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
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Computational models for inferring biochemical networks [PDF]
, 2014 Biochemical networks are of great practical importance. The interaction of biological compounds in cells has been enforced to a proper understanding by the numerous bioinformatics projects, which contributed to a vast amount of biological information ...
Crina Grosan +20 more
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Port-Hamiltonian modeling of non-isothermal chemical reaction networks [PDF]
Journal of Mathematical Chemistry, 2018 zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Wang, Li +2 more
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Forward and Backward Bisimulations for Chemical Reaction Networks [PDF]
, 2015 We present two quantitative behavioral equivalences over species of a chemical reaction network (CRN) with semantics based on ordinary differential equations.
Cardelli, Luca +3 more
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A Theoretical Approach to the Complex Chemical Evolution of Phosphorus in the Interstellar Medium
The Astrophysical Journal, 2023 The study of phosphorus chemistry in the interstellar medium has become a topic of growing interest in astrobiology because it is plausible that a wide range of P-bearing molecules were introduced in the early Earth by the impact of asteroids and comets ...
Marina Fernández-Ruz +2 more
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CompLaB v1.0: a scalable pore-scale model for flow, biogeochemistry, microbial metabolism, and biofilm dynamics [PDF]
Geoscientific Model Development, 2023 Microbial activity and chemical reactions in porous media depend on the local conditions at the pore scale and can involve complex feedback with fluid flow and mass transport.
H. Jung, H. Jung, H.-S. Song, C. Meile
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Prediction of Compound Synthesis Accessibility Based on Reaction Knowledge Graph
Molecules, 2022 With the increasing application of deep-learning-based generative models for de novo molecule design, the quantitative estimation of molecular synthetic accessibility (SA) has become a crucial factor for prioritizing the structures generated from ...
Baiqing Li, Hongming Chen
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Evaluation of rate law approximations in bottom-up kinetic models of metabolism. [PDF]
, 2016 BackgroundThe mechanistic description of enzyme kinetics in a dynamic model of metabolism requires specifying the numerical values of a large number of kinetic parameters.
A Bordbar +49 more
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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
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RuleMonkey: software for stochastic simulation of rule-based models
BMC Bioinformatics, 2010 Background The system-level dynamics of many molecular interactions, particularly protein-protein interactions, can be conveniently represented using reaction rules, which can be specified using model-specification languages, such as the BioNetGen ...
Hlavacek William S +5 more
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