Chemical reaction network knowledge graphs: the OntoRXN ontology [PDF]
Journal of Cheminformatics, 2022 The organization and management of large amounts of data has become a major point in almost all areas of human knowledge. In this context, semantic approaches propose a structure for the target data, defining ontologies that state the types of entities ...
Diego Garay-Ruiz, Carles Bo
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Temporally programmed polymer – solvent interactions using a chemical reaction network [PDF]
Nature Communications, 2022 Out of equilibrium operation of chemical reaction networks. (CRNs) enables materials to autonomously respond to their environment by activation and deactivation of intermolecular interactions but the deactivation to noninteracting building blocks remains
Benjamin Klemm +3 more
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Translated Chemical Reaction Networks [PDF]
Bulletin of Mathematical Biology, 2013 Many biochemical and industrial applications involve complicated networks of simultaneously occurring chemical reactions. Under the assumption of mass action kinetics, the dynamics of these chemical reaction networks are governed by systems of polynomial
Johnston, Matthew D.
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What makes a reaction network “chemical”?
Journal of Cheminformatics, 2022 Background Reaction networks (RNs) comprise a set X of species and a set $$\mathscr {R}$$ R of reactions $$Y\rightarrow Y'$$ Y → Y ′ , each converting a multiset of educts $$Y\subseteq X$$ Y ⊆ X into a multiset $$Y'\subseteq X$$ Y ′ ⊆ X of products.
Stefan Müller +2 more
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Stochastic thermodynamics of chemical reaction networks [PDF]
The Journal of Chemical Physics, 2006 For chemical reaction networks described by a master equation, we define energy and entropy on a stochastic trajectory and develop a consistent nonequilibrium thermodynamic description along a single stochastic trajectory of reaction events.
Andrieux D. +8 more
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CERENA: ChEmical REaction Network Analyzer--A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics. [PDF]
PLoS ONE, 2016 Gene expression, signal transduction and many other cellular processes are subject to stochastic fluctuations. The analysis of these stochastic chemical kinetics is important for understanding cell-to-cell variability and its functional implications, but
Atefeh Kazeroonian +4 more
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PCA-based synthetic sensitivity coefficients for chemical reaction network in cancer [PDF]
Scientific ReportsChemical reaction networks are powerful tools for modeling cell signaling and its disruptions in diseases like cancer. Realistic chemical reaction networks involve hundreds of proteins and reactions, resulting in a model depending on a consistently large
Giorgia Biddau +3 more
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Chemical Reaction Network Theory elucidates sources of multistability in interferon signaling. [PDF]
PLoS Computational Biology, 2017 Bistability has important implications in signaling pathways, since it indicates a potential cell decision between alternative outcomes. We present two approaches developed in the framework of the Chemical Reaction Network Theory for easy and efficient ...
Irene Otero-Muras +2 more
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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
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Multilayered substructures of a non-enzymatic chemical reaction network for synthesizing sugars [PDF]
Communications ChemistryIn biological chemical reactions, substructures formed through multi-step enzymatic reactions organize into large chemical reaction networks (CRNs) that produce complex and sophisticated functions.
Genta Chikatani +9 more
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