Chemical reaction network knowledge graphs: the OntoRXN ontology. [PDF]
J Cheminform, 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 ...
Garay-Ruiz D, Bo C.
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Temporally programmed polymer - solvent interactions using a chemical reaction network. [PDF]
Nat Commun, 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
Klemm B +3 more
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SoftwareX, 2020 Reaction Path Analysis (RPA) is an essential tool in identifying the key reaction pathways that drive chemical transformations of complex reaction networks.
Udit Gupta, Dionisios G Vlachos
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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
Kazeroonian A +4 more
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PCA-based synthetic sensitivity coefficients for chemical reaction network in cancer. [PDF]
Sci RepChemical 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
Biddau G +3 more
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Chemical Reaction Network Theory elucidates sources of multistability in interferon signaling. [PDF]
PLoS Comput Biol, 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 ...
Otero-Muras I, Yordanov P, Stelling J.
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Roles of network topology in the relaxation dynamics of simple chemical reaction network models. [PDF]
Sci RepUnderstanding the relationship between the structure of chemical reaction networks and their reaction dynamics is essential for unveiling the design principles of living organisms.
Himeoka Y +3 more
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Multilayered substructures of a non-enzymatic chemical reaction network for synthesizing sugars. [PDF]
Commun ChemIn biological chemical reactions, substructures formed through multi-step enzymatic reactions organize into large chemical reaction networks (CRNs) that produce complex and sophisticated functions.
Chikatani G +9 more
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Advancing Mathematical Epidemiology and Chemical Reaction Network Theory via Synergies Between Them. [PDF]
Entropy (Basel)Our paper reviews some key concepts in chemical reaction network theory and mathematical epidemiology, and examines their intersection, with three goals.
Avram F, Adenane R, Neagu M.
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Diffusive network connected chemical reaction networks
Systems Science and Control EngineeringA novel type of networked Chemical Reaction Network (CRN) model is proposed in this paper where the CRN subsystem nodes are connected in a bi-directional state-difference-driven way, forming a diffusive network. The diffusive connecting elements can also
Katalin M Hangos +2 more
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