Reduction of dynamical biochemical reactions networks in computational biology

O Radulescu, AN Gorban, A Zinovyev, V Noel - Frontiers in genetics, 2012 - frontiersin.org
Biochemical networks are used in computational biology, to model mechanistic details of
systems involved in cell signaling, metabolism, and regulation of gene expression …

ERODE: a tool for the evaluation and reduction of ordinary differential equations

L Cardelli, M Tribastone, M Tschaikowski… - … 2017, Held as Part of the …, 2017 - Springer
We present ERODE, a multi-platform tool for the solution and exact reduction of systems of
ordinary differential equations (ODEs). ERODE supports two recently introduced …

Forward and backward bisimulations for chemical reaction networks

L Cardelli, M Tribastone, M Tschaikowski… - ar**
L Cardelli, IC Perez-Verona, M Tribastone… - …, 2021 - academic.oup.com
Motivation Stochastic reaction networks are a widespread model to describe biological
systems where the presence of noise is relevant, such as in cell regulatory processes …

Comparing chemical reaction networks: A categorical and algorithmic perspective

L Cardelli, M Tribastone, M Tschaikowski… - Proceedings of the 31st …, 2016 - dl.acm.org
We study chemical reaction networks (CRNs) as a kernel language for concurrency models
with semantics based on ordinary differential equations. We investigate the problem of …

Compositionality of rewriting rules with conditions

N Behr, J Krivine - Compositionality, 2021 - compositionality.episciences.org
We extend the notion of compositional associative rewriting as recently studied in the rule
algebra framework literature to the setting of rewriting rules with conditions. Our …

Syntactic Markovian bisimulation for chemical reaction networks

L Cardelli, M Tribastone, M Tschaikowski… - … , Algorithms, Logics and …, 2017 - Springer
In chemical reaction networks (CRNs) with stochastic semantics based on continuous-time
Markov chains (CTMCs), the typically large populations of species cause combinatorially …

[HTML][HTML] Symbolic computation of differential equivalences

L Cardelli, M Tribastone, M Tschaikowski… - Theoretical Computer …, 2019 - Elsevier
Ordinary differential equations (ODEs) are widespread in many natural sciences including
chemistry, ecology, and systems biology, and in disciplines such as control theory and …