Results 1 to 10 of about 356 (136)
Physics-informed machine learning for automatic model reduction in chemical reaction networks [PDF]
Scientific ReportsPhysics-informed machine learning bridges the gap between the high fidelity of mechanistic models and the adaptive insights of artificial intelligence. In chemical reaction network modeling, this synergy proves valuable, addressing the high computational
Joseph Pateras +4 more
doaj +4 more sources
Roles of network topology in the relaxation dynamics of simple chemical reaction network models [PDF]
Scientific ReportsUnderstanding the relationship between the structure of chemical reaction networks and their reaction dynamics is essential for unveiling the design principles of living organisms.
Yusuke Himeoka +3 more
doaj +5 more sources
On Quantitative Comparison of Chemical Reaction Network Models [PDF]
Electronic Proceedings in Theoretical Computer Science, 2019 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. Their dynamic
Ozan Kahramanoğulları
doaj +7 more sources
Delays in Model Reduction of Chemical Reaction Networks
IFAC-PapersOnLine, 2018 Abstract A novel engineering model reduction method is proposed in this paper that can be applied to a chemical reaction network (CRN) with chains of linear reactions. The reduced model is a delayed CRN with possibly different delays but with less state variables than the original model.
György Lipták, Katalin M. Hangos
openalex +3 more sources
Large deviations theory for Markov jump models of chemical reaction networks [PDF]
The Annals of Applied Probability, 2018 We prove a sample path Large Deviation Principle (LDP) for a class of jump processes whose rates are not uniformly Lipschitz continuous in phase space. Building on it we further establish the corresponding Wentzell-Freidlin (W-F) (infinite time horizon) asymptotic theory.
Andréa Agazzi +2 more
openalex +6 more sources
A spatial measure-valued model for chemical reaction networks in heterogeneous systems [PDF]
The Annals of Applied Probability, 2023 We propose a novel measure valued process which models the behaviour of chemical reaction networks in spatially heterogeneous systems. It models reaction dynamics between different molecular species and continuous movement of molecules in space. Reactions rates at a spatial location are proportional to the mass of different species present locally and ...
Lea Popovic, Amandine Véber
openalex +4 more sources
Piecewise Linear and Boolean Models of Chemical Reaction Networks [PDF]
Bulletin of Mathematical Biology, 2014 This is an extension of previous work arXiv:1201 ...
Alan Veliz‐Cuba +2 more
openalex +6 more sources
Molecule Edit Graph Attention Network: Modeling Chemical Reactions as Sequences of Graph Edits [PDF]
Journal of Chemical Information and Modeling, 2021 The central challenge in automated synthesis planning is to be able to generate and predict outcomes of a diverse set of chemical reactions. In particular, in many cases, the most likely synthesis pathway cannot be applied due to additional constraints, which requires proposing alternative chemical reactions. With this in mind, we present Molecule Edit
Mikołaj Sacha +7 more
openalex +5 more sources
Hybrid models for chemical reaction networks: Multiscale theory and application to gene regulatory systems [PDF]
The Journal of Chemical Physics, 2017 Well-mixed stochastic chemical kinetics are properly modeled by the chemical master equation (CME) and associated Markov jump processes in molecule number space. If the reactants are present in large amounts, however, corresponding simulations of the stochastic dynamics become computationally expensive and model reductions are demanded.
Stefanie Winkelmann, Christof Schütte
openalex +3 more sources
Port-Hamiltonian modeling of non-isothermal chemical reaction networks [PDF]
Journal of Mathematical Chemistry, 2018 Motivated by recent progress on the port-Hamiltonian formulation of isothermal chemical reaction networks and of the continuous stirred tank reactor, the present paper aims to develop a port-Hamiltonian formulation of chemical reaction networks in the non-isothermal case, and to exploit this for equilibrium and stability analysis.
Li Wang +2 more
openalex +5 more sources