaviourally-equivalent CCS processes. Most of the existing related literature focuses on the inverse problem (i.e., encoding process calculi…
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…
We provide a rigorous definition of free-energy transduction and its efficiency in arbitrary -- linear or nonlinear -- open chemical reaction networks (CRNs) operating at steady state. Our method is based on the knowledge of the…
Biochemical processes in cells are governed by complex networks of many chemical species interacting stochastically in diverse ways and on different time scales. Constructing microscopically accurate models of such networks is often…