Searcharxiv⌕ Search
Home/Archive/arXiv

arXiv · 2608.17893

Abstract Simulation of Reaction Networks

Marie-Eva Fabri·Joachim Niehren·Sara Riva·Cristian Versari
View original source ↗Read source document ↗Export metadata ↓

Abstract

Reaction networks model reactions between a finite set of species. These networks can be associated with different semantics, depending on the type of analysis and the phenomena under study. The standard continuous semantics is given by a system of differential equations based on the kinetic expressions of the reactions. To simulate a network under this semantics, the full knowledge of the kinetic laws of each reaction and the initial concentrations of each species is necessary. Since in empirical settings the quantitative information about the reactions can be partially or totally unknown, the challenge is to introduce new semantics that can still be applied. In this direction, a recent approach in the state of the art concerning Reaction Networks proposes a qualitative abstraction that is too coarse to properly capture the time-course continuous behaviour. Starting from the ideas of this approach, in this paper we first introduce the causal continuous semantics for Reaction Networks to capture their continuous-time dynamics, preserving the causality hidden inside each transition. Later, we introduce the differential sign semantics to abstract in a qualitative way the behaviour of a system under the causal continuous semantics. We show that our new method, based on abstract interpretation, yields appropriate Boolean transition graphs that refine those provided by the previous approach.

Explore related subjects

cs.DM

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Marie-Eva Fabri, Joachim Niehren, Sara Riva, Cristian Versari. 2026-08-18. Abstract Simulation of Reaction Networks. https://arxiv.org/abs/2608.17893

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

An FPTAS for Two-Machine Open-Shop Scheduling with a Single Unavailability Interval

We consider the two-machine open-shop scheduling problem in which one machine is unavailable during a fixed interval. We study the resumable setting: an operation interrupted by the unavailability interval may resume, without penalty, when the machine becomes available. The objective is to minimize the makespan. Although the problem is NP-hard and several approximation algorithms are known, whether it admits a fully polynomial-time approximation scheme (FPTAS) has remained open for two decades. We resolve this question affirmatively by giving the first FPTAS, thereby strengthening the previously known polynomial-time approximation scheme (PTAS). As an intermediate result, we develop a new pseudo-polynomial dynamic program with seven state dimensions, improving on the ten-dimensional formulation in the literature.

cs.DM↗
arXiv2026

Generalized Graph Search Trees

Graph search algorithms and their corresponding graph search trees are commonly used in algorithmic graph theory. In recent years, the recognition problem of these graph search trees has received significant attention. So far, the research has focused on two types of search trees: first-in trees that behave like BFS-trees and last-in trees that behave like DFS-trees. The search tree paradigms differ from each other by the parent a vertex is connected to. In first-in trees, it is the first visited neighbor, while in last-in trees it is the last neighbor visited before that vertex. Here, we will generalize these concepts of graph search trees by allowing every preceding neighbor of a vertex to be the parent. We study the complexity of the recognition problem of these generalized graph search trees. We present NP-completeness proofs for most searches. We also show that the problem is trivial for Generic Search and polynomial-time solvable for several searches on bipartite graphs and chordal graphs. We also study the question how fixing the start vertex influences the complexity of the problem.

cs.DM↗
arXiv2026

The exact asymptotic constant in the metric dimension of Jaccard space

Let $X$ be a finite set with $|X|=n$ and let $\mathrm{Jac}(a,b)=|a\,\triangle\, b|/|a\cup b|$ be the Jaccard distance on the power set $2^X$. Lladser and Paradise recently proved that the metric dimension of $(2^X,\mathrm{Jac})$ is $\Theta(n/\ln n)$, with the constant left open; their bounds are $(\ln 2)\,n/\ln n\lesssim \beta(2^X,\mathrm{Jac})\lesssim 2\ln(2e)\,n/\ln n$. We determine the constant: \[ \beta(2^X,\mathrm{Jac})=\frac{2n}{\log_2 n}\,(1+o(1))=(2\ln 2)\,\frac{n}{\ln n}\,(1+o(1)). \] The proof identifies the problem, on each ``slice'' of subsets of fixed cardinality, with the Erd\H{o}s--R\'enyi coin-weighing problem for a spring scale (the problem of \emph{detecting matrices}). The lower bound is the Erd\H{o}s--R\'enyi entropy argument applied to the middle slice; the upper bound follows from the explicit detecting families of Lindstr\"om and of Cantor and Mills, augmented by a single extra landmark that reveals cardinality.

cs.DM↗